ABCB1
Plant size (dwarfism)
Unknown,
Unknown
Cenchrus americanus
(species)
Domesticated
Linkage Mapping
Parvathaneni RK; Jakkula V; Padi FK ; et al. (2013)
Fine-mapping and identification of a candidate gene underlying the d2 dwarfing phenotype in pearl mi[...]
GP00000006
ABCB1
Q9ZR72
Morphology
unknown
Cenchrus americanus
(species)
Cenchrus americanus
(species)
ABCB1
Cenchrus americanus
(species)
Published - Accepted by Curator
ABCB1
Plant size (dwarfism)
Coding,
Insertion
N
Sorghum bicolor
sorghum - (species)
Domesticated
Candidate Gene
Multani DS; Briggs SP; Chamberlin MA ; et al. (2003)
Loss of an MDR transporter in compact stalks of maize br2 and sorghum dw3 mutants.
GP00000007
ABCB1
Q9ZR72
Morphology
882bp direct duplication in exon 5 of the dw3 allele driving loss-of-function N
Sorghum bicolor
sorghum - (species)
Sorghum bicolor
sorghum - (species)
ABCB1
Sorghum bicolor
sorghum - (species)
Published - Accepted by Curator
Abdominal-B
Coloration (male-specific)
Unknown,
Unknown
Drosophila malerkotliana
(species)
Intraspecific
Linkage Mapping
Signor SA; Liu Y; Rebeiz M ; et al. (2016)
Genetic Convergence in the Evolution of Male-Specific Color Patterns in Drosophila.
GP00001548
Abd-B
P09087
Morphology
unknown
Drosophila malerkotliana
(species)
Drosophila malerkotliana
(species)
Abdominal-B
Drosophila malerkotliana
(species)
Published - Accepted by Curator
Abdominal-B
Coloration (male-specific)
Unknown,
Unknown
Drosophila merina
(species)
Interspecific
Linkage Mapping
Signor SA; Liu Y; Rebeiz M ; et al. (2016)
Genetic Convergence in the Evolution of Male-Specific Color Patterns in Drosophila.
GP00001549
Abd-B
P09087
Morphology
unknown
Drosophila ercepeae
(species)
Drosophila merina
(species)
Abdominal-B
Drosophila merina
(species)
Published - Accepted by Curator
Abdominal-B
Coloration (abdomen; male)
Cis-regulatory,
Unknown
Drosophila santomea
(species) D
Interspecific
Linkage Mapping
Liu Y; Ramos-Womack M; Han C ; et al. (2019)
Changes throughout a Genetic Network Mask the Contribution of Hox Gene Evolution.
GP00002021
Abd-B
P09087
Morphology
change in the iab5 cis-regulatory element (15kb long)- exact causing mutation(s) unknown - decreased AbdB abdominal expression
Drosophila yakuba
(species)
Drosophila santomea
(species) D
Abdominal-B
Drosophila santomea
(species)
Published - Accepted by Curator
Abdominal-B
Coloration (abdomen; setae)
Cis-regulatory,
Unknown
Bombus melanopygus
(species)
Intraspecific
Association Mapping
Tian L; Rahman SR; Ezray BD ; et al. (2019)
A homeotic shift late in development drives mimetic color variation in a bumble bee.
GP00002048
Abd-B
P09087
Morphology
4kb region - probably several mutations according to recombinants with intermediate phenotypes
Bombus melanopygus
(species)
Bombus melanopygus
(species)
Abdominal-B
Bombus melanopygus
(species)
Published - Accepted by Curator
achaete-scute complex
Bristle number (abdomen; female-limited)
Cis-regulatory,
Insertion
Drosophila melanogaster
fruit fly - (species) D
Intraspecific
Linkage Mapping
Long AD; Lyman RF; Morgan AH ; et al. (2000)
Both naturally occurring insertions of transposable elements and intermediate frequency polymorphism[...]
GP00000046
sc
P10084
Morphology
transposon insertion in non-coding region
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species) D
achaete-scute complex
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
achaete-scute complex
Bristle number (abdomen)
Cis-regulatory,
Indel
Drosophila melanogaster
fruit fly - (species)
Intraspecific
Linkage Mapping
Long AD; Lyman RF; Morgan AH ; et al. (2000)
Both naturally occurring insertions of transposable elements and intermediate frequency polymorphism[...]
GP00000047
sc
P10084
Morphology
indel MC21 in promoter region of scute
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species)
achaete-scute complex
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
achaete-scute complex
Bristle number (thorax)
Cis-regulatory,
Indel
Drosophila melanogaster
fruit fly - (species)
Intraspecific
Linkage Mapping
Gruber JD; Genissel A; Macdonald SJ ; et al. (2007)
How repeatable are associations between polymorphisms in achaete-scute and bristle number variation [...]
GP00000048
sc
P10084
Morphology
indel MC22 in promoter region of scute
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species)
achaete-scute complex
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
achaete-scute complex
Bristle number (thorax)
Cis-regulatory,
Unknown
Drosophila quadrilineata
(species)
Interspecific
Candidate Gene
Marcellini S; Simpson P (2006)
Two or four bristles: functional evolution of an enhancer of scute in Drosophilidae.
GP00000049
sc
P10084
Morphology
Not identified
Drosophila melanogaster
fruit fly - (species)
Drosophila quadrilineata
(species)
achaete-scute complex
Drosophila quadrilineata
(species)
Published - Accepted by Curator
achaete-scute complex
Bristle number (genitalia; leg sex comb)
3 Mutations:
Cis-regulatory
SNP
Drosophila santomea
(species) D
Interspecific
Linkage Mapping
Nagy O; Nuez I; Savisaar R ; et al. (2018)
Correlated Evolution of Two Copulatory Organs via a Single cis-Regulatory Nucleotide Change.
GP00001680
sc
P10084
Morphology
3 mutations
Drosophila yakuba
(species)
Drosophila santomea
(species) D
achaete-scute complex
Drosophila santomea
(species)
Published - Accepted by Curator
ACS11
Plant architecture (petiole-to-leaf-length ratio)
Coding,
SNP
Arabidopsis thaliana
thale cress - (species)
Intraspecific
Association Mapping
Kooke R; Kruijer W; Bours R ; et al. (2016)
Genome-Wide Association Mapping and Genomic Prediction Elucidate the Genetic Architecture of Morphol[...]
GP00001235
ACS11
Q9S9U6
Morphology
several candidate amino acid changes
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
ACS11
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
ADAMTS10
Body size (height)
Unknown,
Unknown
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Lettre G (2011)
Recent progress in the study of the genetics of height.
GP00000050
ADAMTS10
Q9H324
Morphology
unknown
Homo sapiens
human - (species)
Homo sapiens
human - (species)
ADAMTS10
Homo sapiens
human - (species)
Published - Accepted by Curator
AGAMOUS-LIKE 50
Leaf number (at flowering time)
Unknown,
Unknown
Arabidopsis thaliana
thale cress - (species)
Intraspecific
Association Mapping
Seymour DK; Chae E; Grimm DG ; et al. (2016)
Genetic architecture of nonadditive inheritance in Arabidopsis thaliana hybrids.
GP00001450
AGAMOUS-like 50
Q9XIE7
Morphology
unknown
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
AGAMOUS-LIKE 50
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AGAMOUS-Like6
Plant architecture
Inflorescence architecture
Coding,
SNP
Arabidopsis thaliana
thale cress - (species) D
Intraspecific
Linkage Mapping
Huang X; Effgen S; Meyer RC ; et al. (2012)
Epistatic natural allelic variation reveals a function of AGAMOUS-LIKE6 in axillary bud formation in[...]
GP00000053
AGL6
P29386
Morphology
Morphology
Pro201Leu
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
AGAMOUS-Like6
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
aggrecan
Body size (dwarfism)
Coding,
Insertion
N
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Cavanagh JA; Tammen I; Windsor PA ; et al. (2007)
Bulldog dwarfism in Dexter cattle is caused by mutations in ACAN.
GP00002140
ACAN
P16112
Morphology
2266_2267insGGCA mutation introduces a frameshift and a premature termination codon into exon 11; the frameshift occurs at amino acid position 756 ; the termination codon occurs at position 914 compared to the normal aggrecan product of 2327 amino acids N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
aggrecan
Bos taurus
cattle - (species)
Published - Accepted by Curator
aggrecan
Body size (dwarfism)
Cis-regulatory,
SNP
N
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Cavanagh JA; Tammen I; Windsor PA ; et al. (2007)
Bulldog dwarfism in Dexter cattle is caused by mutations in ACAN.
GP00002141
ACAN
P16112
Morphology
−198C>T transition predicted to introduce a new ATG start codon 199 bp upstream of the normal start codon N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
aggrecan
Bos taurus
cattle - (species)
Published - Accepted by Curator
aggrecan
Body size (dwarfism)
Coding,
Deletion
N
Equus caballus
horse - (species) D
Domesticated
Association Mapping
Eberth JE; Graves KT; MacLeod JN ; et al. (2018)
Multiple alleles of ACAN associated with chondrodysplastic dwarfism in Miniature horses.
GP00002142
ACAN
P16112
Morphology
g.95257458_95257500del ; p.Phe2017-Asp2023del N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
aggrecan
Equus caballus
horse - (species)
Published - Accepted by Curator
aggrecan
Body size (dwarfism)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Metzger J; Gast AC; Schrimpf R ; et al. (2017)
Whole-genome sequencing reveals a potential causal mutation for dwarfism in the Miniature Shetland p[...]
1 Additional References
GP00002143
ACAN
P16112
Morphology
g.95282140C>G ; p.Ala505Pro
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
aggrecan
Equus caballus
horse - (species)
Published - Accepted by Curator
aggrecan
Body size (dwarfism)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Association Mapping
Eberth JE; Graves KT; MacLeod JN ; et al. (2018)
Multiple alleles of ACAN associated with chondrodysplastic dwarfism in Miniature horses.
GP00002144
ACAN
P16112
Morphology
g.95284530C>T ; p.Val424Met
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
aggrecan
Equus caballus
horse - (species)
Published - Accepted by Curator
aggrecan
Body size (dwarfism)
Coding,
Deletion
N
Equus caballus
horse - (species) D
Domesticated
Association Mapping
Eberth JE; Graves KT; MacLeod JN ; et al. (2018)
Multiple alleles of ACAN associated with chondrodysplastic dwarfism in Miniature horses.
GP00002145
ACAN
P16112
Morphology
g.95291270del ; p.Lys82fs N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
aggrecan
Equus caballus
horse - (species)
Published - Accepted by Curator
Agouti
Coloration (coat; dorso-ventral)
Gene Loss,
Deletion
N
Peromyscus polionotus
oldfield mouse - (species)
Intraspecific
Candidate Gene
Kingsley EP; Manceau M; Wiley CD ; et al. (2009)
Melanism in peromyscus is caused by independent mutations in agouti.
GP00000055
Asip
Q03288
Morphology
125kb deletion including 5' CDS of Agouti N
Peromyscus polionotus
oldfield mouse - (species)
Peromyscus polionotus
oldfield mouse - (species)
Agouti
Peromyscus polionotus
oldfield mouse - (species)
Published - Accepted by Curator
Agouti
Coloration (coat; dorso-ventral)
Coding,
SNP
N
Peromyscus polionotus
oldfield mouse - (species)
Intraspecific
Candidate Gene
Kingsley EP; Manceau M; Wiley CD ; et al. (2009)
Melanism in peromyscus is caused by independent mutations in agouti.
GP00000056
Asip
Q03288
Morphology
Premature stop codon at residue 65 N
Peromyscus polionotus
oldfield mouse - (species)
Peromyscus polionotus
oldfield mouse - (species)
Agouti
Peromyscus polionotus
oldfield mouse - (species)
Published - Accepted by Curator
Agouti
Coloration (coat; dorso-ventral)
Cis-regulatory,
Unknown
Peromyscus polionotus leucocephalus
(subspecies) D
Peromyscus polionotus niveiventris
(subspecies) D
Peromyscus polionotus peninsularis
(subspecies) D
Peromyscus polionotus allophrys
(subspecies) D
Peromyscus polionotus trissyllepsis
(subspecies) D
Peromyscus polionotus ammobates
(subspecies) D
Peromyscus polionotus albifrons
(subspecies) D
Peromyscus polionotus subgriseus
(subspecies) D
Intraspecific
Linkage Mapping
Manceau M; Domingues VS; Mallarino R ; et al. (2011)
The developmental role of Agouti in color pattern evolution.
1 Additional References
GP00000057
Asip
Q03288
Morphology
"A closer investigation of this region revealed three SNPs significantly associated with pigment variation, spanning 1,756 bp, in strong linkage disequilibrium (mean r2 = 0.85). A single SNP on chromosome 4 (chr4) at position chr4: 9,845,301 showed a markedly stronger association with pPC1 than the other two (Fig. 3B). This SNP is located between two untranslated exons (exons 1D and 1E), is 120 bp upstream of a cluster of Short Interspersed Nuclear Elements (SINE) in reverse orientation relative to the transcription of Agouti, and is 5,641 bp upstream of the first coding exon (exon 2). "
"Next, we employ an association-mapping approach to identify an ∼2-kb previously uncharacterized noncoding region of Agouti associated with color variation. We then show that this 2-kb region can drive dermal expression in Mus embryos, demonstrating its regulatory activity in the skin during the establishment of pigmentation."
Peromyscus polionotus subgriseus
(subspecies)
Peromyscus polionotus polionotus
(subspecies)
Peromyscus polionotus albifrons
(subspecies)
Peromyscus polionotus leucocephalus
(subspecies) D
Peromyscus polionotus niveiventris
(subspecies) D
Peromyscus polionotus peninsularis
(subspecies) D
Peromyscus polionotus allophrys
(subspecies) D
Peromyscus polionotus trissyllepsis
(subspecies) D
Peromyscus polionotus ammobates
(subspecies) D
Peromyscus polionotus albifrons
(subspecies) D
Peromyscus polionotus subgriseus
(subspecies) D
Agouti
Peromyscus polionotus leucocephalus
(subspecies)
Peromyscus polionotus niveiventris
(subspecies)
Peromyscus polionotus peninsularis
(subspecies)
Peromyscus polionotus allophrys
(subspecies)
Peromyscus polionotus trissyllepsis
(subspecies)
Peromyscus polionotus ammobates
(subspecies)
Peromyscus polionotus albifrons
(subspecies)
Peromyscus polionotus subgriseus
(subspecies)
Published - Accepted by Curator
Agouti
Coloration (coat; dorso-ventral)
Cis-regulatory,
Unknown
Sus scrofa domesticus
domestic pig - (subspecies)
Domesticated
Linkage Mapping
Drögemüller C; Giese A; Martins-Wess F ; et al. (2006)
The mutation causing the black-and-tan pigmentation phenotype of Mangalitza pigs maps to the porcine[...]
GP00000058
Asip
Q03288
Morphology
unknown
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies)
Agouti
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
Agouti
Coloration (coat)
Cis-regulatory,
Insertion
Bos taurus
cattle - (species) D
Domesticated
Candidate Gene
Girardot M; Guibert S; Laforet MP ; et al. (2006)
The insertion of a full-length Bos taurus LINE element is responsible for a transcriptional deregula[...]
GP00000059
Asip
Q03288
Morphology
LINE element insertion in 5' region of gene; over expression of alternative splice forms
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Agouti
Bos taurus
cattle - (species)
Published - Accepted by Curator
Agouti
Coloration (coat)
Coding,
Deletion
N
Equus caballus
horse - (species) D
Intraspecific
Linkage Mapping
Rieder S; Taourit S; Mariat D ; et al. (2001)
Mutations in the agouti (ASIP), the extension (MC1R), and the brown (TYRP1) loci and their associati[...]
1 Additional References
GP00000062
Asip
Q03288
Morphology
11bp deletion in exon 2: g.2174_2184del11 c.191_201del N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Agouti
Equus caballus
horse - (species)
Published - Accepted by Curator
Agouti
Coloration (coat)
Coding,
Deletion
N
Felis catus
domestic cat - (species) D
Domesticated
Linkage Mapping
Eizirik E; Yuhki N; Johnson WE ; et al. (2003)
Molecular genetics and evolution of melanism in the cat family.
GP00000063
Asip
Q03288
Morphology
Deletion of nt 123-124 N
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
Agouti
Felis catus
domestic cat - (species)
Published - Accepted by Curator
Agouti
Coloration (coat)
Coding,
SNP
N
Panthera pardus
leopard - (species) D
Intraspecific
Candidate Gene
Schneider A; David VA; Johnson WE ; et al. (2012)
How the leopard hides its spots: ASIP mutations and melanism in wild cats.
GP00000065
Asip
Q03288
Morphology
nonsense mutation located in exon 4 (C333A) predicted to introduce a stop codon at amino acid position 111 N
Panthera pardus
leopard - (species)
Panthera pardus
leopard - (species) D
Agouti
Panthera pardus
leopard - (species)
Published - Accepted by Curator
Agouti
Coloration (coat)
Coding,
SNP
Catopuma temminckii
Asiatic golden cat - (species)
Intraspecific
Candidate Gene
Schneider A; David VA; Johnson WE ; et al. (2012)
How the leopard hides its spots: ASIP mutations and melanism in wild cats.
GP00000066
Asip
Q03288
Morphology
C128W (384C>G)
Catopuma temminckii
Asiatic golden cat - (species)
Catopuma temminckii
Asiatic golden cat - (species)
Agouti
Catopuma temminckii
Asiatic golden cat - (species)
Published - Accepted by Curator
Agouti
Coloration (coat)
Coding,
Deletion
N
Vulpes vulpes
red fox - (species) D
Domesticated
Candidate Gene
Våge DI; Lu D; Klungland H ; et al. (1997)
A non-epistatic interaction of agouti and extension in the fox, Vulpes vulpes.
GP00000067
Asip
Q03288
Morphology
166 bp deletion in exon 1 N
Vulpes vulpes
red fox - (species)
Vulpes vulpes
red fox - (species) D
Agouti
Vulpes vulpes
red fox - (species)
Published - Accepted by Curator
Agouti
Coloration (feathers)
Coding,
Deletion
N
Coturnix japonica
Japanese quail - (species) D
Domesticated
Linkage Mapping
Hiragaki T; Inoue-Murayama M; Miwa M ; et al. (2008)
Recessive black is allelic to the yellow plumage locus in Japanese quail and associated with a frame[...]
GP00000068
Asip
Q03288
Morphology
8bp frameshift deletion N
Coturnix japonica
Japanese quail - (species)
Coturnix japonica
Japanese quail - (species) D
Agouti
Coturnix japonica
Japanese quail - (species)
Published - Accepted by Curator
Agouti
Coloration (feathers)
Cis-regulatory,
Deletion
Coturnix japonica
Japanese quail - (species) D
Domesticated
Linkage Mapping
Nadeau NJ; Minvielle F; Ito S ; et al. (2008)
Characterization of Japanese quail yellow as a genomic deletion upstream of the avian homolog of the[...]
1 Additional References
GP00000069
Asip
Q03288
Morphology
141162-bp deletion resulting in novel promoter sharing and expression of a RALY-ASIP fusion transcript
Coturnix japonica
Japanese quail - (species)
Coturnix japonica
Japanese quail - (species) D
Agouti
Coturnix japonica
Japanese quail - (species)
Published - Accepted by Curator
Agouti
Coloration (coat)
Coding,
SNP
N
Leopardus colocolo
Colocolo - (species) D
Intraspecific
Candidate Gene
Schneider A; Henegar C; Day K ; et al. (2015)
Recurrent evolution of melanism in South American felids.
GP00001731
Asip
Q03288
Morphology
Arg to Cys substitution in the C-terminal region of ASIP (p.R120C) lies in the critical RFF loop (e.g. a triplet motif made of one arginine and two phenylalanine residues) required for binding to the MC1R N
Leopardus colocolo
Colocolo - (species)
Leopardus colocolo
Colocolo - (species) D
Agouti
Leopardus colocolo
Colocolo - (species)
Published - Accepted by Curator
Agouti
Coloration (coat)
Coding,
SNP
N
Leopardus guigna
Kodkod - (species) D
Intraspecific
Candidate Gene
Schneider A; Henegar C; Day K ; et al. (2015)
Recurrent evolution of melanism in South American felids.
GP00001732
Asip
Q03288
Morphology
Cys to Tyr substitution in ASIP (p.C126Y) which affects the key disulfide bond that stabilizes the RFF loop N
Leopardus guigna
Kodkod - (species)
Leopardus guigna
Kodkod - (species) D
Agouti
Leopardus guigna
Kodkod - (species)
Published - Accepted by Curator
Agouti
Coloration (feathers)
Gene Amplification,
Insertion
Coturnix japonica
Japanese quail - (species) D
Domesticated
Linkage Mapping
Robic A; Morisson M; Leroux S ; et al. (2019)
Two new structural mutations in the 5' region of the ASIP gene cause diluted feather color phenotype[...]
GP00001973
Asip
Q03288
Morphology
71-kb tandem duplication that comprises one unchanged copy of ASIP and one copy present in the ITCH-ASIP fusion gene which leads to a transcript coding for a normal ASIP protein
Coturnix japonica
Japanese quail - (species)
Coturnix japonica
Japanese quail - (species) D
Agouti
Coturnix japonica
Japanese quail - (species)
Published - Accepted by Curator
Agouti
Coloration (coat)
5 Mutations:
Peromyscus maniculatus
North American deer mouse - (species)
Intraspecific
Association Mapping
Linnen CR; Poh YP; Peterson BK ; et al. (2013)
Adaptive evolution of multiple traits through multiple mutations at a single gene.
1 Additional References
GP00001974
Asip
Q03288
Morphology
5 mutations
Peromyscus maniculatus
North American deer mouse - (species)
Peromyscus maniculatus
North American deer mouse - (species)
Agouti
Peromyscus maniculatus
North American deer mouse - (species)
Published - Accepted by Curator
Agouti
Coloration (coat)
Gene Loss,
Deletion
N
Peromyscus maniculatus
North American deer mouse - (species)
Intraspecific
Candidate Gene
Kingsley EP; Manceau M; Wiley CD ; et al. (2009)
Melanism in peromyscus is caused by independent mutations in agouti.
GP00001975
Asip
Q03288
Morphology
125kb deletion ; recessive mutation N
Peromyscus maniculatus
North American deer mouse - (species)
Peromyscus maniculatus
North American deer mouse - (species)
Agouti
Peromyscus maniculatus
North American deer mouse - (species)
Published - Accepted by Curator
Agouti
Coloration (coat)
Coding,
SNP
N
Peromyscus maniculatus
North American deer mouse - (species)
Intraspecific
Association Mapping
Kingsley EP; Manceau M; Wiley CD ; et al. (2009)
Melanism in peromyscus is caused by independent mutations in agouti.
GP00001976
Asip
Q03288
Morphology
recessive mutation at nucleotide position 193 (in exon 3) resulting in a change from glutamine to a stop codon at amino acid position 65 (Q65term) N
Peromyscus maniculatus
North American deer mouse - (species)
Peromyscus maniculatus
North American deer mouse - (species)
Agouti
Peromyscus maniculatus
North American deer mouse - (species)
Published - Accepted by Curator
Agouti
Coloration (coat)
Coding,
SNP
Sciurus niger
fox squirrel - (species) D
Intraspecific
Candidate Gene
McRobie HR; Moncrief ND; Mundy NI (2019)
Multiple origins of melanism in two species of North American tree squirrel (Sciurus).
GP00002335
Morphology
Gly121Cys
Sciurus niger
fox squirrel - (species)
Sciurus niger
fox squirrel - (species) D
Agouti
Sciurus niger
fox squirrel - (species)
Published - Accepted by Curator
Agouti
Coloration (coat)
Cis-regulatory,
Insertion
Mus musculus molossinus
Japanese wild mouse - (subspecies) D
Intraspecific
Candidate Gene
Tanave A; Imai Y; Koide T (2019)
Nested retrotransposition in the East Asian mouse genome causes the classical nonagouti mutation.
GP00002386
Asip
Q03288
Morphology
Mus musculus molossinus
Japanese wild mouse - (subspecies)
Mus musculus molossinus
Japanese wild mouse - (subspecies) D
Agouti
Mus musculus molossinus
Japanese wild mouse - (subspecies)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Coding,
SNP
Canis lupus familiaris
dog - (subspecies)
Domesticated
Candidate Gene
Berryere TG; Kerns JA; Barsh GS ; et al. (2005)
Association of an Agouti allele with fawn or sable coat color in domestic dogs.
GP00000060
Asip
Q03288
Morphology
c.244G>T + 248G>A ; p.A82S + p.R83H
A82S and R83H in Linkage Disequilibrium
a G-to-T transversion and a G-to-A transition in exon 4 at positions corresponding to residues 244 and 248 of the cDNA sequence
It is unknown if one or both substitutions alter Agouti protein function
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies)
Agouti (ASIP)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Kerns JA; Newton J; Berryere TG ; et al. (2004)
Characterization of the dog Agouti gene and a nonagoutimutation in German Shepherd Dogs.
1 Additional References
GP00000061
Asip
Q03288
Morphology
R96C ; g.23393552C>T c.286C>T p.R96C
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
Agouti (ASIP)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (skin; hair)
Cis-regulatory,
Unknown
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Bonilla C; Boxill LA; Donald SA ; et al. (2005)
The 8818G allele of the agouti signaling protein (ASIP) gene is ancestral and is associated with dar[...]
2 Additional References
GP00000070
Asip
Q03288
Morphology
unknown
Homo sapiens
human - (species)
Homo sapiens
human - (species)
Agouti (ASIP)
Homo sapiens
human - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Gene Amplification,
Insertion
Ovis aries
sheep - (species) D
Domesticated
Candidate Gene
Norris BJ; Whan VA (2008)
A gene duplication affecting expression of the ovine ASIP gene is responsible for white and black sh[...]
1 Additional References
GP00001324
Asip
Q03288
Morphology
~190kb gene duplication causing dominant white phenotype. Duplication was facilitated by homologous recombination between two non-LTR SINE sequences flanking the duplicated segment ; possible involvement of gene conversion.
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
Agouti (ASIP)
Ovis aries
sheep - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Cis-regulatory,
SNP
Ovis aries
sheep - (species) D
Domesticated
Candidate Gene
Norris BJ; Whan VA (2008)
A gene duplication affecting expression of the ovine ASIP gene is responsible for white and black sh[...]
GP00001325
Asip
Q03288
Morphology
unidentified promoter silencing
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
Agouti (ASIP)
Ovis aries
sheep - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Cis-regulatory,
Unknown
Vermivora cyanoptera
blue-winged warbler - (species)
Interspecific
Association Mapping
Toews DP; Taylor SA; Vallender R ; et al. (2016)
Plumage Genes and Little Else Distinguish the Genomes of Hybridizing Warblers.
GP00001331
Asip
Q03288
Morphology
unknown - the divergent region falls in the 5prime region that is directly upstream of the associated coding region
Vermivora chrysoptera
Golden-winged warbler - (species)
Vermivora cyanoptera
blue-winged warbler - (species)
Agouti (ASIP)
Vermivora cyanoptera
blue-winged warbler - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Coding,
SNP
Monarcha castaneiventris
Makira monarch - (species) D
Intraspecific
Association Mapping
Uy JA; Cooper EA; Cutie S ; et al. (2016)
Mutations in different pigmentation genes are associated with parallel melanism in island flycatcher[...]
GP00001334
Asip
Q03288
Morphology
Ile55Thr
Monarcha castaneiventris
Makira monarch - (species)
Monarcha castaneiventris
Makira monarch - (species) D
Agouti (ASIP)
Monarcha castaneiventris
Makira monarch - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Coding,
SNP
Equus asinus
ass - (species) D
Domesticated
Candidate Gene
Abitbol M; Legrand R; Tiret L (2015)
A missense mutation in the agouti signaling protein gene (ASIP) is associated with the no light poin[...]
GP00001335
Asip
Q03288
Morphology
c.349T>C p.Cys117Arg
Equus asinus
ass - (species)
Equus asinus
ass - (species) D
Agouti (ASIP)
Equus asinus
ass - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Cis-regulatory,
Insertion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Dreger DL; Schmutz SM (2011 Sep-Oct)
A SINE insertion causes the black-and-tan and saddle tan phenotypes in domestic dogs.
GP00001336
Asip
Q03288
Morphology
A 239bp SINE insertion in reverse orientation in intron 1
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
Agouti (ASIP)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Lifespan
2 Mutations:
Coding
N
Ovis aries
sheep - (species) D
Intraspecific
Linkage Mapping
Gratten J; Pilkington JG; Brown EA ; et al. (2010)
The genetic basis of recessive self-colour pattern in a wild sheep population.
1 Additional References
GP00001356
Asip
Q03288
Morphology
Physiology
2 mutations
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
Agouti (ASIP)
Ovis aries
sheep - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Coding,
Insertion
N
Oryctolagus cuniculus
rabbit - (species) D
Domesticated
Candidate Gene
Fontanesi L; Forestier L; Allain D ; et al. (2010)
Characterization of the rabbit agouti signaling protein (ASIP) gene: transcripts and phylogenetic an[...]
1 Additional References
GP00001968
Asip
Q03288
Morphology
an insertion in exon 2 of the black nonagouti allele = c.5_6insA mutation which causes a frameshift and a predicted truncated protein of only 21 amino acids N
Oryctolagus cuniculus
rabbit - (species)
Oryctolagus cuniculus
rabbit - (species) D
Agouti (ASIP)
Oryctolagus cuniculus
rabbit - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Coding,
Deletion
N
D
Intraspecific
Candidate Gene
Miller SM; Guthrie AJ; Harper CK (2016)
Single base-pair deletion in ASIP exon 3 associated with recessive black phenotype in impala (Aepyce[...]
GP00001977
Asip
Q03288
Morphology
recessive c.174delA was found in all black phenotype sequences ; premature stop codon (239–241 bp) N
D
Agouti (ASIP)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Coding,
Deletion
N
Camelus dromedarius
Arabian camel - (species) D
Domesticated
Candidate Gene
Almathen F; Elbir H; Bahbahani H ; et al. (2018)
Polymorphisms in MC1R and ASIP Genes are Associated with Coat Color Variation in the Arabian Camel.
1 Additional References
GP00001978
Asip
Q03288
Morphology
1-bp deletion at position 23 resulting in frameshift N
Camelus dromedarius
Arabian camel - (species)
Camelus dromedarius
Arabian camel - (species) D
Agouti (ASIP)
Camelus dromedarius
Arabian camel - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Cis-regulatory,
Unknown
Lepus americanus
snowshoe hare - (species) D
Intraspecific
Association Mapping
Jones MR; Mills LS; Alves PC ; et al. (2018)
Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares.
GP00002060
Asip
Q03288
Morphology
exact mutation(s) unknown
Lepus americanus
snowshoe hare - (species)
Lepus americanus
snowshoe hare - (species) D
Agouti (ASIP)
Lepus americanus
snowshoe hare - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Cis-regulatory,
Unknown
Lepus timidus
Mountain hare - (species) D
Intraspecific
Association Mapping
Giska I; Farelo L; Pimenta J ; et al. (2019)
Introgression drives repeated evolution of winter coat color polymorphism in hares.
GP00002061
Asip
Q03288
Morphology
exact mutation(s) unknown
Lepus timidus
Mountain hare - (species)
Lepus timidus
Mountain hare - (species) D
Agouti (ASIP)
Lepus timidus
Mountain hare - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Cis-regulatory,
Insertion
Mus musculus
house mouse - (species) D
Domesticated
Candidate Gene
Morgan HD; Sutherland HG; Martin DI ; et al. (1999)
Epigenetic inheritance at the agouti locus in the mouse.
GP00002107
Asip
Q03288
Morphology
insertion of an intra-cisternal A particle (IAP) retrotransposon upstream of the agouti gene (A). This activates transcription and causes ectopic expression of agouti protein; resulting in yellow fur; obesity; diabetes and increased susceptibility to tumours. The pleiotropic effects of ectopic agouti expression are presumably due to effects of the paracrine signal on other tissues.
Mus musculus
house mouse - (species)
Mus musculus
house mouse - (species) D
Agouti (ASIP)
Mus musculus
house mouse - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (skin)
Cis-regulatory,
Unknown
Gallus gallus
chicken - (species)
Domesticated
Candidate Gene
Yu S; Wang G; Liao J (2019)
Association of a novel SNP in the ASIP gene with skin color in black-bone chicken.
GP00002130
Asip
Q03288
Morphology
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
Agouti (ASIP)
Gallus gallus
chicken - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Coding,
SNP
Vicugna pacos
alpaca - (species) D
Domesticated
Candidate Gene
Chandramohan B; Renieri C; La Manna V ; et al. (2013)
The alpaca agouti gene: genomic locus, transcripts and causative mutations of eumelanic and pheomela[...]
GP00002336
Asip
Q03288
Morphology
p.R98C likely affecting conformation in a cysteine-rich domain
Vicugna pacos
alpaca - (species)
Vicugna pacos
alpaca - (species) D
Agouti (ASIP)
Vicugna pacos
alpaca - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Cis-regulatory,
Insertion
Bubalus bubalis
water buffalo - (species) D
Domesticated
Association Mapping
Liang D; Zhao P; Si J ; et al. (2021)
Genomic Analysis Revealed a Convergent Evolution of LINE-1 in Coat Color: A Case Study in Water Buff[...]
GP00002370
Asip
Q03288
Morphology
"2,809-bp-long LINE-1 insertion in the ASIP (agouti signaling protein) gene is the causative mutation for the white coat phenotype in swamp buffalo (Bubalus bubalis). This LINE-1 insertion (3′ truncated and containing only 5′ UTR) functions as a strong proximal promoter that leads to a 10-fold increase in the transcription of ASIP in white buffalo skin. The 165 bp of 5′ UTR transcribed from the LINE-1 is spliced into the first coding exon of ASIP, resulting in a chimeric transcript. The increased expression of ASIP prevents melanocyte maturation, leading to the absence of pigment in white buffalo skin and hairs. Phylogenetic analyses indicate that the white buffalo-specific ASIP allele originated from a recent genetic transposition event in swamp buffalo. Interestingly, as a similar LINE-1 insertion has been identified in the cattle ASIP gene, we discuss the convergent mechanism of coat color evolution in the Bovini tribe."
Bubalus bubalis
water buffalo - (species)
Bubalus bubalis
water buffalo - (species) D
Agouti (ASIP)
Bubalus bubalis
water buffalo - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat; dorso-ventral)
Coding,
Insertion
N
Oryctolagus cuniculus
rabbit - (species) D
Domesticated
Candidate Gene
Letko A; Ammann B; Jagannathan V ; et al. (2020)
A deletion spanning the promoter and first exon of the hair cycle-specific ASIP transcript isoform i[...]
GP00002373
Asip
Q03288
Morphology
"The structural variant represented an approximately 11 kb deletion (NC_013672.1:g.5,455,408_5,466,123del; Fig. 2). In rabbit, there are currently two ASIP transcript isoforms annotated (NCBI annotation release 102). The deletion removes the entire first 5′-untranslated exon of one of these transcripts (NM_001122939.1). (...) he deletion removed the transcription start site and the first untranslated exon of the presumably hair cycle-specific transcript isoform, suggesting that this is the most likely causative variant for the black and tan phenotype." N
Oryctolagus cuniculus
rabbit - (species)
Oryctolagus cuniculus
rabbit - (species) D
Agouti (ASIP)
Oryctolagus cuniculus
rabbit - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration
Gene Amplification,
Insertion
Capra hircus
goat - (species) D
Domesticated
Association Mapping
Guo J; Sun X; Mao A ; et al. (2022)
A 13.42-kb tandem duplication at the ASIP locus is strongly associated with the depigmentation pheno[...]
GP00002380
Asip
Q03288
Morphology
"We confirmed that a genomic region harboring the ASIP gene is a major locus affecting the coat color phenotype of Swiss markings in goats. Although the molecular genetic mechanisms remain unsolved, the 13,420-bp duplication upstream of ASIP is a necessary but not sufficient condition for this phenotype in goats. Moreover, the variations in the copy number of the duplication across different goat breeds do not lead to phenotypic heterogeneity."
Capra hircus
goat - (species)
Capra hircus
goat - (species) D
Agouti (ASIP)
Capra hircus
goat - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Gene Amplification,
Insertion
Capra hircus
goat - (species) D
Domesticated
Candidate Gene
Henkel J; Dubacher A; Bangerter E ; et al. (2021)
Introgression of ASIP and TYRP1 Alleles Explains Coat Color Variation in Valais Goats.
GP00002381
Asip
Q03288
Morphology
"The white Capra Sempione carried one copy of the AWt allele, which is commonly found in Saanen and Appenzell goats. AWt involves a triplication of ~155 kb comprising the coding sequence of the ASIP, AHCY and ITCH genes (Fontanesi et al. 2009; Henkel et al. 2019). Closer inspection of the short-read alignments revealed that the sequenced Capra Sempione had acquired additional smaller structural alterations compared to the original AWt allele, which comprised a duplication of 1053 bp inserted into a 10 194 bp deletion of the original AWt CNV allele (Supplementary Figure S1)."
Capra hircus
goat - (species)
Capra hircus
goat - (species) D
Agouti (ASIP)
Capra hircus
goat - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Gene Amplification,
Insertion
Capra hircus
goat - (species) D
Domesticated
Candidate Gene
Henkel J; Dubacher A; Bangerter E ; et al. (2021)
Introgression of ASIP and TYRP1 Alleles Explains Coat Color Variation in Valais Goats.
GP00002382
Asip
Q03288
Morphology
"The greyish Grüenochte goat carried one copy of the Apc allele, which causes the characteristic black and white pattern of Swiss Peacock goats (Henkel et al. 2019). The Apc allele consists of a central quadruplication of ~45 kb with triplicated adjacent flanking regions comprising ~28 kb and ~42 kb, respectively."
Capra hircus
goat - (species)
Capra hircus
goat - (species) D
Agouti (ASIP)
Capra hircus
goat - (species)
Published - Accepted by Curator
Agouti-related peptide 2 (agrp2)
Coloration (stripes)
Cis-regulatory,
Unknown
Haplochromis sauvagei
(species)
Haplochromis chilotes
(species)
Interspecific
Linkage Mapping
Kratochwil CF; Liang Y; Gerwin J ; et al. (2018)
Agouti-related peptide 2 facilitates convergent evolution of stripe patterns across cichlid fish rad[...]
1 Additional References
GP00001764
asip2b
J3JQX9
Morphology
Causal mutation(s) are in a 1.1-kb interval within the first agrp2 intron
Pundamilia nyererei
(species)
Haplochromis sauvagei
(species)
Haplochromis chilotes
(species)
Agouti-related peptide 2 (agrp2)
Haplochromis sauvagei
(species)
Haplochromis chilotes
(species)
Published - Accepted by Curator
Agouti-related peptide 2 (agrp2)
Coloration (stripes)
Cis-regulatory,
Unknown
Haplochromis sauvagei
(species)
Haplochromis chilotes
(species)
Interspecific
Linkage Mapping
Kratochwil CF; Liang Y; Gerwin J ; et al. (2018)
Agouti-related peptide 2 facilitates convergent evolution of stripe patterns across cichlid fish rad[...]
1 Additional References
GP00001960
asip2b
J3JQX9
Morphology
Causal mutation(s) are in a 1.1-kb interval within the first agrp2 intron
Pundamilia nyererei
(species)
Haplochromis sauvagei
(species)
Haplochromis chilotes
(species)
Agouti-related peptide 2 (agrp2)
Haplochromis sauvagei
(species)
Haplochromis chilotes
(species)
Published - Accepted by Curator
agrecan
Body size (height)
Unknown,
Unknown
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Lettre G (2011)
Recent progress in the study of the genetics of height.
GP00000072
ACAN
P16112
Morphology
unknown
Homo sapiens
human - (species)
Homo sapiens
human - (species)
agrecan
Homo sapiens
human - (species)
Published - Accepted by Curator
ALX1
Beak size
Unknown,
Unknown
Geospiza
(genus) D
Interspecific
Association Mapping
Lamichhaney S; Berglund J; Almén MS ; et al. (2015)
Evolution of Darwin's finches and their beaks revealed by genome sequencing.
1 Additional References
GP00000081
Alx1
Q8C8B0
Morphology
240kb haplotype with complex variation
Geospiza
(genus)
Geospiza
(genus) D
ALX1
Geospiza
(genus)
Published - Accepted by Curator
an2-like (Stan2)
Coloration (tuber skin)
Cis-regulatory,
Unknown
Solanum tuberosum
potato - (species)
Domesticated
Linkage Mapping
Jung CS; Griffiths HM; De Jong DM ; et al. (2009)
The potato developer (D) locus encodes an R2R3 MYB transcription factor that regulates expression of[...]
GP00000088
AN2
A4GRU8
Morphology
unknown
Solanum tuberosum
potato - (species)
Solanum tuberosum
potato - (species)
an2-like (Stan2)
Solanum tuberosum
potato - (species)
Published - Accepted by Curator
anthocyanin2 (an2)
Coloration (fruit)
Cis-regulatory,
Unknown
Capsicum chinense
(species)
Domesticated
Linkage Mapping
Borovsky Y; Oren-Shamir M; Ovadia R ; et al. (2004)
The A locus that controls anthocyanin accumulation in pepper encodes a MYB transcription factor homo[...]
GP00000087
AN2
A4GRU8
Morphology
unknown
Capsicum annuum
(species)
Capsicum chinense
(species)
anthocyanin2 (an2)
Capsicum chinense
(species)
Published - Accepted by Curator
anthocyanin2 (an2)
Coloration (flowers)
Coding,
Deletion
N
Petunia axillaris
(species) D
Intraspecific
Candidate Gene
Quattrocchio F; Wing J; van der Woude K ; et al. (1999)
Molecular analysis of the anthocyanin2 gene of petunia and its role in the evolution of flower color[...]
GP00000089
AN2
A4GRU8
Morphology
1bp deletion at a.a. 127; premature stop N
Petunia integrifolia
(species)
Petunia axillaris
(species) D
anthocyanin2 (an2)
Petunia axillaris
(species)
Published - Accepted by Curator
anthocyanin2 (an2)
Coloration (flowers)
Coding,
Insertion
N
Petunia axillaris
(species) D
Intraspecific
Candidate Gene
Quattrocchio F; Wing J; van der Woude K ; et al. (1999)
Molecular analysis of the anthocyanin2 gene of petunia and its role in the evolution of flower color[...]
GP00000090
AN2
A4GRU8
Morphology
4bp insertion at a.a. 127; premature stop N
Petunia integrifolia
(species)
Petunia axillaris
(species) D
anthocyanin2 (an2)
Petunia axillaris
(species)
Published - Accepted by Curator
anthocyanin2 (an2)
Coloration (flowers)
Coding,
SNP
N
Petunia axillaris
(species)
Intraspecific
Candidate Gene
Quattrocchio F; Wing J; van der Woude K ; et al. (1999)
Molecular analysis of the anthocyanin2 gene of petunia and its role in the evolution of flower color[...]
GP00000091
AN2
A4GRU8
Morphology
W196* N
Petunia integrifolia
(species)
Petunia axillaris
(species)
anthocyanin2 (an2)
Petunia axillaris
(species)
Published - Accepted by Curator
anthocyanin2 (an2)
Coloration (flowers)
Coding,
Deletion
N
Petunia axillaris
(species) D
Intraspecific
Candidate Gene
Hoballah ME; Gübitz T; Stuurman J ; et al. (2007)
Single gene-mediated shift in pollinator attraction in Petunia.
GP00000092
AN2
A4GRU8
Morphology
1bp deletion; premature stop N
Petunia integrifolia
(species)
Petunia axillaris
(species) D
anthocyanin2 (an2)
Petunia axillaris
(species)
Published - Accepted by Curator
anthocyanin2 (an2)
Coloration (flowers)
Coding,
SNP
N
Petunia axillaris
(species)
Interspecific
Candidate Gene
Hoballah ME; Gübitz T; Stuurman J ; et al. (2007)
Single gene-mediated shift in pollinator attraction in Petunia.
GP00000093
AN2
A4GRU8
Morphology
1 aa substitution; premature stop N
Petunia integrifolia
(species)
Petunia axillaris
(species)
anthocyanin2 (an2)
Petunia axillaris
(species)
Published - Accepted by Curator
anthocyanin2 (an2)
Coloration (flowers)
Coding,
SNP
N
Petunia axillaris
(species)
Interspecific
Candidate Gene
Hoballah ME; Gübitz T; Stuurman J ; et al. (2007)
Single gene-mediated shift in pollinator attraction in Petunia.
GP00000094
AN2
A4GRU8
Morphology
1 aa substitution; premature stop N
Petunia integrifolia
(species)
Petunia axillaris
(species)
anthocyanin2 (an2)
Petunia axillaris
(species)
Published - Accepted by Curator
apontic-like
Coloration (larval color pattern)
Cis-regulatory,
Unknown
Bombyx mori
domestic silkworm - (species) D
Domesticated
Linkage Mapping
Yoda S; Yamaguchi J; Mita K ; et al. (2014)
The transcription factor Apontic-like controls diverse colouration pattern in caterpillars.
2 Additional References
GP00001386
apt
O61602
Morphology
233-kb region around apt-like (pS) refined as 33kb interval in apt-like Intron 1 (+p) with uncharacterized haplotype driving apt-like upregulation in derived phenotypes
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
apontic-like
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
AR
Sensory vibrissae (loss)
Penile spine (loss)
Cis-regulatory,
Deletion
Homo sapiens
human - (species) D
Interspecific
Candidate Gene
McLean CY; Reno PL; Pollen AA ; et al. (2011)
Human-specific loss of regulatory DNA and the evolution of human-specific traits.
GP00000102
AR
P10275
Morphology
Morphology
Enhancer loss
Pan troglodytes
chimpanzee - (species)
Homo sapiens
human - (species) D
AR
Homo sapiens
human - (species)
Published - Accepted by Curator
ARHGAP11B
Neocortex development (basal progenitor amplification)
Coding,
SNP
N
Homo sapiens
human - (species) D
Intraspecific
Candidate Gene
Florio M; Namba T; Pääbo S ; et al. (2016)
A single splice site mutation in human-specific ARHGAP11B causes basal progenitor amplification.
GP00001442
ARHGAP11B
Q3KRB8
Morphology
c.661C>G new splice site mutation removing 55nt from exon 5 truncating a GAP domain N
Homo sapiens
human - (species)
Homo sapiens
human - (species) D
ARHGAP11B
Homo sapiens
human - (species)
Published - Accepted by Curator
aristaless
Coloration (wing, Mullerian mimicry)
Cis-regulatory,
Unknown
Heliconius cydno
(species) D
Intraspecific
Linkage Mapping
Westerman EL; VanKuren NW; Massardo D ; et al. (2018)
Aristaless Controls Butterfly Wing Color Variation Used in Mimicry and Mate Choice.
GP00002059
al
Q06453
Morphology
gain of expression - exact mutation unknown
Heliconius cydno
(species)
Heliconius cydno
(species) D
aristaless
Heliconius cydno
(species)
Published - Accepted by Curator
arrow
Coloration (wing)
Cis-regulatory,
Unknown
Danaus chrysippus
African queen - (species)
Intraspecific
Association Mapping
Martin SH; Singh KS; Gordon IJ ; et al. (2020)
Whole-chromosome hitchhiking driven by a male-killing endosymbiont.
GP00002431
cnn
P54623
Morphology
The strongest associations with forewing tip (C locus) occur at the gene arrow and a phylogenetic network for a 100-kb region around this gene similarly clusters individuals by phenotype. In Drosophila Arrow is essential for Wnt signalling in wing development
Danaus chrysippus
African queen - (species)
Danaus chrysippus
African queen - (species)
arrow
Danaus chrysippus
African queen - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Gene Loss,
Complex Change
N
Arabidopsis thaliana
thale cress - (species)
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000106
GA20OX1
Q39110
Morphology
Whole gene deletion N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
Deletion
N
Arabidopsis thaliana
thale cress - (species) D
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000107
GA20OX1
Q39110
Morphology
-2bp at +297 N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
Deletion
N
Arabidopsis thaliana
thale cress - (species) D
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000108
GA20OX1
Q39110
Morphology
-1bp "G" at +324 N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
Deletion
N
Arabidopsis thaliana
thale cress - (species) D
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000109
GA20OX1
Q39110
Morphology
-5bp "G" at +545 N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
Deletion
N
Arabidopsis thaliana
thale cress - (species) D
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000110
GA20OX1
Q39110
Morphology
-10bp "G" at +784 N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
Deletion
N
Arabidopsis thaliana
thale cress - (species) D
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000111
GA20OX1
Q39110
Morphology
-29bp at +426 N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
Deletion
N
Arabidopsis thaliana
thale cress - (species) D
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000112
GA20OX1
Q39110
Morphology
-444bp at +985 N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
Insertion
N
Arabidopsis thaliana
thale cress - (species) D
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000113
GA20OX1
Q39110
Morphology
+1bp "G" at +256 N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
Insertion
N
Arabidopsis thaliana
thale cress - (species) D
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000114
GA20OX1
Q39110
Morphology
+7bp "G" at +961 N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
Insertion
N
Arabidopsis thaliana
thale cress - (species) D
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000115
GA20OX1
Q39110
Morphology
+1bp at +1270 N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
Insertion
N
Arabidopsis thaliana
thale cress - (species) D
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000116
GA20OX1
Q39110
Morphology
Transposon insertion at +1355 N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
SNP
N
Arabidopsis thaliana
thale cress - (species)
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000117
GA20OX1
Q39110
Morphology
W46* N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
SNP
N
Arabidopsis thaliana
thale cress - (species)
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
1 Additional References
GP00000118
GA20OX1
Q39110
Morphology
W271* -G816A according to Fig.3 of Xu et al. 1995 N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
SNP
N
Arabidopsis thaliana
thale cress - (species)
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000119
GA20OX1
Q39110
Morphology
E312* N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
2 Mutations:
Coding
SNP
Arabidopsis thaliana
thale cress - (species) D
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000120
GA20OX1
Q39110
Morphology
2 mutations
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Plant size (dwarfism)
2 Mutations:
Coding
SNP
Arabidopsis thaliana
thale cress - (species) D
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000121
GA20OX1
Q39110
Morphology
Morphology
2 mutations
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
2 Mutations:
Coding
SNP
Arabidopsis thaliana
thale cress - (species) D
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000122
GA20OX1
Q39110
Morphology
2 mutations
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
SNP
Arabidopsis thaliana
thale cress - (species)
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000123
GA20OX1
Q39110
Morphology
Splice Site mutation G742A
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
Deletion
N
Arabidopsis thaliana
thale cress - (species) D
Intraspecific
Linkage Mapping
Luo Y; Dong X; Yu T ; et al. (2015)
A Single Nucleotide Deletion in Gibberellin20-oxidase1 Causes Alpine Dwarfism in Arabidopsis.
GP00001243
GA20OX1
Q39110
Morphology
-1bp at position 184 causing premature stop N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
2 Mutations:
Coding
SNP
Arabidopsis thaliana
thale cress - (species)
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00001685
GA20OX1
Q39110
Morphology
2 mutations
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtMYC1
Trichome density (leaf)
Coding,
SNP
Arabidopsis thaliana
thale cress - (species)
Intraspecific
Linkage Mapping
Symonds VV; Hatlestad G; Lloyd AM (2011)
Natural allelic variation defines a role for ATMYC1: trichome cell fate determination.
1 Additional References
GP00001268
BHLH12
Q8W2F1
Morphology
P189A
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
AtMYC1
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
B2
Coloration (bulb)
Cis-regulatory,
Insertion
N
Allium cepa
onion - (species) D
Domesticated
Linkage Mapping
Jo C; Kim S (2019)
Transposition of a non-autonomous DNA transposon in the gene coding for a bHLH transcription factor [...]
GP00002058
Morphology
577-bp insertion of a transposable element named AcWHITE in the 5′ upstream region of the white allele of B2. A 8-bp target site duplication (GTTATA AC) and a 7-bp terminal inverted repeat (CAAGGTT) were identified at both ends of this insertion - no SNP detected in the coding region N
Allium cepa
onion - (species)
Allium cepa
onion - (species) D
B2
Allium cepa
onion - (species)
Published - Accepted by Curator
B4GALT7
Body size (dwarfism)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Association Mapping
Leegwater PA; Vos-Loohuis M; Ducro BJ ; et al. (2016)
Dwarfism with joint laxity in Friesian horses is associated with a splice site mutation in B4GALT7.
GP00002151
B4GALT7
Q9UBV7
Morphology
g.3,772,591C>T ; c.50G>A ; p.R17K ; last nucleotide of exon 1 and leads to a splicing deficiency of B4GALT7 transcripts ; All 29 dwarfs of which DNA was available were homozygous for the mutation . . . the 8 obligate carriers were heterozygous
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
B4GALT7
Equus caballus
horse - (species)
Published - Accepted by Curator
bab
Coloration (abdomen; female)
Cis-regulatory,
Unknown
Drosophila yakuba
(species)
Interspecific
Candidate Gene
Rogers WA; Salomone JR; Tacy DJ ; et al. (2013)
Recurrent modification of a conserved cis-regulatory element underlies fruit fly pigmentation divers[...]
GP00002008
bab1
Q9W0K7
Morphology
causing mutation(s) unknown. Cis-regulatory element assayed with a GFP reporter in D. melanogaster.
Drosophila melanogaster
fruit fly - (species)
Drosophila yakuba
(species)
bab
Drosophila yakuba
(species)
Published - Accepted by Curator
bab
Coloration (abdomen; female)
Cis-regulatory,
Unknown
Drosophila fuyamai
(species)
Interspecific
Candidate Gene
Rogers WA; Salomone JR; Tacy DJ ; et al. (2013)
Recurrent modification of a conserved cis-regulatory element underlies fruit fly pigmentation divers[...]
GP00002009
bab1
Q9W0K7
Morphology
causing mutation(s) unknown. Cis-regulatory element assayed with a GFP reporter in D. melanogaster.
Drosophila melanogaster
fruit fly - (species)
Drosophila fuyamai
(species)
bab
Drosophila fuyamai
(species)
Published - Accepted by Curator
bab
Coloration (abdomen; female)
Cis-regulatory,
Unknown
Drosophila auraria
(species)
Interspecific
Candidate Gene
Rogers WA; Salomone JR; Tacy DJ ; et al. (2013)
Recurrent modification of a conserved cis-regulatory element underlies fruit fly pigmentation divers[...]
GP00002010
bab1
Q9W0K7
Morphology
causing mutation(s) unknown. Cis-regulatory element assayed with a GFP reporter in D. melanogaster.
Drosophila melanogaster
fruit fly - (species)
Drosophila auraria
(species)
bab
Drosophila auraria
(species)
Published - Accepted by Curator
bab
Coloration (abdomen ; sexual trait ; plasticity)
Cis-regulatory,
Deletion
Drosophila melanogaster
fruit fly - (species) D
Intraspecific
Linkage Mapping
De Castro S; Peronnet F; Gilles JF ; et al. (2018)
bric à brac (bab), a central player in the gene regulatory network that mediates thermal plasticity [...]
GP00002423
bab1
Q9W0K7
Morphology
a 56-bp deletion that removes two binding sites for Abdominal B (Abd-B), a direct activator of bab, is present in a cis-regulatiry region of bab1 (within the first intron of bab1) in the Dark line.
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species) D
bab
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
bab
Coloration (wing; male ; irridescence)
Cis-regulatory,
Unknown
Interspecific
Linkage Mapping
Ficarrotta V; Hanly JJ; Loh LS ; et al. (2022)
A genetic switch for male UV iridescence in an incipient species pair of sulphur butterflies.
GP00002425
bab1
Q9W0K7
Morphology
no fixed coding variation at the bab locus between the sister species. Lower expression of bab in the irridescent scale species. CRISPR bab mutants show that bab is a negative regulator of irridescent scales.
Colias philodice
clouded sulphur butterfly - (species)
bab
Published - Accepted by Curator
bab
Coloration (abdomen; female)
2 Mutations:
Cis-regulatory
SNP
Drosophila melanogaster
fruit fly - (species)
Intraspecific
Candidate Gene
Rogers WA; Salomone JR; Tacy DJ ; et al. (2013)
Recurrent modification of a conserved cis-regulatory element underlies fruit fly pigmentation divers[...]
GP00002610
bab1
Q9W0K7
Morphology
2 mutations
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species)
bab
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
bab
Coloration (abdomen; female)
2 Mutations:
Cis-regulatory
SNP
Drosophila melanogaster
fruit fly - (species)
Intraspecific
Candidate Gene
Rogers WA; Salomone JR; Tacy DJ ; et al. (2013)
Recurrent modification of a conserved cis-regulatory element underlies fruit fly pigmentation divers[...]
GP00002611
bab1
Q9W0K7
Morphology
2 mutations
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species)
bab
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
bab1
Coloration (abdomen)
3 Mutations:
Cis-regulatory
Unknown
Drosophila melanogaster
fruit fly - (species)
Intraspecific
Linkage Mapping
Kopp A; Graze RM; Xu S ; et al. (2003)
Quantitative trait loci responsible for variation in sexually dimorphic traits in Drosophila melanog[...]
1 Additional References
GP00000130
bab1
Q9W0K7
Morphology
3 mutations
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species)
bab1
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
bab1
Coloration (abdomen)
Cis-regulatory,
Unknown
Drosophila melanogaster
fruit fly - (species) D
Interspecific
Candidate Gene
Williams TM; Selegue JE; Werner T ; et al. (2008)
The regulation and evolution of a genetic switch controlling sexually dimorphic traits in Drosophila[...]
GP00000131
bab1
Q9W0K7
Morphology
inter - ABD-B- and DSX- binding site spacing was reduced in regions I, II, and III
gain of ABD-B binding site 13
Drosophila willistoni
(species)
Drosophila melanogaster
fruit fly - (species) D
bab1
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
BarH1
Coloration (wing; sex-specific; female-specific)
Cis-regulatory,
Insertion
Colias croceus
clouded yellow - (species) D
Intraspecific
Association Mapping
Woronik A; Tunström K; Perry MW ; et al. (2019)
A transposable element insertion is associated with an alternative life history strategy.
GP00002095
B-H1
Q24255
Morphology
insertion of a Jockey-like transposable element 6 kb downstream of the Colias homolog of BarH-1. BarH-1 expression suppresses orange coloration in the wings.
Colias croceus
clouded yellow - (species)
Colias croceus
clouded yellow - (species) D
BarH1
Colias croceus
clouded yellow - (species)
Published - Accepted by Curator
Barren inflorescence2 (BIF2)
Plant architecture
Inflorescence architecture
Unknown,
Unknown
Zea mays
(species)
Domesticated
Linkage Mapping
Pressoir G; Brown PJ; Zhu W ; et al. (2009)
Natural variation in maize architecture is mediated by allelic differences at the PINOID co-ortholog[...]
1 Additional References
GP00000135
bif2
A6MW92
Morphology
Morphology
unknown
Zea mays
(species)
Zea mays
(species)
Barren inflorescence2 (BIF2)
Zea mays
(species)
Published - Accepted by Curator
BCO2 = beta-carotene oxygenase 2
Coloration (coat)
Cis-regulatory,
Unknown
Vermivora cyanoptera
blue-winged warbler - (species)
Interspecific
Association Mapping
Toews DP; Taylor SA; Vallender R ; et al. (2016)
Plumage Genes and Little Else Distinguish the Genomes of Hybridizing Warblers.
GP00001332
BCO2
Q9BYV7
Morphology
unknown - the divergent region falls in the 5prime region that is directly upstream of the associated coding region
Vermivora chrysoptera
Golden-winged warbler - (species)
Vermivora cyanoptera
blue-winged warbler - (species)
BCO2 = beta-carotene oxygenase 2
Vermivora cyanoptera
blue-winged warbler - (species)
Published - Accepted by Curator
BCO2 = beta-carotene oxygenase 2
Carotenoid content (bill, legs)
Coding,
SNP
N
Serinus canaria
common canary - (species) D
Domesticated
Association Mapping
Gazda MA; Toomey MB; Araújo PM ; et al. (2020)
GENETIC BASIS OF DE NOVO APPEARANCE OF CAROTENOID ORNAMENTATION IN BARE-PARTS OF CANARIES.
GP00002039
BCO2
Q9BYV7
Morphology
point mutation at nucleotide position 837,806 that is predicted to be a nonsynonymous mutation in the exon 9 of the BCO2 gene. This variant results in the substitution of a histidine for an arginine at residue 413 of the protein (R413H) . In silico analysis suggests that the R413H could cause structural distortion of the protein and lead to a possible loss of activity. In vitro assays with the urucum BCO2 variant show that the enzyme activity is lost. N
Serinus canaria
common canary - (species)
Serinus canaria
common canary - (species) D
BCO2 = beta-carotene oxygenase 2
Serinus canaria
common canary - (species)
Published - Accepted by Curator
BCO2 = beta-carotene oxygenase 2
Coloration (ventral scales)
Cis-regulatory,
Unknown
Podarcis muralis
Common wall lizard - (species)
Intraspecific
Association Mapping
Andrade P; Pinho C; Pérez I de Lanuza G ; et al. (2019)
Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall [...]
GP00002120
Bco2
Q99NF1
Morphology
Podarcis muralis
Common wall lizard - (species)
Podarcis muralis
Common wall lizard - (species)
BCO2 = beta-carotene oxygenase 2
Podarcis muralis
Common wall lizard - (species)
Published - Accepted by Curator
BCO2 = beta-carotene oxygenase 2
Carotenoid content (sexual dichromatism, male-specific)
Unknown,
Unknown
Serinus canaria
common canary - (species)
Intergeneric or Higher
Linkage Mapping
Gazda MA; Araújo PM; Lopes RJ ; et al. (2020)
A genetic mechanism for sexual dichromatism in birds.
GP00002139
BCO2
Q9BYV7
Morphology
Gene expression study suggests a cis-regulatory difference ; and coding mutations are unlikely to be causal
Spinus cucullatus
red siskin - (species)
Serinus canaria
common canary - (species)
BCO2 = beta-carotene oxygenase 2
Serinus canaria
common canary - (species)
Published - Accepted by Curator
BCO2 = beta-carotene oxygenase 2
Coloration (beak)
Cis-regulatory,
Unknown
Geospiza scandens
(species) D
Geospiza fortis
medium ground-finch - (species) D
Geospiza conirostris
(species) D
Geospiza magnirostris
(species) D
Geospiza fuliginosa
(species) D
Camarhynchus parvulus
(species) D
Camarhynchus pauper
(species) D
Camarhynchus pallidus
woodpecker finch - (species) D
Geospiza difficilis
(species) D
Intraspecific
Association Mapping
Enbody ED; Sprehn CG; Abzhanov A ; et al. (2021)
A multispecies BCO2 beak color polymorphism in the Darwin's finch radiation.
GP00002384
BCO2
Q9BYV7
Morphology
"By closely inspecting this region in a combined sample of all 456 finches of the two species we identified a single exonic SNP with a likelihood ratio test (LRT) statistic exceeding 166 (Figure 1C). It is also the only consistently elevated SNP in an analysis of each species alone (Figure S1), is the best fit variant under a recessive model (STAR Methods), and occurs on multiple haplotypes (Figure S1C). This SNP (chr24:6,166,878; p6166878 hereafter) leads to a synonymous change 32 bp into exon 4 of BCO2. "
"The functional importance of the observed synonymous change is uncertain, and the presence of an unidentified linked causal variant cannot be completely ruled out (see Conclusions). However, a functional explanation is possible because codon usage can be under strong selection30 and may have functional consequences on translation,30 RNA stability,31 and transcription.32 Notably, p6166878 changes the highest frequency valine codon (ƒGTG = 27.3%) to the lowest (ƒGTA = 7.6%) in the reference genome. This is in line with the observed phenotypic effect of the yellow mutation because a lower abundance codon is expected to be associated with lower protein expression.33 In this case, less BCO2 activity results in more carotenoid deposition in the yellow morph. In fact, we found that yellow homozygotes showed significantly lower BCO2 expression compared to pink homozygotes in the upper beak of developing embryos (Figure 1F) that were sourced from a variety of different species and islands (Table S1): small sample sizes prohibit species-specific analysis. Among the six heterozygous individuals, the pink allele was expressed more than the yellow allele in five samples tested using a droplet-digital PCR (Figure S2C). Differences in expression between the two alleles, and in the absence of alternative splice variants (STAR Methods), raise the possibility that the synonymous change alters transcription factor binding affinity in exon 4. Further research into tissue-specific expression and the specific transcription factors that regulate BCO2 is warranted."
Geospiza scandens
(species)
Geospiza fortis
medium ground-finch - (species)
Geospiza conirostris
(species)
Geospiza magnirostris
(species)
Geospiza fuliginosa
(species)
Camarhynchus parvulus
(species)
Camarhynchus pauper
(species)
Camarhynchus pallidus
woodpecker finch - (species)
Geospiza difficilis
(species)
Geospiza scandens
(species) D
Geospiza fortis
medium ground-finch - (species) D
Geospiza conirostris
(species) D
Geospiza magnirostris
(species) D
Geospiza fuliginosa
(species) D
Camarhynchus parvulus
(species) D
Camarhynchus pauper
(species) D
Camarhynchus pallidus
woodpecker finch - (species) D
Geospiza difficilis
(species) D
BCO2 = beta-carotene oxygenase 2
Geospiza scandens
(species)
Geospiza fortis
medium ground-finch - (species)
Geospiza conirostris
(species)
Geospiza magnirostris
(species)
Geospiza fuliginosa
(species)
Camarhynchus parvulus
(species)
Camarhynchus pauper
(species)
Camarhynchus pallidus
woodpecker finch - (species)
Geospiza difficilis
(species)
Published - Accepted by Curator
BCO2 = beta-carotene oxygenase 2
Coloration (feather)
Unknown,
Unknown
Setophaga petechia
yellow warbler - (species) D
Interspecific
Association Mapping
Baiz MD; Wood AW; Brelsford A ; et al. (2021)
Pigmentation Genes Show Evidence of Repeated Divergence and Multiple Bouts of Introgression in Setop[...]
GP00002387
BCO2
Q9BYV7
Morphology
Setophaga pensylvanica
Chestnut-sided warbler - (species)
Setophaga petechia
yellow warbler - (species) D
BCO2 = beta-carotene oxygenase 2
Setophaga petechia
yellow warbler - (species)
Published - Accepted by Curator
BCO2 = beta-carotene oxygenase 2
Coloration (feather)
Unknown,
Unknown
Setophaga citrina
hooded warbler - (species) D
Interspecific
Association Mapping
Baiz MD; Wood AW; Brelsford A ; et al. (2021)
Pigmentation Genes Show Evidence of Repeated Divergence and Multiple Bouts of Introgression in Setop[...]
GP00002388
BCO2
Q9BYV7
Morphology
Setophaga ruticilla
(species)
Setophaga citrina
hooded warbler - (species) D
BCO2 = beta-carotene oxygenase 2
Setophaga citrina
hooded warbler - (species)
Published - Accepted by Curator
Bh4
Coloration (seed hull)
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Zhu BF; Si L; Wang Z ; et al. (2011)
Genetic control of a transition from black to straw-white seed hull in rice domestication.
1 Additional References
GP00000143
Bh4
A0A0H3ZGK8
Morphology
22-bp deletion N
Oryza rufipogon
(species)
Oryza sativa
rice - (species) D
Bh4
Oryza sativa
rice - (species)
Published - Accepted by Curator
bHLH2
Coloration (flower; seed)
Coding,
Insertion
N
Ipomoea purpurea
common morning-glory - (species) D
Domesticated
Candidate Gene
Park KI; Ishikawa N; Morita Y ; et al. (2007)
A bHLH regulatory gene in the common morning glory, Ipomoea purpurea, controls anthocyanin biosynthe[...]
GP00002078
BHLH2
Q9CAD0
Morphology
two copies of 3.9-kb Tip100 integrated into bHLH2 exon 7 and intron 2 N
Ipomoea purpurea
common morning-glory - (species)
Ipomoea purpurea
common morning-glory - (species) D
bHLH2
Ipomoea purpurea
common morning-glory - (species)
Published - Accepted by Curator
bHLH2
Coloration (flower; seed)
Coding,
Insertion
N
Ipomoea purpurea
common morning-glory - (species) D
Domesticated
Candidate Gene
Park KI; Ishikawa N; Morita Y ; et al. (2007)
A bHLH regulatory gene in the common morning glory, Ipomoea purpurea, controls anthocyanin biosynthe[...]
GP00002085
BHLH2
Q9CAD0
Morphology
only one copy of Tip100 in exon 7 and no apparent footprint of Tip100 in intron 2 N
Ipomoea purpurea
common morning-glory - (species)
Ipomoea purpurea
common morning-glory - (species) D
bHLH2
Ipomoea purpurea
common morning-glory - (species)
Published - Accepted by Curator
bHLH2
Coloration (flower; seed)
Coding,
Insertion
N
Ipomoea purpurea
common morning-glory - (species) D
Domesticated
Candidate Gene
Park KI; Ishikawa N; Morita Y ; et al. (2007)
A bHLH regulatory gene in the common morning glory, Ipomoea purpurea, controls anthocyanin biosynthe[...]
GP00002086
BHLH2
Q9CAD0
Morphology
insertion of 838 bp IpMu1 in exon 2 N
Ipomoea purpurea
common morning-glory - (species)
Ipomoea purpurea
common morning-glory - (species) D
bHLH2
Ipomoea purpurea
common morning-glory - (species)
Published - Accepted by Curator
bHLH2
Coloration (flowers; seeds)
Coding,
Insertion
N
Ipomoea tricolor
(species) D
Domesticated
Candidate Gene
Park KI; Choi JD; Hoshino A ; et al. (2004)
An intragenic tandem duplication in a transcriptional regulatory gene for anthocyanin biosynthesis c[...]
GP00002091
BHLH2
Q9CAD0
Morphology
intragenic tandem duplication of 3.3 kbp of the bHLH2 gene. Each of the tandem repeats is flanked by a 3-bp sequence AAT; indicating that the 3-bp microhomology is used to generate the tandem duplication. The transcripts in the pale-blue flower buds of the mutant contain an internal 583-bp tandem duplication that results in the production of a truncated polypeptide lacking the bHLH domain. The mRNA accumulation of most of the structural genes encoding enzymes for anthocyanin biosynthesis in the flower buds of the mutant was significantly reduced. The transcripts identical to the wild-type mRNAs for the transcriptional activator were present abundantly in blue spots of the variegated flowers whereas the transcripts containing the 583-bp tandem duplication were predominant in the pale-blue background of the same flowers. The flower and seed variegations studied here are likely to be caused by somatic homologous recombination between an intragenic tandem duplication in the gene encoding a bHLH transcriptional activator for anthocyanin biosynthesis. N
Ipomoea tricolor
(species)
Ipomoea tricolor
(species) D
bHLH2
Ipomoea tricolor
(species)
Published - Accepted by Curator
bHLH2
Coloration (flowers)
Coding,
Insertion
N
Petunia axillaris
(species) D
Domesticated
Candidate Gene
Spelt C; Quattrocchio F; Mol J ; et al. (2002)
ANTHOCYANIN1 of petunia controls pigment synthesis, vacuolar pH, and seed coat development by geneti[...]
GP00002092
BHLH2
Q9CAD0
Morphology
insertion of a dTph1 transposon in the AN1 gene N
Petunia axillaris
(species)
Petunia axillaris
(species) D
bHLH2
Petunia axillaris
(species)
Published - Accepted by Curator
Bm-iAANAT
Coloration (larva)
Coding,
Deletion
N
Bombyx mori
domestic silkworm - (species) D
Domesticated
Linkage Mapping
Zhan S; Guo Q; Li M ; et al. (2010)
Disruption of an N-acetyltransferase gene in the silkworm reveals a novel role in pigmentation.
1 Additional References
GP00000145
Aanat
D6MKR2
Morphology
126-bp deletion overlapping with end of exon 4 and resulting in misplicing. Linkage analysis and genomic studies have shown that Bombyx arylalkamine-N-acetyl transferase, the homologous gene (Dat) that converts dopamine into N-acetyl dopamine, encodes a precursor of N-acetyl dopamine, sclerotin in Drosophila and it is the gene responsible for mln. N
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
Bm-iAANAT
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
BMP2
Fertility (egg production)
Bird head morphology (male comb)
Cis-regulatory,
Unknown
Gallus gallus
chicken - (species)
Domesticated
Linkage Mapping
Johnsson M; Gustafson I; Rubin CJ ; et al. (2012)
A sexual ornament in chickens is affected by pleiotropic alleles at HAO1 and BMP2, selected during d[...]
1 Additional References
GP00000151
BMP2
Q90751
Physiology
Morphology
unknown; but intergenic QTL peak with decomposed effects on expression of BMP2 and HAO1
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
BMP2
Gallus gallus
chicken - (species)
Published - Accepted by Curator
BMP3 or PRKG2
Cranio-facial morphology
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Schoenebeck JJ; Hutchinson SA; Byers A ; et al. (2012)
Variation of BMP3 contributes to dog breed skull diversity.
GP00000152
Bmp3
Q8BHE5
Morphology
F452L in BMP3 ; this missense mutation is in a conserved position and correlates well with small breeds. However; the functional data (zebrafish BMP3 morpholino knockdown) proposed in this article is inconsistent with the mice BMP3 null-mutation
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
BMP3 or PRKG2
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
BMP4 (uncertain)
Cranio-facial morphology
Unknown,
Unknown
Maylandia zebra
zebra mbuna - (species)
Interspecific
Linkage Mapping
Albertson RC; Streelman JT; Kocher TD ; et al. (2005)
Integration and evolution of the cichlid mandible: the molecular basis of alternate feeding strategi[...]
2 Additional References
GP00000153
bmp4
O13107
Morphology
Not identified
Labeotropheus fuelleborni
blue mbuna - (species)
Maylandia zebra
zebra mbuna - (species)
BMP4 (uncertain)
Maylandia zebra
zebra mbuna - (species)
Published - Accepted by Curator
BMP6
Tooth number
Cis-regulatory,
Unknown
Gasterosteus aculeatus
three-spined stickleback - (species) D
Intraspecific
Linkage Mapping
Cleves PA; Ellis NA; Jimenez MT ; et al. (2014)
Evolved tooth gain in sticklebacks is associated with a cis-regulatory allele of Bmp6.
2 Additional References
GP00000154
Bmp6
P20722
Morphology
Candidate enhancer of 190bp recapitulating tooth and fin expression of BMP6
Gasterosteus aculeatus
three-spined stickleback - (species)
Gasterosteus aculeatus
three-spined stickleback - (species) D
BMP6
Gasterosteus aculeatus
three-spined stickleback - (species)
Published - Accepted by Curator
BRANCHED1a (BRC1a)
Plant architecture
Inflorescence architecture
Coding,
SNP
Solanum
(genus) D
Intergeneric or Higher
Candidate Gene
Nicolas M; Rodríguez-Buey ML; Franco-Zorrilla JM ; et al. (2015)
A Recently Evolved Alternative Splice Site in the BRANCHED1a Gene Controls Potato Plant Architecture[...]
GP00000156
BRC1A
F6KB94
Morphology
Morphology
Evolution of an alternative splice site (G>A) that unlocks a short isoform
Capsicum annuum
(species)
Solanum
(genus) D
BRANCHED1a (BRC1a)
Solanum
(genus)
Published - Accepted by Curator
Brassinosteroid-deficient dwarf1 (brd1)
Plant size (height)
Unknown,
Unknown
Zea mays
(species)
Intraspecific
Linkage Mapping
Peiffer JA; Romay MC; Gore MA ; et al. (2014)
The genetic architecture of maize height.
GP00001628
ZEAMMB73_Zm00001d033180
A0A1D6KWT1
Morphology
On chromosome 1 two C>T transitions reduce plant height in 18RIL families
Zea mays
(species)
Zea mays
(species)
Brassinosteroid-deficient dwarf1 (brd1)
Zea mays
(species)
Published - Accepted by Curator
Brevis radix (BRX)
Root size (shorter)
Coding,
SNP
N
Arabidopsis thaliana
thale cress - (species)
Intraspecific
Linkage Mapping
Mouchel CF; Briggs GC; Hardtke CS (2004)
Natural genetic variation in Arabidopsis identifies BREVIS RADIX, a novel regulator of cell prolifer[...]
GP00000157
BRX
Q17TI5
Morphology
premature stop codon in exon 4; TGG>TGA; truncated protein missing approximately two-thirds of the C terminus N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
Brevis radix (BRX)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
Brevis radix (BRX)
Root growth
Coding,
Deletion
Arabidopsis thaliana
thale cress - (species) D
Intraspecific
Linkage Mapping
Beuchat J; Li S; Ragni L ; et al. (2010)
A hyperactive quantitative trait locus allele of Arabidopsis BRX contributes to natural variation in[...]
GP00001262
BRX
Q17TI5
Morphology
21bp deletion at position in spacer 3 (position not given)
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
Brevis radix (BRX)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
c1
Coloration (seed)
Cis-regulatory,
Insertion
Zea mays
(species) D
Domesticated
Linkage Mapping
Hattori T; Vasil V; Rosenkrans L ; et al. (1992)
The Viviparous-1 gene and abscisic acid activate the C1 regulatory gene for anthocyanin biosynthesis[...]
1 Additional References
GP00000167
C1
P10290
Morphology
5bp insertion in the proximal promoter that creates a new binding site for VP1; a transcription factor that regulates kernel maturation; so that the pigment pathway is turned on while the kernel matures; giving blue kernels
Zea mays
(species)
Zea mays
(species) D
c1
Zea mays
(species)
Published - Accepted by Curator
Camta3
Plant size (height)
Unknown,
Unknown
Zea mays
(species)
Intraspecific
Association Mapping
Peiffer JA; Romay MC; Gore MA ; et al. (2014)
The genetic architecture of maize height.
GP00001629
CAMTA3
Q8GSA7
Morphology
C>T transition on chromosome 3
Zea mays
(species)
Zea mays
(species)
Camta3
Zea mays
(species)
Published - Accepted by Curator
cardinal
Coloration (eyes)
Coding,
Insertion
N
Tribolium castaneum
red flour beetle - (species) D
Domesticated
Candidate Gene
Shirai Y; Daimon T (2020)
Mutations in cardinal are responsible for the red-1 and peach eye color mutants of the red flour bee[...]
GP00002665
cd
Q9VCW2
Morphology
A fragment of a transposable element (about 5 kb - 99% identical in amino acids to a putative retrotransposon (XP_015838217)) is inserted into exon 6. This insertion introduced a premature stop codon just after the insertion site. Amino acid residues near the C-terminal end of the haem peroxidase domain are thus disrupted. N
Tribolium castaneum
red flour beetle - (species)
Tribolium castaneum
red flour beetle - (species) D
cardinal
Tribolium castaneum
red flour beetle - (species)
Published - Accepted by Curator
cardinal
Coloration (eyes)
Coding,
Deletion
N
Tribolium castaneum
red flour beetle - (species) D
Domesticated
Candidate Gene
Shirai Y; Daimon T (2020)
Mutations in cardinal are responsible for the red-1 and peach eye color mutants of the red flour bee[...]
GP00002666
cd
Q9VCW2
Morphology
1-bp deletion in exon 6 that causes a frameshift mutation. Amino acid residues near the C-terminal end of the haem peroxidase domain are thus disrupted. N
Tribolium castaneum
red flour beetle - (species)
Tribolium castaneum
red flour beetle - (species) D
cardinal
Tribolium castaneum
red flour beetle - (species)
Published - Accepted by Curator
cardinal
Coloration (eyes)
Coding,
SNP
N
Bombyx mori
domestic silkworm - (species) D
Domesticated
Candidate Gene
Osanai-Futahashi M; Tatematsu KI; Futahashi R ; et al. (2016)
Positional cloning of a Bombyx pink-eyed white egg locus reveals the major role of cardinal in ommoc[...]
GP00002667
cd
Q9VCW2
Morphology
Missense mutation in a conserved motif in exon 9. The tryptophan residue which is converted to arginine in the two pe strains is widely conserved in holometabolous insects. N
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
cardinal
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
Carotenoid-binding protein (CBP)
Coloration (silk)
Gene Amplification,
Complex Change
Bombyx mori
domestic silkworm - (species) D
Domesticated
Linkage Mapping
Sakudoh T; Nakashima T; Kuroki Y ; et al. (2011)
Diversity in copy number and structure of a silkworm morphogenetic gene as a result of domestication[...]
1 Additional References
GP00000169
Q1HE01
Morphology
Copy Number Variation (up to 20 copies in B. mori ; only one in the wild form; B. mandarina)
Bombyx mandarina
wild silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
Carotenoid-binding protein (CBP)
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
Catecholamines up
Bristle number
Lifespan
Locomotor activity
Sleep
Coding,
Unknown
Drosophila melanogaster
fruit fly - (species)
Intraspecific
Linkage Mapping
Carbone MA; Jordan KW; Lyman RF ; et al. (2006)
Phenotypic variation and natural selection at catsup, a pleiotropic quantitative trait gene in Droso[...]
1 Additional References
GP00000172
Catsup
Q9V3A4
Morphology
Physiology
Behavior
Behavior
unknown; but most large-effect variants appear to be coding
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species)
Catecholamines up
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
Cauliflower (BoCAL)
Inflorescence morphology
Coding,
SNP
N
Brassica oleracea var. botrytis
(varietas) D
Domesticated
Candidate Gene
Kempin SA; Savidge B; Yanofsky MF (1995)
Molecular basis of the cauliflower phenotype in Arabidopsis.
1 Additional References
GP00000173
CAL
Q39081
Morphology
GAG>TAG; E151*; protein truncated after only 150 of the 255 amino acids of the wild-type protein N
Brassica oleracea
wild cabbage - (species)
Brassica oleracea var. botrytis
(varietas) D
Cauliflower (BoCAL)
Brassica oleracea var. botrytis
(varietas)
Published - Accepted by Curator
ccdc170
Coloration
Unknown,
Unknown
Anolis sagrei
Brown anole - (species)
Intraspecific
Association Mapping
Feiner N; Brun-Usan M; Andrade P ; et al. (2022)
A single locus regulates a female-limited color pattern polymorphism in a reptile.
GP00002363
Ccdc170
D3YXL0
Morphology
Anolis sagrei
Brown anole - (species)
Anolis sagrei
Brown anole - (species)
ccdc170
Anolis sagrei
Brown anole - (species)
Published - Accepted by Curator
CDKN2A
Coloration (feathers ; sex-linked dilution)
2 Mutations:
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Schwochow Thalmann D; Ring H; Sundström E ; et al. (2017)
The evolution of Sex-linked barring alleles in chickens involves both regulatory and coding changes [...]
1 Additional References
GP00000178
CDKN2A
P42771
Morphology
2 mutations
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
CDKN2A
Gallus gallus
chicken - (species)
Published - Accepted by Curator
CDKN2A
Coloration (feathers ; sex-linked barring)
2 Mutations:
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Schwochow Thalmann D; Ring H; Sundström E ; et al. (2017)
The evolution of Sex-linked barring alleles in chickens involves both regulatory and coding changes [...]
1 Additional References
GP00002162
CDKN2A
P42771
Morphology
2 mutations
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
CDKN2A
Gallus gallus
chicken - (species)
Published - Accepted by Curator
Chalcone synthase D (CHS-D)
Coloration (flower)
Unknown,
Insertion
Ipomoea purpurea
common morning-glory - (species) D
Intraspecific
Candidate Gene
Habu Y; Hisatomi Y; Iida S (1998)
Molecular characterization of the mutable flaked allele for flower variegation in the common morning[...]
GP00001459
CHSD
O22045
Morphology
insertion of a 3.9kb long transposable element Tip100 in intron
Ipomoea purpurea
common morning-glory - (species)
Ipomoea purpurea
common morning-glory - (species) D
Chalcone synthase D (CHS-D)
Ipomoea purpurea
common morning-glory - (species)
Published - Accepted by Curator
Chalcone synthase D (CHS-D)
Coloration (flower)
Unknown,
Insertion
Ipomoea purpurea
common morning-glory - (species) D
Intraspecific
Candidate Gene
Habu Y; Hisatomi Y; Iida S (1998)
Molecular characterization of the mutable flaked allele for flower variegation in the common morning[...]
GP00001460
CHSD
O22045
Morphology
2 insertions of Tip100 in opposite orientation at different sites within the same intron
Ipomoea purpurea
common morning-glory - (species)
Ipomoea purpurea
common morning-glory - (species) D
Chalcone synthase D (CHS-D)
Ipomoea purpurea
common morning-glory - (species)
Published - Accepted by Curator
Chalk5
Grain chalkiness
Amylose content
Grain yield
Cis-regulatory,
SNP
Oryza sativa
rice - (species)
Intraspecific
Linkage Mapping
Li Y; Fan C; Xing Y ; et al. (2014)
Chalk5 encodes a vacuolar H(+)-translocating pyrophosphatase influencing grain chalkiness in rice.
GP00001309
Chalk5
A2Y0L3
Morphology
Physiology
Physiology
Two candidate SNPs at positions -721 and - 485 in promoter region
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Chalk5
Oryza sativa
rice - (species)
Published - Accepted by Curator
chordin
Fin morphology (skeleton; dorsal fin; caudal fin; tail; paired fin)
Coding,
SNP
N
Carassius auratus
goldfish - (species) D
Domesticated
Candidate Gene
Abe G; Lee SH; Chang M ; et al. (2014)
The origin of the bifurcated axial skeletal system in the twin-tail goldfish.
1 Additional References
GP00002346
chdA
W8VTE1
Morphology
stop codon in codon 127. GAG (E) -> TAG (STOP). Predicted to result in a truncated protein lacking the second to fourth CR domains. N
Carassius auratus
goldfish - (species)
Carassius auratus
goldfish - (species) D
chordin
Carassius auratus
goldfish - (species)
Published - Accepted by Curator
CLV3
Fruit size
Cis-regulatory,
Inversion
Solanum lycopersicum
tomato - (species) D
Domesticated
Linkage Mapping
Xu C; Liberatore KL; MacAlister CA ; et al. (2015)
A cascade of arabinosyltransferases controls shoot meristem size in tomato.
GP00001565
CLV3
Q9XF04
Morphology
A 294 kb inversion with a breakpoint 1 kb upstream of CLV3
Solanum pimpinellifolium
(species)
Solanum lycopersicum
tomato - (species) D
CLV3
Solanum lycopersicum
tomato - (species)
Published - Accepted by Curator
cly1
Pollen shedding (Cleistogamy; lodicule size)
Cis-regulatory,
SNP
Hordeum vulgare
(species) D
Domesticated
Linkage Mapping
Nair SK; Wang N; Turuspekov Y ; et al. (2010)
Cleistogamous flowering in barley arises from the suppression of microRNA-guided HvAP2 mRNA cleavage[...]
1 Additional References
GP00001314
AP2
P47927
Morphology
A>G @position 3084; in a miRNA targeting site.
Hordeum vulgare
(species)
Hordeum vulgare
(species) D
cly1
Hordeum vulgare
(species)
Published - Accepted by Curator
cly1
Pollen shedding (Cleistogamy; lodicule size)
Cis-regulatory,
SNP
Hordeum vulgare
(species) D
Domesticated
Linkage Mapping
Nair SK; Wang N; Turuspekov Y ; et al. (2010)
Cleistogamous flowering in barley arises from the suppression of microRNA-guided HvAP2 mRNA cleavage[...]
1 Additional References
GP00001315
AP2
P47927
Morphology
A>C @position 3090; in a miRNA targeting site.
Hordeum vulgare
(species)
Hordeum vulgare
(species) D
cly1
Hordeum vulgare
(species)
Published - Accepted by Curator
cly1
Pollen shedding (Cleistogamy; lodicule size)
Cis-regulatory,
Epigenetic Change
Hordeum vulgare
(species) D
Domesticated
Linkage Mapping
Wang N; Ning S; Wu J ; et al. (2015)
An epiallele at cly1 affects the expression of floret closing (cleistogamy) in barley.
GP00001316
AP2
P47927
Morphology
T>C @position -245; creating differential methylation
Hordeum vulgare
(species)
Hordeum vulgare
(species) D
cly1
Hordeum vulgare
(species)
Published - Accepted by Curator
coatomer protein complex subunit alpha (COPA)
Coloration (coat)
Coding,
SNP
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Dorshorst B; Henegar C; Liao X ; et al. (2015)
Dominant Red Coat Color in Holstein Cattle Is Associated with a Missense Mutation in the Coatomer Pr[...]
GP00001329
COPA
P53621
Morphology
c.C>T p.Arg160Cys
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
coatomer protein complex subunit alpha (COPA)
Bos taurus
cattle - (species)
Published - Accepted by Curator
colored plant 1
Coloration (seed)
Cis-regulatory,
Unknown
Zea mays
(species)
Domesticated
Linkage Mapping
Radicella JP; Brown D; Tolar LA ; et al. (1992)
Allelic diversity of the maize B regulatory gene: different leader and promoter sequences of two B a[...]
GP00000190
b1
W5S3Q3
Morphology
Not identified
Zea mays
(species)
Zea mays
(species)
colored plant 1
Zea mays
(species)
Published - Accepted by Curator
CORIN
Coloration (coat)
Coding,
SNP
Panthera tigris
tiger - (species) D
Intraspecific
Linkage Mapping
Xu X; Dong GX; Schmidt-Küntzel A ; et al. (2017)
The genetics of tiger pelage color variations.
GP00002169
Corin
Q9Z319
Morphology
c.1759C >T p.H587Y
Panthera tigris
tiger - (species)
Panthera tigris
tiger - (species) D
CORIN
Panthera tigris
tiger - (species)
Published - Accepted by Curator
cortex
Coloration (wing ; industrial melanism ; camouflage)
Cis-regulatory,
Insertion
Biston betularia
pepper-and-salt moth - (species) D
Intraspecific
Linkage Mapping
Van't Hof AE; Campagne P; Rigden DJ ; et al. (2016)
The industrial melanism mutation in British peppered moths is a transposable element.
GP00001804
cort
Q960N3
Morphology
Putative transposon insertion within the first intron ; consists of of ~9 kb tandemly repeated 2.3 times + three short tandem subrepeat units
Biston betularia
pepper-and-salt moth - (species)
Biston betularia
pepper-and-salt moth - (species) D
cortex
Biston betularia
pepper-and-salt moth - (species)
Published - Accepted by Curator
cortex
Coloration (wing)
Cis-regulatory,
Deletion
Heliconius melpomene
postman butterfly - (species) D
Domesticated
Association Mapping
Hanly JJ; Livraghi L; Heryanto C ; et al. (2022)
A large deletion at the cortex locus eliminates butterfly wing patterning.
GP00001805
cort
Q960N3
Morphology
78-kb deletion in the 5′ region of the cortex gene that includes a facultative 5′UTR exon detected in larval wing disk transcriptomes. Phenotypic effect confirmed by CRISPR mutagenesis of this exon. The ivory deletion causes the loss of 1 of 2 promoters.
Heliconius melpomene
postman butterfly - (species)
Heliconius melpomene
postman butterfly - (species) D
cortex
Heliconius melpomene
postman butterfly - (species)
Published - Accepted by Curator
cortex
Coloration (wing ; leaf mimicry ; camouflage)
Cis-regulatory,
Complex Change
Kallima inachus
orange oakleaf - (species) D
Intraspecific
Association Mapping
Wang S; Teng D; Li X ; et al. (2022)
The evolution and diversification of oakleaf butterflies.
GP00002413
cort
Q960N3
Morphology
Kallima inachus
orange oakleaf - (species)
Kallima inachus
orange oakleaf - (species) D
cortex
Kallima inachus
orange oakleaf - (species)
Published - Accepted by Curator
cortex
Coloration (wing ; leaf mimicry ; camouflage)
Cis-regulatory,
Unknown
Kallima inachus
orange oakleaf - (species) D
Intraspecific
Association Mapping
Wang S; Teng D; Li X ; et al. (2022)
The evolution and diversification of oakleaf butterflies.
GP00002414
cort
Q960N3
Morphology
Kallima inachus
orange oakleaf - (species)
Kallima inachus
orange oakleaf - (species) D
cortex
Kallima inachus
orange oakleaf - (species)
Published - Accepted by Curator
cortex
Coloration (wing ; leaf mimicry ; camouflage)
Cis-regulatory,
Unknown
Kallima inachus
orange oakleaf - (species) D
Intraspecific
Association Mapping
Wang S; Teng D; Li X ; et al. (2022)
The evolution and diversification of oakleaf butterflies.
GP00002415
cort
Q960N3
Morphology
Kallima inachus
orange oakleaf - (species)
Kallima inachus
orange oakleaf - (species) D
cortex
Kallima inachus
orange oakleaf - (species)
Published - Accepted by Curator
cortex
Coloration (wing ; leaf mimicry ; camouflage)
Cis-regulatory,
Unknown
Kallima inachus
orange oakleaf - (species) D
Intraspecific
Association Mapping
Wang S; Teng D; Li X ; et al. (2022)
The evolution and diversification of oakleaf butterflies.
GP00002416
cort
Q960N3
Morphology
Large inversion and many mutations in the large inverted region.
Kallima inachus
orange oakleaf - (species)
Kallima inachus
orange oakleaf - (species) D
cortex
Kallima inachus
orange oakleaf - (species)
Published - Accepted by Curator
cortex
Coloration (wing ; body)
Unknown,
Unknown
Bombyx mori
domestic silkworm - (species)
Domesticated
Linkage Mapping
Ito K; Katsuma S; Kuwazaki S ; et al. (2016)
Mapping and recombination analysis of two moth colour mutations, Black moth and Wild wing spot, in t[...]
GP00002417
cort
Q960N3
Morphology
Mapping to a 2-Mb-long region which contains the cortex gene.
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species)
cortex
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
cortex
Coloration (wing)
Unknown,
Unknown
Bombyx mori
domestic silkworm - (species)
Domesticated
Linkage Mapping
Ito K; Katsuma S; Kuwazaki S ; et al. (2016)
Mapping and recombination analysis of two moth colour mutations, Black moth and Wild wing spot, in t[...]
GP00002418
cort
Q960N3
Morphology
Mapping to a 100-kb-long region which contains the cortex gene.
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species)
cortex
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
cortex
Coloration (wing; mimicry)
Unknown,
Unknown
Papilio clytia
common mime swallowtail - (species)
Intraspecific
Association Mapping
VanKuren NW; Massardo D; Nallu S ; et al. (2019)
Butterfly Mimicry Polymorphisms Highlight Phylogenetic Limits of Gene Reuse in the Evolution of Dive[...]
GP00002419
cort
Q960N3
Morphology
Mapping to a 500-kb region that contains the cortex gene
Papilio clytia
common mime swallowtail - (species)
Papilio clytia
common mime swallowtail - (species)
cortex
Papilio clytia
common mime swallowtail - (species)
Published - Accepted by Curator
cortex
Coloration (wing; seasonal)
Cis-regulatory,
Unknown
Junonia coenia
buckeye - (species) D
Experimental Evolution
Association Mapping
van der Burg KRL; Lewis JJ; Brack BJ ; et al. (2020)
Genomic architecture of a genetically assimilated seasonal color pattern.
GP00002420
cort
Q960N3
Morphology
No variation in coding region. Strong association with cis-regulatory SNP.
Junonia coenia
buckeye - (species)
Junonia coenia
buckeye - (species) D
cortex
Junonia coenia
buckeye - (species)
Published - Accepted by Curator
cortex
Coloration (wing)
Cis-regulatory,
Insertion
Heliconius melpomene
postman butterfly - (species) D
Intraspecific
Association Mapping
Livraghi L; Hanly JJ; Van Bellghem SM ; et al. (2021)
Cortex cis-regulatory switches establish scale colour identity and pattern diversity in Heliconius.
GP00002660
cort
Q960N3
Morphology
Insertion of two transposable elements (BovB-like and Helitron-like)
Heliconius melpomene
postman butterfly - (species)
Heliconius melpomene
postman butterfly - (species) D
cortex
Heliconius melpomene
postman butterfly - (species)
Published - Accepted by Curator
CREBRF
Body size (obesity)
Coding,
SNP
Homo sapiens
human - (species) D
Intraspecific
Association Mapping
Minster RL; Hawley NL; Su CT ; et al. (2016)
A thrifty variant in CREBRF strongly influences body mass index in Samoans.
GP00001444
CREBRF
Q8IUR6
Morphology
c.1370G>A p.Arg457Gln
Homo sapiens
human - (species)
Homo sapiens
human - (species) D
CREBRF
Homo sapiens
human - (species)
Published - Accepted by Curator
Cryptochrome 2 (CRY2) EDI allele
Flowering time
Fruit shape (fruit length)
Flower morphology (ovule number per fruit)
Fertility (percentage of unfertilized ovules)
Coding,
SNP
Arabidopsis thaliana
thale cress - (species)
Intraspecific
Linkage Mapping
El-Din El-Assal S; Alonso-Blanco C; Peeters AJ ; et al. (2001)
A QTL for flowering time in Arabidopsis reveals a novel allele of CRY2.
3 Additional References
GP00000192
CRY2
Q96524
Physiology
Morphology
Morphology
Physiology
V367M
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
Cryptochrome 2 (CRY2) EDI allele
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
csf1
Coloration
Cis-regulatory,
Unknown
Oryzias woworae
(species) D
Interspecific
Linkage Mapping
Ansai S; Mochida K; Fujimoto S ; et al. (2021)
Genome editing reveals fitness effects of a gene for sexual dichromatism in Sulawesian fishes.
GP00002366
CSF1
P09603
Morphology
Oryzias celebensis
Celebes medaka - (species)
Oryzias woworae
(species) D
csf1
Oryzias woworae
(species)
Published - Accepted by Curator
csf1a
Coloration (loss of stripes)
Cis-regulatory,
Unknown
Danio albolineatus
pearl danio - (species) D
Interspecific
Candidate Gene
Patterson LB; Bain EJ; Parichy DM (2014)
Pigment cell interactions and differential xanthophore recruitment underlying zebrafish stripe reite[...]
GP00002123
csf1a
A0A0B5JQ49
Morphology
Danio rerio
zebrafish - (species)
Danio albolineatus
pearl danio - (species) D
csf1a
Danio albolineatus
pearl danio - (species)
Published - Accepted by Curator
CYC-like HaCYC2c
Flower morphology
Cis-regulatory,
Insertion
Helianthus annuus
common sunflower - (species) D
Intraspecific
Linkage Mapping
Chapman MA; Tang S; Draeger D ; et al. (2012)
Genetic analysis of floral symmetry in Van Gogh's sunflowers reveals independent recruitment of CYCL[...]
GP00000193
CYC
O49250
Morphology
999bp insertion in promoter
Helianthus annuus
common sunflower - (species)
Helianthus annuus
common sunflower - (species) D
CYC-like HaCYC2c
Helianthus annuus
common sunflower - (species)
Published - Accepted by Curator
CYC-like RAY1/RAY2
Flower morphology
Gene Amplification,
Complex Change
Senecio vulgaris
(species)
Intraspecific
Linkage Mapping
Kim M; Cui ML; Cubas P ; et al. (2008)
Regulatory genes control a key morphological and ecological trait transferred between species.
GP00000194
CYC
O49250
Morphology
Gene gain by hybridization
Senecio vulgaris
(species)
Senecio vulgaris
(species)
CYC-like RAY1/RAY2
Senecio vulgaris
(species)
Published - Accepted by Curator
Cycloidea (Lcyc)
Flower morphology
Cis-regulatory,
Epigenetic Change
Linaria vulgaris
common toadflax - (species) D
Intraspecific
Linkage Mapping
Cubas P; Vincent C; Coen E (1999)
An epigenetic mutation responsible for natural variation in floral symmetry.
GP00000197
CYC
O49250
Morphology
Stable methylation
Linaria vulgaris
common toadflax - (species)
Linaria vulgaris
common toadflax - (species) D
Cycloidea (Lcyc)
Linaria vulgaris
common toadflax - (species)
Published - Accepted by Curator
CYP(T)
Flower morphology (style length)
Coding,
Insertion
N
Primula vulgaris
(species) D
Intraspecific
Linkage Mapping
Li J; Cocker JM; Wright J ; et al. (2016)
Genetic architecture and evolution of the S locus supergene in Primula vulgaris.
GP00001394
CYP734A1
O48786
Morphology
single base insertion in exon 2 introduces a disruptive premature stop codon N
Primula vulgaris
(species)
Primula vulgaris
(species) D
CYP(T)
Primula vulgaris
(species)
Published - Accepted by Curator
CYP(T)
Flower morphology (style length)
Coding,
SNP
Primula vulgaris
(species) D
Intraspecific
Linkage Mapping
Li J; Cocker JM; Wright J ; et al. (2016)
Genetic architecture and evolution of the S locus supergene in Primula vulgaris.
GP00001395
CYP734A1
O48786
Morphology
G>C p.Asp126His in exon 2
Primula vulgaris
(species)
Primula vulgaris
(species) D
CYP(T)
Primula vulgaris
(species)
Published - Accepted by Curator
CYP19A1
Coloration (feathers)
Cis-regulatory,
Insertion
Gallus gallus
chicken - (species) D
Domesticated
Candidate Gene
Li J; Davis BW; Jern P ; et al. (2019)
Characterization of the endogenous retrovirus insertion in CYP19A1 associated with henny feathering [...]
GP00002050
CYP19A1
P11511
Morphology
7524 bp insertion at the 5'end of CYP19A1 of an intact endogenous retrovirus (99% sequence identity to the avian leukosis virus ev-1 and ev-21 strains suggesting a recent integration) - The ERV 3'LTR contains a powerful transcriptional enhancer and core promoter with TATA box.
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
CYP19A1
Gallus gallus
chicken - (species)
Published - Accepted by Curator
CYP2J19
Coloration (feathers)
Unknown,
Unknown
Serinus canaria
common canary - (species)
Interspecific
Linkage Mapping
Lopes RJ; Johnson JD; Toomey MB ; et al. (2016)
Genetic Basis for Red Coloration in Birds.
GP00000201
CYP2J2
P51589
Morphology
unknown
Spinus cucullatus
red siskin - (species)
Serinus canaria
common canary - (species)
CYP2J19
Serinus canaria
common canary - (species)
Published - Accepted by Curator
CYP2J19
Coloration (red vs yellow beak)
Gene Loss,
Deletion
N
Taeniopygia guttata
zebra finch - (species) D
Domesticated
Linkage Mapping
Mundy NI; Stapley J; Bennison C ; et al. (2016)
Red Carotenoid Coloration in the Zebra Finch Is Controlled by a Cytochrome P450 Gene Cluster.
GP00000202
CYP2J2
P51589
Morphology
13kb deletion including complete loss of the CYP2J19A copy and cis-regulatory effects on CYP2J19B N
Taeniopygia guttata
zebra finch - (species)
Taeniopygia guttata
zebra finch - (species) D
CYP2J19
Taeniopygia guttata
zebra finch - (species)
Published - Accepted by Curator
CYP76AD1
Coloration
Coding,
Insertion
N
Beta vulgaris
(species) D
Domesticated
Linkage Mapping
Hatlestad GJ; Sunnadeniya RM; Akhavan NA ; et al. (2012)
The beet R locus encodes a new cytochrome P450 required for red betalain production.
GP00000210
CYP76AD1
I3PFJ5
Morphology
5bp insertion resulting in frameshift N
Beta vulgaris
(species)
Beta vulgaris
(species) D
CYP76AD1
Beta vulgaris
(species)
Published - Accepted by Curator
Dat
Coloration (puparium)
Unknown,
Unknown
Drosophila virilis
(species)
Interspecific
Linkage Mapping
Ahmed-Braimah YH; Sweigart AL (2015)
A single gene causes an interspecific difference in pigmentation in Drosophila.
GP00001403
AANAT1
Q94521
Morphology
unknown
Drosophila americana
(species)
Drosophila virilis
(species)
Dat
Drosophila virilis
(species)
Published - Accepted by Curator
DC-STAMP domain containing 2 (DCST2)
Body size
Unknown,
Unknown
Homo sapiens
human - (species)
Intraspecific
Association Mapping
van der Valk RJ; Kreiner-Møller E; Kooijman MN ; et al. (2015)
A novel common variant in DCST2 is associated with length in early life and height in adulthood.
GP00001509
DCST2
Q5T1A1
Morphology
SNP rs905938 C allele associated with an increase in birth length but probably not the causative mutation
Homo sapiens
human - (species)
Homo sapiens
human - (species)
DC-STAMP domain containing 2 (DCST2)
Homo sapiens
human - (species)
Published - Accepted by Curator
Dca (=smp-30)
Wing size
Cis-regulatory,
Unknown
Drosophila melanogaster
fruit fly - (species)
Intraspecific
Candidate Gene
Lee SF; Chen Y; Varan AK ; et al. (2011)
Molecular basis of adaptive shift in body size in Drosophila melanogaster: functional and sequence a[...]
1 Additional References
GP00000214
smp-30
Q9VFG5
Morphology
Non-coding
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species)
Dca (=smp-30)
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
DCAR-032551
Carotenoid content
Coding,
Insertion
N
Daucus carota
carrot - (species) D
Domesticated
Linkage Mapping
Iorizzo M; Ellison S; Senalik D ; et al. (2016)
A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid[...]
GP00001568
DCAR_032551
A0A162A3G8
Morphology
A 212-nt insertion in exon 2 that creates a frameshift mutation N
Daucus carota
carrot - (species)
Daucus carota
carrot - (species) D
DCAR-032551
Daucus carota
carrot - (species)
Published - Accepted by Curator
DDB1
Resistance to UV irradiation (sun exposure to skin)
Cis-regulatory,
Complex Change
Homo sapiens
human - (species) D
Intraspecific
Association Mapping
Crawford NG; Kelly DE; Hansen MEB ; et al. (2017)
Loci associated with skin pigmentation identified in African populations.
GP00001363
DDB1
Q16531
Morphology
most strongly associated SNPs are located in a region conserved across vertebrates flanked by TMEM138 and TMEM216 ~36 to 44 kb upstream of DDB1 and in high LD ; includes rs7948623 located 172 bp downstream of TMEM138 which shows enhancer activity in melanoma cells and interacts with the promoters of DDB1
Homo sapiens
human - (species)
Homo sapiens
human - (species) D
DDB1
Homo sapiens
human - (species)
Published - Accepted by Curator
DEEPER ROOTING 1
Drought tolerance
Root growth
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Uga Y; Sugimoto K; Ogawa S ; et al. (2013)
Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought condition[...]
GP00000215
Dro1
Q69P88
Physiology
Morphology
1bp deletion within exon 4 N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
DEEPER ROOTING 1
Oryza sativa
rice - (species)
Published - Accepted by Curator
DEFICIENS
Fruit shape
Cis-regulatory,
Epigenetic Change
Elaeis guineensis
African oil palm - (species) D
Domesticated
Association Mapping
Ong-Abdullah M; Ordway JM; Jiang N ; et al. (2015)
Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm.
GP00002100
AP3
P35632
Morphology
hypomethylation of the 3.2 kb oil palm Karma transposable element located within an intron of the DEFICIENS gene - this results in unmasking of a cryptic splice acceptor site and a premature termination signal and causes the mantled fruit phenotype- epigenetic derepression of a TE associated with a deleterious phenotype
Elaeis guineensis
African oil palm - (species)
Elaeis guineensis
African oil palm - (species) D
DEFICIENS
Elaeis guineensis
African oil palm - (species)
Published - Accepted by Curator
Delta
Bristle number (abdomen)
Cis-regulatory,
Unknown
Drosophila melanogaster
fruit fly - (species)
Intraspecific
Linkage Mapping
Long AD; Lyman RF; Langley CH ; et al. (1998)
Two sites in the Delta gene region contribute to naturally occurring variation in bristle number in [...]
1 Additional References
GP00000216
Dl
P10041
Morphology
unknown; associated site in intron 5
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species)
Delta
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
Delta
Bristle number (thorax)
Cis-regulatory,
Unknown
Drosophila melanogaster
fruit fly - (species)
Intraspecific
Linkage Mapping
Long AD; Lyman RF; Langley CH ; et al. (1998)
Two sites in the Delta gene region contribute to naturally occurring variation in bristle number in [...]
1 Additional References
GP00000217
Dl
P10041
Morphology
unknown; associated site in intron 2
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species)
Delta
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
DEP1
Grain yield
Coding,
Indel
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Huang X; Qian Q; Liu Z ; et al. (2009)
Natural variation at the DEP1 locus enhances grain yield in rice.
GP00000218
P0046G12.12-1
Q67UU9
Morphology
replacement of a 637bp stretch of the middle of exon5 by a 12-bp sequence creating a premature stop codon and consequently a loss of 230 residues from the C-terminus N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
DEP1
Oryza sativa
rice - (species)
Published - Accepted by Curator
determinant of gall color (dgc)
Coloration (induced gall)
Cis-regulatory,
Unknown
Hormaphis cornu
(species)
Intraspecific
Association Mapping
Korgaonkar A; Han C; Lemire AL ; et al. (2021)
A novel family of secreted insect proteins linked to plant gall development.
GP00002392
Morphology
almost complete silencing of dgc expression in salivary glands of aphids carrying the red gall allele
Hormaphis cornu
(species)
Hormaphis cornu
(species)
determinant of gall color (dgc)
Hormaphis cornu
(species)
Published - Accepted by Curator
Dihydroflavonol 4 reductase (MlDfr)
Coloration (flower)
Coding,
Insertion
N
Erythranthe lewisii
(species) D
Intraspecific
Candidate Gene
Wu CA; Streisfeld MA; Nutter LI ; et al. (2013)
The genetic basis of a rare flower color polymorphism in Mimulus lewisii provides insight into the r[...]
GP00001457
DFRA
P51102
Morphology
A 2 nt (TG) insertion at position 265 causing a frameshift and a greatly truncated protein of 106 aa only about one-fourth of its functional length N
Erythranthe lewisii
(species)
Erythranthe lewisii
(species) D
Dihydroflavonol 4 reductase (MlDfr)
Erythranthe lewisii
(species)
Published - Accepted by Curator
dihydroflavonol reductase (DFR)
Coloration (flowers)
Coding,
Deletion
Iochroma calycinum
(species) D
Intraspecific
Candidate Gene
Coburn RA; Griffin RH; Smith SD (2015)
Genetic basis for a rare floral mutant in an Andean species of Solanaceae.
GP00000224
DFRA
P51102
Morphology
33bp (11 a.a) deletion In coding sequence
Iochroma calycinum
(species)
Iochroma calycinum
(species) D
dihydroflavonol reductase (DFR)
Iochroma calycinum
(species)
Published - Accepted by Curator
dihydroflavonol reductase (DFR)
Coloration (flowers)
Coding,
SNP
Iochroma cyaneum
(species)
Intraspecific
Linkage Mapping
Smith SD; Rausher MD (2011)
Gene loss and parallel evolution contribute to species difference in flower color.
GP00000225
DFRA
P51102
Morphology
12 candidate a.a. substitution in cluding one at a residue known to influence substrate specificity
Iochroma cyaneum
(species)
Iochroma cyaneum
(species)
dihydroflavonol reductase (DFR)
Iochroma cyaneum
(species)
Published - Accepted by Curator
dihydroflavonol reductase (DFR)
Coloration (tuber skin)
Coding,
Unknown
Solanum tuberosum
potato - (species)
Domesticated
Linkage Mapping
De Jong WS; De Jong DM; De Jong H ; et al. (2003)
An allele of dihydroflavonol 4-reductase associated with the ability to produce red anthocyanin pigm[...]
1 Additional References
GP00000226
DFRA
P51102
Morphology
unknown; 10 a.a variable positions
Solanum tuberosum
potato - (species)
Solanum tuberosum
potato - (species)
dihydroflavonol reductase (DFR)
Solanum tuberosum
potato - (species)
Published - Accepted by Curator
Distal-less
Coloration (wing)
Cis-regulatory,
Unknown
Bicyclus anynana
squinting bush brown - (species)
Domesticated
Linkage Mapping
Beldade P; Brakefield PM; Long AD (2002)
Contribution of Distal-less to quantitative variation in butterfly eyespots.
GP00000229
Dll
P20009
Morphology
unknown
Bicyclus anynana
squinting bush brown - (species)
Bicyclus anynana
squinting bush brown - (species)
Distal-less
Bicyclus anynana
squinting bush brown - (species)
Published - Accepted by Curator
Dopa-decarboxylase
Bristle number (abdomen)
Cis-regulatory,
Unknown
Drosophila melanogaster
fruit fly - (species)
Intraspecific
Linkage Mapping
Mackay TF; Lyman RF (2005)
Drosophila bristles and the nature of quantitative genetic variation.
GP00000232
Ddc
P05031
Morphology
Promoter variation
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species)
Dopa-decarboxylase
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
Dopamine N-acetyltransferase (Dat)
Coloration (puparium)
Unknown,
Unknown
Drosophila virilis
(species) D
Interspecific
Linkage Mapping
Ahmed-Braimah YH; Sweigart AL (2015)
A single gene causes an interspecific difference in pigmentation in Drosophila.
GP00000234
AANAT1
Q94521
Morphology
Not identified ; 11kb mapped interval including regulatory region and first exon
Drosophila americana
(species)
Drosophila virilis
(species) D
Dopamine N-acetyltransferase (Dat)
Drosophila virilis
(species)
Published - Accepted by Curator
Doublesex
Bristle number (male sex comb tooth number)
Cis-regulatory,
Complex Change
obscura group
(species group)
Interspecific
Candidate Gene
Tanaka K; Barmina O; Sanders LE ; et al. (2011)
Evolution of sex-specific traits through changes in HOX-dependent doublesex expression.
GP00000235
dsx
P23023
Morphology
Acquisition of Scr binding sites in enhancer
Sophophora
(subgenus)
obscura group
(species group)
Doublesex
obscura group
(species group)
Published - Accepted by Curator
Doublesex
Coloration (wing ; Batesian mimicry)
Unknown,
Unknown
Papilio polytes
common Mormon - (species)
Intraspecific
Linkage Mapping
Kunte K; Zhang W; Tenger-Trolander A ; et al. (2014)
doublesex is a mimicry supergene.
2 Additional References
GP00001966
dsx
P23023
Morphology
More than 1000 nucleotide substitutions differentiate mimetic and non-mimetic dsx alleles. The non-mimetic Cyrus Dsx protein folds much like other insects (such as Bombyx mori) whereas the mimetic polytes protein structure is highly divergent. Knockdown experiments show that female-specific dsx isoforms expressed from the inverted H allele (dsx(H)) induce mimetic coloration patterns and simultaneously repress non-mimetic patterns.
Papilio polytes
common Mormon - (species)
Papilio polytes
common Mormon - (species)
Doublesex
Papilio polytes
common Mormon - (species)
Published - Accepted by Curator
Doublesex
Coloration (wing ; Batesian mimicry)
Unknown,
Unknown
Papilio memnon
(species)
Intraspecific
Candidate Gene
Iijima T; Kajitani R; Komata S ; et al. (2018)
Parallel evolution of Batesian mimicry supergene in two Papilio butterflies, P. polytes and P. memno[...]
1 Additional References
GP00001967
dsx
P23023
Morphology
A locus containing three genes (dsx; Nach-like and UXT) displays dimorphic sequences strictly associated with the mimetic/nonmimetic phenotypes. Expression of dox; UXT but not Nach-like showed differences correlated with phenotype in female hind wings.
Papilio memnon
(species)
Papilio memnon
(species)
Doublesex
Papilio memnon
(species)
Published - Accepted by Curator
Doublesex (or neighbouring gene prospero)
Wing shape (sex-specific)
Cis-regulatory,
Unknown
Nasonia giraulti
(species)
Interspecific
Linkage Mapping
Loehlin DW; Oliveira DC; Edwards R ; et al. (2010)
Non-coding changes cause sex-specific wing size differences between closely related species of Nason[...]
GP00000236
dsx
P23023
Morphology
various
Nasonia vitripennis
jewel wasp - (species)
Nasonia giraulti
(species)
Doublesex (or neighbouring gene prospero)
Nasonia giraulti
(species)
Published - Accepted by Curator
Dvl2
Organ size (tail)
Coding,
Deletion
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Mansour TA; Lucot K; Konopelski SE ; et al. (2018)
Whole genome variant association across 100 dogs identifies a frame shift mutation in DISHEVELLED 2 [...]
GP00002110
DVL2
O14641
Morphology
single base deletion found on CFA 5(g.32195043_32195044del) that is homozygous in the three screw tail breeds - predicted to lead to a frameshift mutation and cause a premature stop codon that truncates the translated protein by 23 amino acids (p.Pro684LeufsX26) - 26 altered amino acids are predicted to be present in the highly conserved C-terminus of the mutant protein. N
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
Dvl2
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
dwarf-8 (d8)
Plant size (dwarfism)
Coding,
Deletion
N
Zea mays
(species) D
Domesticated
Linkage Mapping
Peng J; Richards DE; Hartley NM ; et al. (1999)
'Green revolution' genes encode mutant gibberellin response modulators.
2 Additional References
GP00000241
D8
Q9ST48
Morphology
330bp deletion to V84 N
Zea mays
(species)
Zea mays
(species) D
dwarf-8 (d8)
Zea mays
(species)
Published - Accepted by Curator
DYM
Body size (height)
Unknown,
Unknown
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Lettre G (2011)
Recent progress in the study of the genetics of height.
GP00000242
DYM
Q7RTS9
Morphology
unknown
Homo sapiens
human - (species)
Homo sapiens
human - (species)
DYM
Homo sapiens
human - (species)
Published - Accepted by Curator
EARLY FLOWERING 3(ELF3) [possible pseudo-replicate]
Plant growth (hypocotyl elongation ; temperature-dependent)
Coding,
SNP
Arabidopsis thaliana
thale cress - (species)
Intraspecific
Linkage Mapping
Raschke A; Ibañez C; Ullrich KK ; et al. (2015)
Natural variants of ELF3 affect thermomorphogenesis by transcriptionally modulating PIF4-dependent a[...]
GP00001245
ELF3
O82804
Morphology
A362V
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
EARLY FLOWERING 3(ELF3) [possible pseudo-replicate]
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
ebony
Coloration (abdomen)
Cis-regulatory,
Unknown
Drosophila novamexicana
(species) D
Intraspecific
Linkage Mapping
Wittkopp PJ; Stewart EE; Arnold LL ; et al. (2009)
Intraspecific polymorphism to interspecific divergence: genetics of pigmentation in Drosophila.
1 Additional References
GP00000248
e
O76858
Morphology
Not identified
Drosophila americana
(species)
Drosophila novamexicana
(species) D
ebony
Drosophila novamexicana
(species)
Published - Accepted by Curator
ebony
Coloration (thorax)
Cis-regulatory,
Unknown
Drosophila melanogaster
fruit fly - (species)
Intraspecific
Linkage Mapping
Takahashi A; Takahashi K; Ueda R ; et al. (2007)
Natural variation of ebony gene controlling thoracic pigmentation in Drosophila melanogaster.
1 Additional References
GP00000249
e
O76858
Morphology
Not identified
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species)
ebony
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
ebony
Coloration (posterior abdomen)
Cis-regulatory,
Unknown
Drosophila auraria
(species) D
Intraspecific
Candidate Gene
Johnson WC; Ordway AJ; Watada M ; et al. (2015)
Genetic Changes to a Transcriptional Silencer Element Confers Phenotypic Diversity within and betwee[...]
GP00000250
e
O76858
Morphology
Inactivation of a conserved silencer resulting in gain-of-expression; the increase in ebony expression in the light strain occurred primarily through mutations affecting the ebony male-specific silencer element
Drosophila auraria
(species)
Drosophila auraria
(species) D
ebony
Drosophila auraria
(species)
Published - Accepted by Curator
ebony
Coloration (posterior abdomen)
Cis-regulatory,
Unknown
Drosophila serrata
(species) D
Interspecific
Candidate Gene
Johnson WC; Ordway AJ; Watada M ; et al. (2015)
Genetic Changes to a Transcriptional Silencer Element Confers Phenotypic Diversity within and betwee[...]
GP00000251
e
O76858
Morphology
loss of the ebony male-specific silencer function - increased expression of ebony
Drosophila jambulina
(species)
Drosophila serrata
(species) D
ebony
Drosophila serrata
(species)
Published - Accepted by Curator
ebony
Coloration (posterior abdomen)
Cis-regulatory,
Unknown
Drosophila melanogaster
fruit fly - (species)
Intraspecific
Linkage Mapping
Takahashi A; Takano-Shimizu T (2011)
Divergent enhancer haplotype of ebony on inversion In(3R)Payne associated with pigmentation variatio[...]
GP00000252
e
O76858
Morphology
17 nucleotide sites and 2 indels in complete association with the thoracic trident pigmentation intensity in a 13kb region
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species)
ebony
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
ebony
Coloration (posterior abdomen)
5 Mutations:
Cis-regulatory
SNP
Drosophila melanogaster
fruit fly - (species)
Intraspecific
Linkage Mapping
Rebeiz M; Pool JE; Kassner VA ; et al. (2009)
Stepwise modification of a modular enhancer underlies adaptation in a Drosophila population.
GP00000253
e
O76858
Morphology
5 mutations
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species)
ebony
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
ebony
Coloration (male-specific)
Cis-regulatory,
SNP
Drosophila malerkotliana
(species)
Intraspecific
Linkage Mapping
Signor SA; Liu Y; Rebeiz M ; et al. (2016)
Genetic Convergence in the Evolution of Male-Specific Color Patterns in Drosophila.
GP00001544
e
O76858
Morphology
5 changes including 4 SNP and 1bp indel in the first intron
Drosophila malerkotliana
(species)
Drosophila malerkotliana
(species)
ebony
Drosophila malerkotliana
(species)
Published - Accepted by Curator
ebony
Coloration (male-specific)
Cis-regulatory,
Unknown
Drosophila pseudoananassae
(species)
Intraspecific
Linkage Mapping
Signor SA; Liu Y; Rebeiz M ; et al. (2016)
Genetic Convergence in the Evolution of Male-Specific Color Patterns in Drosophila.
GP00001545
e
O76858
Morphology
unknown
Drosophila pseudoananassae
(species)
Drosophila pseudoananassae
(species)
ebony
Drosophila pseudoananassae
(species)
Published - Accepted by Curator
ebony
Coloration (male-specific)
Unknown,
Unknown
Drosophila merina
(species)
Interspecific
Linkage Mapping
Signor SA; Liu Y; Rebeiz M ; et al. (2016)
Genetic Convergence in the Evolution of Male-Specific Color Patterns in Drosophila.
GP00001546
e
O76858
Morphology
unknown
Drosophila ercepeae
(species)
Drosophila merina
(species)
ebony
Drosophila merina
(species)
Published - Accepted by Curator
ebony
Coloration (male-specific)
Unknown,
Unknown
Drosophila bipectinata
(species)
Interspecific
Linkage Mapping
Signor SA; Liu Y; Rebeiz M ; et al. (2016)
Genetic Convergence in the Evolution of Male-Specific Color Patterns in Drosophila.
GP00001547
e
O76858
Morphology
unknown
Drosophila parabipectinata
(species)
Drosophila bipectinata
(species)
ebony
Drosophila bipectinata
(species)
Published - Accepted by Curator
ebony
Coloration (abdomen; male)
Cis-regulatory,
Insertion
Drosophila santomea
(species) D
Interspecific
Linkage Mapping
Liu Y; Ramos-Womack M; Han C ; et al. (2019)
Changes throughout a Genetic Network Mask the Contribution of Hox Gene Evolution.
GP00002024
e
O76858
Morphology
insertion of a partial 481 bp fragment related to a transposable element of the helitron class - maybe other causing mutations as well at this ebony locus (including one fixed amino acid change whose phenotypic effect has not been investigated) - increased expression associated with lighter pigmentation
Drosophila yakuba
(species)
Drosophila santomea
(species) D
ebony
Drosophila santomea
(species)
Published - Accepted by Curator
Ectodysplasin (EDA)
Dermal bone (loss of armor plates)
Cis-regulatory,
Unknown
Gasterosteus aculeatus
three-spined stickleback - (species) D
Interspecific
Linkage Mapping
Colosimo PF; Hosemann KE; Balabhadra S ; et al. (2005)
Widespread parallel evolution in sticklebacks by repeated fixation of Ectodysplasin alleles.
2 Additional References
GP00000254
Eda
O54693
Morphology
large haplotype- includes a T-> G regulatory change that affect expression based on differential responsiveness to Wnt signaling
Gasterosteus aculeatus
three-spined stickleback - (species)
Gasterosteus aculeatus
three-spined stickleback - (species) D
Ectodysplasin (EDA)
Gasterosteus aculeatus
three-spined stickleback - (species)
Published - Accepted by Curator
Ectodysplasin (EDA)
Scales (loss)
Femoral glands (absent)
Tooth number
Coding,
Insertion
Pogona vitticeps
central bearded dragon - (species) D
Intraspecific
Candidate Gene
Di-Poï N; Milinkovitch MC (2016)
The anatomical placode in reptile scale morphogenesis indicates shared ancestry among skin appendage[...]
GP00002040
Eda
O54693
Morphology
Morphology
Morphology
5′688–bp insertion of a transposon of the LTR-Gypsy family which generates a new splice donor site (gt) 42 bases upstream of the wild-type donor site; thus generating a 14–amino acid deletion in the corresponding transcript
Pogona vitticeps
central bearded dragon - (species)
Pogona vitticeps
central bearded dragon - (species) D
Ectodysplasin (EDA)
Pogona vitticeps
central bearded dragon - (species)
Published - Accepted by Curator
EDAR
Hair thickness
Eccrine gland density
Ear traits = lobe size / lobe attachment / helix rolling / ear protrusion
Tooth morphology (shovel-shaped incisors)
Coding,
SNP
Homo sapiens
human - (species) D
Intraspecific
Association Mapping
Fujimoto A; Kimura R; Ohashi J ; et al. (2008)
A scan for genetic determinants of human hair morphology: EDAR is associated with Asian hair thickne[...]
4 Additional References
GP00000256
EDAR
Q9UNE0
Morphology
Morphology
Morphology
Morphology
p.Val370Ala; functionally validated in mouse
Homo sapiens
human - (species)
Homo sapiens
human - (species) D
EDAR
Homo sapiens
human - (species)
Published - Accepted by Curator
EDAR
Scales (reduced)
Coding,
Deletion
N
Sinocyclocheilus anshuiensis
(species) D
Sinocyclocheilus grahami
(species) D
Sinocyclocheilus rhinocerous
(species) D
Interspecific
Candidate Gene
Yang J; Chen X; Bai J ; et al. (2016)
The Sinocyclocheilus cavefish genome provides insights into cave adaptation.
GP00002359
EDAR
Q9UNE0
Morphology
Several deletions in the EDAR1 coding region. N
Danio rerio
zebrafish - (species)
Sinocyclocheilus anshuiensis
(species) D
Sinocyclocheilus grahami
(species) D
Sinocyclocheilus rhinocerous
(species) D
EDAR
Sinocyclocheilus anshuiensis
(species)
Sinocyclocheilus grahami
(species)
Sinocyclocheilus rhinocerous
(species)
Published - Accepted by Curator
EDN3
Coloration (hyperpigmentation)
Gene Amplification,
Complex Change
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Dorshorst B; Molin AM; Rubin CJ ; et al. (2011)
A complex genomic rearrangement involving the endothelin 3 locus causes dermal hyperpigmentation in [...]
3 Additional References
GP00000258
EDN3
P14138
Morphology
Large duplication
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
EDN3
Gallus gallus
chicken - (species)
Published - Accepted by Curator
EDN3
Coloration (coat)
Coloration (eyes)
Hearing (loss)
Unknown,
Unknown
Lama glama
llama - (species) D
Vicugna pacos
alpaca - (species) D
Domesticated
Candidate Gene
Fan R; Gu Z; Guang X ; et al. (2020)
Genomic analysis of the domestication and post-Spanish conquest evolution of the llama and alpaca.
GP00002182
EDN3
P14138
Morphology
Morphology
Physiology
Introgression from alpacas to lamas and clear correlation wit phenotype but no information on the mutation(s)
Vicugna vicugna
vicugna - (species)
Lama glama
llama - (species) D
Vicugna pacos
alpaca - (species) D
EDN3
Lama glama
llama - (species)
Vicugna pacos
alpaca - (species)
Published - Accepted by Curator
EDN3
Coloration
Cis-regulatory,
Unknown
Ambystoma mexicanum
axolotl - (species) D
Domesticated
Candidate Gene
Woodcock MR; Vaughn-Wolfe J; Elias A ; et al. (2017)
Identification of Mutant Genes and Introgressed Tiger Salamander DNA in the Laboratory Axolotl, Amby[...]
GP00002377
EDN3
P14138
Morphology
Ambystoma mexicanum
axolotl - (species)
Ambystoma mexicanum
axolotl - (species) D
EDN3
Ambystoma mexicanum
axolotl - (species)
Published - Accepted by Curator
edn3b
Coloration (reduced number of stripes)
Cis-regulatory,
Unknown
Danio nigrofasciatus
dwarf danio - (species)
Interspecific
Candidate Gene
Spiewak JE; Bain EJ; Liu J ; et al. (2018)
Evolution of Endothelin signaling and diversification of adult pigment pattern in Danio fishes.
GP00002124
edn3b
E9QFS0
Morphology
pigment pattern differences between these species are clearly polygenic, and it seems likely that additional loci, of the endothelin pathway or other pathways, will be identified as contributing to attenuated stripes and interstripes of D. nigrofasciatus compared to D. rerio.
Danio rerio
zebrafish - (species)
Danio nigrofasciatus
dwarf danio - (species)
edn3b
Danio nigrofasciatus
dwarf danio - (species)
Published - Accepted by Curator
EDNRA
Coloration (coat ; white-spotting)
Gene Amplification,
Insertion
Capra hircus
goat - (species) D
Domesticated
Association Mapping
Menzi F; Keller I; Reber I ; et al. (2016)
Genomic amplification of the caprine EDNRA locus might lead to a dose dependent loss of pigmentation[...]
GP00002170
Ednra
Q61614
Morphology
1 Mb copy number variant (CNV) harboring 5 genes including EDNRA ; The duplicated EDNRA copies contain a missense variant (p.Tyr129His) predicted to increase the affinity of the encoded mutant receptor for endothelin 3. Menzi et al. proposed a hypothesis whereby ectopic overexpression of a mutant EDNRA scavenges EDN3 required for EDNRB signaling and normal melanocyte development and thus likely leads to an absence of melanocytes in the non-pigmented body areas of Boer goats (thanks to OMIA for the summary)
Capra hircus
goat - (species)
Capra hircus
goat - (species) D
EDNRA
Capra hircus
goat - (species)
Published - Accepted by Curator
EGFR
Wing shape (length)
Unknown,
Unknown
Drosophila melanogaster
fruit fly - (species)
Intraspecific
Linkage Mapping
Dworkin I; Palsson A; Gibson G (2005)
Replication of an Egfr-wing shape association in a wild-caught cohort of Drosophila melanogaster.
1 Additional References
GP00000259
Egfr
P04412
Morphology
unknown
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species)
EGFR
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
EGFR
Coloration (skin)
Unknown,
Unknown
Homo sapiens
human - (species) D
Intraspecific
Association Mapping
Quillen EE; Bauchet M; Bigham AW ; et al. (2012)
OPRM1 and EGFR contribute to skin pigmentation differences between Indigenous Americans and European[...]
GP00001537
EGFR
P00533
Morphology
A>T associated SNP
Homo sapiens
human - (species)
Homo sapiens
human - (species) D
EGFR
Homo sapiens
human - (species)
Published - Accepted by Curator
EIF2AK3
Body size (height)
Unknown,
Unknown
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Lettre G (2011)
Recent progress in the study of the genetics of height.
GP00000264
EIF2AK3
Q9NZJ5
Morphology
unknown
Homo sapiens
human - (species)
Homo sapiens
human - (species)
EIF2AK3
Homo sapiens
human - (species)
Published - Accepted by Curator
EIF2S2
Coloration (skin)
Unknown,
Unknown
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Liu F; Visser M; Duffy DL ; et al. (2015)
Genetics of skin color variation in Europeans: genome-wide association studies with functional follo[...]
GP00001359
EIF2S2
P20042
Morphology
unknown
Homo sapiens
human - (species)
Homo sapiens
human - (species)
EIF2S2
Homo sapiens
human - (species)
Published - Accepted by Curator
Endothelin receptor B
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Metallinos DL; Bowling AT; Rine J (1998)
A missense mutation in the endothelin-B receptor gene is associated with Lethal White Foal Syndrome:[...]
2 Additional References
GP00000269
Ednrb
P48302
Morphology
Ile118Lys
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Endothelin receptor B
Equus caballus
horse - (species)
Published - Accepted by Curator
Endothelin receptor B
Coloration (feathers ; white-spotting)
Coding,
SNP
Coturnix japonica
Japanese quail - (species) D
Domesticated
Linkage Mapping
Miwa M; Inoue-Murayama M; Aoki H ; et al. (2007)
Endothelin receptor B2 (EDNRB2) is associated with the panda plumage colour mutation in Japanese qua[...]
GP00000270
Ednrb
P48302
Morphology
c.995G>A p.R332H
Coturnix japonica
Japanese quail - (species)
Coturnix japonica
Japanese quail - (species) D
Endothelin receptor B
Coturnix japonica
Japanese quail - (species)
Published - Accepted by Curator
Endothelin receptor B2
Coloration (feathers)
Coding,
SNP
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Kinoshita K; Akiyama T; Mizutani M ; et al. (2014)
Endothelin receptor B2 (EDNRB2) is responsible for the tyrosinase-independent recessive white (mo(w)[...]
GP00001360
EDNRB2
W8VUK4
Morphology
c.1008G>T p.Cys244Phe
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
Endothelin receptor B2
Gallus gallus
chicken - (species)
Published - Accepted by Curator
Endothelin receptor B2
Coloration (feathers)
Coding,
SNP
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Kinoshita K; Akiyama T; Mizutani M ; et al. (2014)
Endothelin receptor B2 (EDNRB2) is responsible for the tyrosinase-independent recessive white (mo(w)[...]
GP00001361
EDNRB2
W8VUK4
Morphology
c.G1272A p.Arg332His
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
Endothelin receptor B2
Gallus gallus
chicken - (species)
Published - Accepted by Curator
Endothelin receptor B2
Coloration (feathers ; white-spotting)
Coding,
SNP
Anas platyrhynchos
mallard - (species) D
Domesticated
Candidate Gene
Li L; Li D; Liu L ; et al. (2015)
Endothelin Receptor B2 (EDNRB2) Gene Is Associated with Spot Plumage Pattern in Domestic Ducks (Anas[...]
GP00002378
EDNRB2
W8VUK4
Morphology
Anas platyrhynchos
mallard - (species)
Anas platyrhynchos
mallard - (species) D
Endothelin receptor B2
Anas platyrhynchos
mallard - (species)
Published - Accepted by Curator
Endothelin receptor B2
Coloration (feathers ; white-spotting)
Cis-regulatory,
Unknown
Anas platyrhynchos
mallard - (species) D
Domesticated
Association Mapping
Xi Y; Xu Q; Huang Q ; et al. (2021)
Genome-wide association analysis reveals that EDNRB2 causes a dose-dependent loss of pigmentation in[...]
GP00002383
EDNRB2
W8VUK4
Morphology
"The GWAS results identified a 198 kb (Chr4: 10,149,651 bp to 10,348,068 bp) genetic region that was significantly associated with the black spot phenotype. The conditional GWAS and linkage disequilibrium (LD) analysis further narrowed the ultimate candidate region to 167 kb (Chr4: 10,180,939 bp to 10,348,068 bp). A key gene regulating melanoblast migration and differentiation, EDNRB2 (Endothelin B receptor-like), was found in the candidate region and having significant mRNA expression level changes in embryonic duck skin tissue with different spot sizes. The significant SNPs (single nucleotide polymorphisms) associated with the EDNRB2 gene were annotated, and two mutations (Chr4: 10,180,939 T > C and Chr4: 10,190,671 A > T) were found to result in the loss of binding sites for two trans-factors, XBP1 and cMYB. The phenotypic effect of these two mutations suggested that they can regulate the size of black spots in a dose-dependent manner, and Chr4: 10,180,939 T > C was the major allele locus."
Anas platyrhynchos
mallard - (species)
Anas platyrhynchos
mallard - (species) D
Endothelin receptor B2
Anas platyrhynchos
mallard - (species)
Published - Accepted by Curator
engrailed
Coloration (wing ; Batesian mimicry)
Cis-regulatory,
Unknown
Papilio dardanus
African swallowtail butterfly - (species) D
Intraspecific
Linkage Mapping
Timmermans MJTN; Srivathsan A; Collins S ; et al. (2020)
Mimicry diversification in Papilio dardanus via a genomic inversion in the regulatory region of engr[...]
GP00002428
en
P02836
Morphology
Association with many nucleotide changes in a cis-regulatory region of engrailed. The diverged region exhibits a discrete chromosomal inversion of 40 kb relative to the ancestral orientation that is associated with the cenea morph, but not with the bottom-recessive hippocoonides morph or with non-mimetic allopatric populations.
Papilio dardanus
African swallowtail butterfly - (species)
Papilio dardanus
African swallowtail butterfly - (species) D
engrailed
Papilio dardanus
African swallowtail butterfly - (species)
Published - Accepted by Curator
EOMES (eomesodermin)
Bird head comb (reduced)
Gene Amplification,
Insertion
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Dorshorst B; Harun-Or-Rashid M; Bagherpoor AJ ; et al. (2015)
A genomic duplication is associated with ectopic eomesodermin expression in the embryonic chicken co[...]
GP00000271
Eomes
O54839
Morphology
a 20 Kb tandem duplication containing several conserved putative regulatory elements located 200 Kb upstream of the eomesodermin gene
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
EOMES (eomesodermin)
Gallus gallus
chicken - (species)
Published - Accepted by Curator
EphB2
Feathers (crest morphology)
Coding,
SNP
Columba livia
rock pigeon - (species) D
Domesticated
Association Mapping
Shapiro MD; Kronenberg Z; Li C ; et al. (2013)
Genomic diversity and evolution of the head crest in the rock pigeon.
1 Additional References
GP00000275
EPHB2
P28693
Morphology
Arg758Cys (C>T) p.R758C
Columba livia
rock pigeon - (species)
Columba livia
rock pigeon - (species) D
EphB2
Columba livia
rock pigeon - (species)
Published - Accepted by Curator
EphB2
Feathers (crest morphology)
Coding,
SNP
Streptopelia risoria
ringneck dove - (species) D
Domesticated
Candidate Gene
Vickrey AI; Domyan ET; Horvath MP ; et al. (2015)
Convergent Evolution of Head Crests in Two Domesticated Columbids Is Associated with Different Misse[...]
GP00000276
EPHB2
P28693
Morphology
Gly636Arg (G>A)
Streptopelia risoria
ringneck dove - (species)
Streptopelia risoria
ringneck dove - (species) D
EphB2
Streptopelia risoria
ringneck dove - (species)
Published - Accepted by Curator
ephrin-a4
Coloration (scales)
Unknown,
Unknown
Tropheops sp. 'red cheek'
(species)
Interspecific
Linkage Mapping
Albertson RC; Powder KE; Hu Y ; et al. (2014)
Genetic basis of continuous variation in the levels and modular inheritance of pigmentation in cichl[...]
GP00001420
EFNA4
P52798
Morphology
unknown
Labeotropheus fuelleborni
blue mbuna - (species)
Tropheops sp. 'red cheek'
(species)
ephrin-a4
Tropheops sp. 'red cheek'
(species)
Published - Accepted by Curator
ERECTA
Plant architecture
Leaf architecture
Transpiration
Unknown,
Unknown
Arabidopsis thaliana
thale cress - (species)
Intraspecific
Linkage Mapping
Masle J; Gilmore SR; Farquhar GD (2005)
The ERECTA gene regulates plant transpiration efficiency in Arabidopsis.
2 Additional References
GP00000280
ERECTA
Q42371
Morphology
Morphology
Physiology
unknown
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
ERECTA
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
ETC2
Trichome density (leaf)
Coding,
SNP
Arabidopsis thaliana
thale cress - (species)
Intraspecific
Linkage Mapping
Hilscher J; Schlötterer C; Hauser MT (2009)
A single amino acid replacement in ETC2 shapes trichome patterning in natural Arabidopsis population[...]
GP00001237
ETC2
Q84RD1
Morphology
K19E
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
ETC2
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
fasciated
Fruit size
Fruit architecture
Cis-regulatory,
Unknown
Solanum lycopersicum
tomato - (species)
Domesticated
Linkage Mapping
Cong B; Barrero LS; Tanksley SD (2008)
Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during t[...]
GP00000305
fasciated
B2YHV8
Morphology
Morphology
Possibly 7-bp and 6- to 8-kb insertion in the first intron
Solanum pennellii
(species)
Solanum lycopersicum
tomato - (species)
fasciated
Solanum lycopersicum
tomato - (species)
Published - Accepted by Curator
FASCIATED EAR2
Grain yield (kernel row number)
Unknown,
Unknown
Zea mays
(species)
Domesticated
Linkage Mapping
Bommert P; Nagasawa NS; Jackson D (2013)
Quantitative variation in maize kernel row number is controlled by the FASCIATED EAR2 locus.
GP00000306
FEA2
Q940E8
Morphology
Not identified
Zea mays
(species)
Zea mays
(species)
FASCIATED EAR2
Zea mays
(species)
Published - Accepted by Curator
Fezf2
Cerebral cortex layered organization
Cis-regulatory,
Complex Change
Mammalia
mammals - (class) D
Intergeneric or Higher
Candidate Gene
Shim S; Kwan KY; Li M ; et al. (2012)
Cis-regulatory control of corticospinal system development and evolution.
GP00000307
Fezf2
Q9ESP5
Morphology
Acquisition of SOX binding sites in enhancer E4
Amniota
amniotes - (no rank)
Mammalia
mammals - (class) D
Fezf2
Mammalia
mammals - (class)
Published - Accepted by Curator
FGF20
Organ loss (feathers ; scales)
Coding,
SNP
N
Gallus gallus
chicken - (species) D
Domesticated
Association Mapping
Wells KL; Hadad Y; Ben-Avraham D ; et al. (2012)
Genome-wide SNP scan of pooled DNA reveals nonsense mutation in FGF20 in the scaleless line of feath[...]
GP00002171
FGF20
Q9NP95
Morphology
g.62878803A>T c.535A>T p.R179* N
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
FGF20
Gallus gallus
chicken - (species)
Published - Accepted by Curator
FGF3; FGF4; FGF19; ORAOV1
Coloration (coat; dog Ridgeback phenotype)
Gene Amplification,
Complex Change
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Linkage Mapping
Salmon Hillbertz NH; Isaksson M; Karlsson EK ; et al. (2007)
Duplication of FGF3, FGF4, FGF19 and ORAOV1 causes hair ridge and predisposition to dermoid sinus in[...]
GP00000308
FGF4
J9P3I7
Morphology
Gene duplication
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
FGF3; FGF4; FGF19; ORAOV1
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
FGF4 retrogene
Limb size
Unknown,
Insertion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Parker HG; VonHoldt BM; Quignon P ; et al. (2009)
An expressed fgf4 retrogene is associated with breed-defining chondrodysplasia in domestic dogs.
GP00000309
FGF4
J9P3I7
Morphology
Gene retroposition : 5kb insertion containing a FGF4 retrogene; 25Mb away from the complete (original) FGF4 gene
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
FGF4 retrogene
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
FGF5
Hair length
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Cadieu E; Neff MW; Quignon P ; et al. (2009)
Coat variation in the domestic dog is governed by variants in three genes.
GP00000310
Fgf5
P15656
Morphology
Cys95Phe
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
FGF5
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
FGF5
Hair length (length)
Coding,
Deletion
N
Felis catus
domestic cat - (species) D
Domesticated
Candidate Gene
Drögemüller C; Rüfenacht S; Wichert B ; et al. (2007)
Mutations within the FGF5 gene are associated with hair length in cats.
1 Additional References
GP00000311
Fgf5
P15656
Morphology
c.474delT resulting in frameshift N
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
FGF5
Felis catus
domestic cat - (species)
Published - Accepted by Curator
FGF5
Hair length
Coding,
Deletion
N
Equus asinus
ass - (species) D
Domesticated
Candidate Gene
Legrand R; Tiret L; Abitbol M (2014)
Two recessive mutations in FGF5 are associated with the long-hair phenotype in donkeys.
GP00001369
Fgf5
P15656
Morphology
c.433_434delAT frameshift deletion leading to a stop codon at position 159 N
Equus asinus
ass - (species)
Equus asinus
ass - (species) D
FGF5
Equus asinus
ass - (species)
Published - Accepted by Curator
FGF5
Hair length
Coding,
SNP
N
Equus asinus
ass - (species) D
Domesticated
Candidate Gene
Legrand R; Tiret L; Abitbol M (2014)
Two recessive mutations in FGF5 are associated with the long-hair phenotype in donkeys.
GP00001370
Fgf5
P15656
Morphology
c.245G>A p.W82* nonsense mutation leading to stop codon at position 82 N
Equus asinus
ass - (species)
Equus asinus
ass - (species) D
FGF5
Equus asinus
ass - (species)
Published - Accepted by Curator
FGF5
Hair length (length)
Coding,
Insertion
N
Felis catus
domestic cat - (species) D
Domesticated
Candidate Gene
Drögemüller C; Rüfenacht S; Wichert B ; et al. (2007)
Mutations within the FGF5 gene are associated with hair length in cats.
1 Additional References
GP00002172
Fgf5
P15656
Morphology
c.ins356T resulting in frameshift N
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
FGF5
Felis catus
domestic cat - (species)
Published - Accepted by Curator
FGF5
Hair length
Coding,
Deletion
N
Mesocricetus auratus
golden hamster - (species) D
Domesticated
Candidate Gene
Yoshizawa Y; Wada K; Shimoi G ; et al. (2015)
A 1-bp deletion in Fgf5 causes male-dominant long hair in the Syrian hamster.
GP00002173
Fgf5
P15656
Morphology
c.546delG p.Arg184GlyfsX6 N
Mesocricetus auratus
golden hamster - (species)
Mesocricetus auratus
golden hamster - (species) D
FGF5
Mesocricetus auratus
golden hamster - (species)
Published - Accepted by Curator
FGF5
Hair length
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Dierks C; Mömke S; Philipp U ; et al. (2013)
Allelic heterogeneity of FGF5 mutations causes the long-hair phenotype in dogs.
1 Additional References
GP00002174
Fgf5
P15656
Morphology
g.4528639C>T c.578C>T p.A193V
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
FGF5
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
FGF5
Hair length
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Dierks C; Mömke S; Philipp U ; et al. (2013)
Allelic heterogeneity of FGF5 mutations causes the long-hair phenotype in dogs.
1 Additional References
GP00002175
Fgf5
P15656
Morphology
g.8193T>A splice site
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
FGF5
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
FGF5
Hair length
Coding,
Insertion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Dierks C; Mömke S; Philipp U ; et al. (2013)
Allelic heterogeneity of FGF5 mutations causes the long-hair phenotype in dogs.
1 Additional References
GP00002176
Fgf5
P15656
Morphology
c.559_560dupGG p.R188Afs*73
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
FGF5
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
FGF5
Hair length
Coding,
Deletion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Dierks C; Mömke S; Philipp U ; et al. (2013)
Allelic heterogeneity of FGF5 mutations causes the long-hair phenotype in dogs.
1 Additional References
GP00002177
Fgf5
P15656
Morphology
c.556_571del16 p.A186Tfs*69
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
FGF5
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
FGF5
Hair length
Coding,
SNP
N
Cavia porcellus
domestic guinea pig - (species) D
Domesticated
Candidate Gene
Yu F; Liu Z; Jiao S ; et al. (2018)
A nonsense mutation in the FGF5 gene is associated with the long-haired phenotype in domestic guinea[...]
GP00002178
Fgf5
P15656
Morphology
c.403C>T p.Arg135* N
Cavia porcellus
domestic guinea pig - (species)
Cavia porcellus
domestic guinea pig - (species) D
FGF5
Cavia porcellus
domestic guinea pig - (species)
Published - Accepted by Curator
FGF5
Hair length
Coding,
Indel
N
Lama glama
llama - (species) D
Domesticated
Candidate Gene
Daverio MS; Vidal-Rioja L; Frank EN ; et al. (2017)
Molecular characterization of the llama FGF5 gene and identification of putative loss of function mu[...]
GP00002179
Fgf5
P15656
Morphology
a single base deletion (c.348delA) + a 12-bp insertion (c.351_352insCATATAACATAG) N
Lama guanicoe
guanaco - (species)
Lama glama
llama - (species) D
FGF5
Lama glama
llama - (species)
Published - Accepted by Curator
FGF5
Hair length
Coding,
SNP
N
Lama glama
llama - (species) D
Vicugna pacos
alpaca - (species) D
Domesticated
Candidate Gene
Daverio MS; Vidal-Rioja L; Frank EN ; et al. (2017)
Molecular characterization of the llama FGF5 gene and identification of putative loss of function mu[...]
2 Additional References
GP00002180
Fgf5
P15656
Morphology
transition C>T at position 499 downstream of the ATG codon with transcriptional readthrough ; difference in post-transcriptional readthrough may underlie the different fleece types of the alpaca suri and huacaya breeds ; derived allele was introgressed from lamas to alpacas N
Lama guanicoe
guanaco - (species)
Lama glama
llama - (species) D
Vicugna pacos
alpaca - (species) D
FGF5
Lama glama
llama - (species)
Vicugna pacos
alpaca - (species)
Published - Accepted by Curator
FGF5
Hair length
Coding,
Deletion
N
Mus musculus
house mouse - (species) D
Domesticated
Candidate Gene
Hébert JM; Rosenquist T; Götz J ; et al. (1994)
FGF5 as a regulator of the hair growth cycle: evidence from targeted and spontaneous mutations.
1 Additional References
GP00002441
Fgf5
P15656
Morphology
Deletion which extends at least 2kb upstream of the Fgf5 translational start site and terminates at the end of the first exon or beginning of the first intron. N
Mus musculus
house mouse - (species)
Mus musculus
house mouse - (species) D
FGF5
Mus musculus
house mouse - (species)
Published - Accepted by Curator
FGF5
Hair length
Coding,
Deletion
N
Mus musculus
house mouse - (species) D
Domesticated
Candidate Gene
Mizuno S; Iijima S; Okano T ; et al. (2011)
Retrotransposon-mediated Fgf5(go-Utr) mutant mice with long pelage hair.
GP00002442
Fgf5
P15656
Morphology
Deletion of a 9.3-kb region in the Fgf5 gene including exon 3 and its 5' and 3' flanking sequences. The genomic deletion site also shows insertion of a 498-bp early transposon element long terminal repeat. N
Mus musculus
house mouse - (species)
Mus musculus
house mouse - (species) D
FGF5
Mus musculus
house mouse - (species)
Published - Accepted by Curator
FGF5
Hair length
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Housley DJ; Venta PJ (2006)
The long and the short of it: evidence that FGF5 is a major determinant of canine 'hair'-itability.
GP00002443
Fgf5
P15656
Morphology
Presence of a duplication in a relatively non-conserved region of the gene and a missense mutation resulting in the substitution of Phe for Cys in a highly conserved region. Genotyping of 218 dogs from three breeds fixed for long hair; eight breeds fixed for short hair and five breeds in which long hair is segregating provided evidence that the missense mutation is associated with the hair-length differences among these breeds.
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
FGF5
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Fgfr1a1
Scales (loss)
Coding,
Deletion
N
Cyprinus carpio
common carp - (species) D
Domesticated
Candidate Gene
Rohner N; Bercsényi M; Orbán L ; et al. (2009)
Duplication of fgfr1 permits Fgf signaling to serve as a target for selection during domestication.
GP00000312
fgfr1a
Q90Z00
Morphology
deletion of 310 bp N
Cyprinus carpio
common carp - (species)
Cyprinus carpio
common carp - (species) D
Fgfr1a1
Cyprinus carpio
common carp - (species)
Published - Accepted by Curator
Fgfr1a1
Scales (loss)
Coding,
SNP
Cyprinus carpio
common carp - (species) D
Domesticated
Candidate Gene
Rohner N; Bercsényi M; Orbán L ; et al. (2009)
Duplication of fgfr1 permits Fgf signaling to serve as a target for selection during domestication.
GP00000313
fgfr1a
Q90Z00
Morphology
Glu664Lys
Cyprinus carpio
common carp - (species)
Cyprinus carpio
common carp - (species) D
Fgfr1a1
Cyprinus carpio
common carp - (species)
Published - Accepted by Curator
FGFR2
Hair thickness
Cis-regulatory,
Unknown
Homo sapiens
human - (species)
Intraspecific
Candidate Gene
Fujimoto A; Nishida N; Kimura R ; et al. (2009)
FGFR2 is associated with hair thickness in Asian populations.
GP00000314
FGFR2
P21802
Morphology
Unknown
Homo sapiens
human - (species)
Homo sapiens
human - (species)
FGFR2
Homo sapiens
human - (species)
Published - Accepted by Curator
FGFR3
Body size (bone length)
Coding,
SNP
Ovis aries
sheep - (species) D
Domesticated
Linkage Mapping
Beever JE; Smit MA; Meyers SN ; et al. (2006)
A single-base change in the tyrosine kinase II domain of ovine FGFR3 causes hereditary chondrodyspla[...]
1 Additional References
GP00002184
FGFR3
P22607
Morphology
c.1719T>A p.V700E
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
FGFR3
Ovis aries
sheep - (species)
Published - Accepted by Curator
fiz
Body size
3 Mutations:
Cis-regulatory
SNP
Drosophila melanogaster
fruit fly - (species) D
Intraspecific
Candidate Gene
Glaser-Schmitt A; Parsch J (2018)
Functional characterization of adaptive variation within a cis-regulatory element influencing Drosop[...]
GP00002017
fiz
Q9VY04
Morphology
3 mutations
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species) D
fiz
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
Flavonoid 3'-hydroxylase (F3'H)
Coloration (flowers; pubescence; seeds)
Coding,
Deletion
N
Glycine soja
(species) D
Intraspecific
Candidate Gene
Guo Y; Qiu LJ (2013)
Allele-specific marker development and selection efficiencies for both flavonoid 3'-hydroxylase and [...]
GP00000315
CYP75B1
Q9SD85
Morphology
-1bp at +973 resulting in premature stop codon N
Glycine max
soybean - (species)
Glycine soja
(species) D
Flavonoid 3'-hydroxylase (F3'H)
Glycine soja
(species)
Published - Accepted by Curator
Flavonoid 3'-hydroxylase (F3'H)
Coloration (flowers; pubescence; seeds)
Coding,
Deletion
N
Glycine soja
(species) D
Intraspecific
Candidate Gene
Guo Y; Qiu LJ (2013)
Allele-specific marker development and selection efficiencies for both flavonoid 3'-hydroxylase and [...]
GP00000316
CYP75B1
Q9SD85
Morphology
-1bp at +1164 resulting in premature stop codon N
Glycine max
soybean - (species)
Glycine soja
(species) D
Flavonoid 3'-hydroxylase (F3'H)
Glycine soja
(species)
Published - Accepted by Curator
Flavonoid 3'-hydroxylase (F3'H)
Coloration (flowers; pubescence; seeds)
Coding,
Indel
Glycine soja
(species)
Intraspecific
Candidate Gene
Guo Y; Qiu LJ (2013)
Allele-specific marker development and selection efficiencies for both flavonoid 3'-hydroxylase and [...]
GP00000317
CYP75B1
Q9SD85
Morphology
a single base insertion of an adenine at position 965 as well as a single base deletion of adenine at position 973 resulting in N322K and Q324T - exact causing mutation(s) unknown
Glycine max
soybean - (species)
Glycine soja
(species)
Flavonoid 3'-hydroxylase (F3'H)
Glycine soja
(species)
Published - Accepted by Curator
flavonoid 3'-hydroxylase (F3'H)
Coloration (flowers)
Cis-regulatory,
Insertion
Glycine max
soybean - (species) D
Domesticated
Candidate Gene
Zabala G; Vodkin LO (2005)
The wp mutation of Glycine max carries a gene-fragment-rich transposon of the CACTA superfamily.
GP00000318
CYP75B1
Q9SD85
Morphology
Transposon insertion in intron 2
Glycine max
soybean - (species)
Glycine max
soybean - (species) D
flavonoid 3'-hydroxylase (F3'H)
Glycine max
soybean - (species)
Published - Accepted by Curator
flavonoid 3'-hydroxylase (F3'H)
Coloration (flowers)
Coding,
Insertion
N
Ipomoea purpurea
common morning-glory - (species) D
Domesticated
Candidate Gene
Zufall RA; Rausher MD (2003 Nov-Dec)
The genetic basis of a flower color polymorphism in the common morning glory (Ipomoea purpurea).
3 Additional References
GP00000319
CYP75B1
Q9SD85
Morphology
insertion of the 0.55-kb DNA transposable element Tip201 belonging to the Ac/Ds superfamily. No excision of Tip201 from the F3'H gene could be detected. Both splicing and polyadenylation patterns of the F3'H transcripts were affected by the Tip201 integration. N
Ipomoea purpurea
common morning-glory - (species)
Ipomoea purpurea
common morning-glory - (species) D
flavonoid 3'-hydroxylase (F3'H)
Ipomoea purpurea
common morning-glory - (species)
Published - Accepted by Curator
flavonoid 3'-hydroxylase (F3'H)
Coloration (flowers)
Unknown,
Unknown
Petunia x hybrida
(species)
Domesticated
Candidate Gene
Brugliera F; Barri-Rewell G; Holton TA ; et al. (1999)
Isolation and characterization of a flavonoid 3'-hydroxylase cDNA clone corresponding to the Ht1 loc[...]
GP00000320
CYP75B1
Q9SD85
Morphology
Not identified
Petunia x hybrida
(species)
Petunia x hybrida
(species)
flavonoid 3'-hydroxylase (F3'H)
Petunia x hybrida
(species)
Published - Accepted by Curator
flavonoid 3'-hydroxylase (F3'H)
Coloration (seed; pods)
Coding,
Deletion
N
Glycine max
soybean - (species) D
Domesticated
Linkage Mapping
Toda K; Yang D; Yamanaka N ; et al. (2002)
A single-base deletion in soybean flavonoid 3'-hydroxylase gene is associated with gray pubescence c[...]
1 Additional References
GP00000321
CYP75B1
Q9SD85
Morphology
1bp deletion resulting in frameshift N
Glycine max
soybean - (species)
Glycine max
soybean - (species) D
flavonoid 3'-hydroxylase (F3'H)
Glycine max
soybean - (species)
Published - Accepted by Curator
flavonoid 3'-hydroxylase (F3'H)
Coloration (flowers)
Coding,
SNP
N
Ipomoea nil
Japanese morning glory - (species) D
Domesticated
Candidate Gene
Hoshino A; Morita Y; Choi JD ; et al. (2003)
Spontaneous mutations of the flavonoid 3'-hydroxylase gene conferring reddish flowers in the three m[...]
GP00002087
CYP75B1
Q9SD85
Morphology
nonsense mutation caused by a single C to T base transition generating the stop codon TGA. N
Ipomoea nil
Japanese morning glory - (species)
Ipomoea nil
Japanese morning glory - (species) D
flavonoid 3'-hydroxylase (F3'H)
Ipomoea nil
Japanese morning glory - (species)
Published - Accepted by Curator
flavonoid 3'-hydroxylase (F3'H)
Coloration (flowers)
Coding,
Insertion
N
Ipomoea tricolor
(species) D
Domesticated
Candidate Gene
Hoshino A; Morita Y; Choi JD ; et al. (2003)
Spontaneous mutations of the flavonoid 3'-hydroxylase gene conferring reddish flowers in the three m[...]
GP00002088
CYP75B1
Q9SD85
Morphology
a single T insertion generating the stop codon TAG. The accumulation of the F3'H transcripts is drastically reduced by the nonsense-mediated RNA decay. N
Ipomoea tricolor
(species)
Ipomoea tricolor
(species) D
flavonoid 3'-hydroxylase (F3'H)
Ipomoea tricolor
(species)
Published - Accepted by Curator
flavonoid 3';5'-hydroxylase (F3'5'H)
Coloration (flowers; pubescence; seeds)
Coding,
Insertion
N
Glycine soja
(species) D
Intraspecific
Candidate Gene
Guo Y; Qiu LJ (2013)
Allele-specific marker development and selection efficiencies for both flavonoid 3'-hydroxylase and [...]
GP00000322
CYP75A2
P37120
Morphology
53bp insertion at +1352 N
Glycine max
soybean - (species)
Glycine soja
(species) D
flavonoid 3';5'-hydroxylase (F3'5'H)
Glycine soja
(species)
Published - Accepted by Curator
flavonoid 3';5'-hydroxylase (F3'5'H)
Coloration (flowers)
Coding,
SNP
Glycine soja
(species)
Intraspecific
Linkage Mapping
Takahashi R; Dubouzet JG; Matsumura H ; et al. (2010)
A new allele of flower color gene W1 encoding flavonoid 3'5'-hydroxylase is responsible for light pu[...]
GP00000323
CYP75A2
P37120
Morphology
V210M (uncertain); no expression level differences detected
Glycine soja
(species)
Glycine soja
(species)
flavonoid 3';5'-hydroxylase (F3'5'H)
Glycine soja
(species)
Published - Accepted by Curator
flavonoid 3';5'-hydroxylase (F3'5'H)
Coloration (flowers)
Gene Loss,
Complex Change
N
Iochroma cyaneum
(species)
Interspecific
Linkage Mapping
Smith SD; Rausher MD (2011)
Gene loss and parallel evolution contribute to species difference in flower color.
GP00000324
CYP75A2
P37120
Morphology
Large deletion N
Iochroma cyaneum
(species)
Iochroma cyaneum
(species)
flavonoid 3';5'-hydroxylase (F3'5'H)
Iochroma cyaneum
(species)
Published - Accepted by Curator
flavonoid 3';5'-hydroxylase (F3'5'H)
Coloration (flowers)
Cis-regulatory,
Unknown
Phlox drummondii
(species)
Intraspecific
Linkage Mapping
Hopkins R; Rausher MD (2011)
Identification of two genes causing reinforcement in the Texas wildflower Phlox drummondii.
GP00000325
CYP75A2
P37120
Morphology
unknown
Phlox drummondii
(species)
Phlox drummondii
(species)
flavonoid 3';5'-hydroxylase (F3'5'H)
Phlox drummondii
(species)
Published - Accepted by Curator
flavonoid 3';5'-hydroxylase (F3'5'H)
Coloration (flowers)
Coding,
SNP
Pisum sativum
pea - (species)
Domesticated
Candidate Gene
Moreau C; Ambrose MJ; Turner L ; et al. (2012)
The B gene of pea encodes a defective flavonoid 3',5'-hydroxylase, and confers pink flower color.
GP00000326
CYP75A2
P37120
Morphology
G111E
Pisum sativum
pea - (species)
Pisum sativum
pea - (species)
flavonoid 3';5'-hydroxylase (F3'5'H)
Pisum sativum
pea - (species)
Published - Accepted by Curator
flavonoid 3';5'-hydroxylase (F3'5'H)
Coloration (flowers)
Coding,
Deletion
N
Pisum sativum
pea - (species) D
Domesticated
Linkage Mapping
Moreau C; Ambrose MJ; Turner L ; et al. (2012)
The B gene of pea encodes a defective flavonoid 3',5'-hydroxylase, and confers pink flower color.
GP00000327
CYP75A2
P37120
Morphology
23bp deletion reuslting in frameshift and truncated protein N
Pisum sativum
pea - (species)
Pisum sativum
pea - (species) D
flavonoid 3';5'-hydroxylase (F3'5'H)
Pisum sativum
pea - (species)
Published - Accepted by Curator
flavonoid 3';5'-hydroxylase (F3'5'H)
Coloration (tuber skin)
Cis-regulatory,
Unknown
Solanum tuberosum
potato - (species)
Domesticated
Linkage Mapping
Jung CS; Griffiths HM; De Jong DM ; et al. (2005)
The potato P locus codes for flavonoid 3',5'-hydroxylase.
GP00000328
CYP75A2
P37120
Morphology
unknown
Solanum tuberosum
potato - (species)
Solanum tuberosum
potato - (species)
flavonoid 3';5'-hydroxylase (F3'5'H)
Solanum tuberosum
potato - (species)
Published - Accepted by Curator
follistatin
Limb morphology (wing dimorphism)
Flight behavior (wing dimorphism)
Gene Amplification,
Insertion
Acyrthosiphon pisum
pea aphid - (species) D
Intraspecific
Linkage Mapping
Li B; Bickel RD; Parker BJ ; et al. (2020)
A large genomic insertion containing a duplicated follistatin gene is linked to the pea aphid male w[...]
GP00002138
Fs
Q86NV3
Morphology
Behavior
the api allele from winged males is a 120kb insertion that includes a copy of the follistatin gene
Acyrthosiphon pisum
pea aphid - (species)
Acyrthosiphon pisum
pea aphid - (species) D
follistatin
Acyrthosiphon pisum
pea aphid - (species)
Published - Accepted by Curator
February 9, 2021 22:00
FOXI3
Hair (hypotrichosis)
Coding,
Insertion
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Drögemüller C; Karlsson EK; Hytönen MK ; et al. (2008)
A mutation in hairless dogs implicates FOXI3 in ectodermal development.
GP00000351
FOXI3
B5RHS5
Morphology
Frameshift; 7-bp duplication within exon 1 N
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
FOXI3
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
FOXL2
Horns absence
Somatic sex change
Cis-regulatory,
Deletion
Capra hircus
goat - (species) D
Domesticated
Linkage Mapping
Pailhoux E; Vigier B; Chaffaux S ; et al. (2001)
A 11.7-kb deletion triggers intersexuality and polledness in goats.
2 Additional References
GP00000352
FOXL2
Q8MIP2
Morphology
Physiology
11.7 kbp deletion of mainly repetitive sequences ; Alters transcription of two flanking genes; but FOXL2 in particular is proposed as the main determinant of the phenotype
Capra hircus
goat - (species)
Capra hircus
goat - (species) D
FOXL2
Capra hircus
goat - (species)
Published - Accepted by Curator
foxo
Body size (wing)
Starvation resistance
Unknown,
Unknown
Drosophila melanogaster
fruit fly - (species)
Intraspecific
Candidate Gene
Betancourt NJ; Rajpurohit S; Durmaz E ; et al. (2021)
Allelic polymorphism at foxo contributes to local adaptation in Drosophila melanogaster.
1 Additional References
GP00002661
foxo
Q95V55
Morphology
Morphology; Physiology
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species)
foxo
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
FRIZZLED8
Neocortex development
Cis-regulatory,
Unknown
Homo sapiens
human - (species) D
Interspecific
Candidate Gene
Boyd JL; Skove SL; Rouanet JP ; et al. (2015)
Human-chimpanzee differences in a FZD8 enhancer alter cell-cycle dynamics in the developing neocorte[...]
GP00001443
FZD8
Q9H461
Morphology
10 mutations fixed on the human branch in the Hs-HARE5 genomic locus resulting in enhancer activity in developing neocortex
Pan troglodytes
chimpanzee - (species)
Homo sapiens
human - (species) D
FRIZZLED8
Homo sapiens
human - (species)
Published - Accepted by Curator
FST/MOCS2
coloration (head feathers)
Cis-regulatory,
Unknown
Erythrura gouldiae
Gouldian finch - (species)
Intraspecific
Association Mapping
Toomey MB; Marques CI; Andrade P ; et al. (2018)
A non-coding region near Follistatin controls head colour polymorphism in the Gouldian finch.
1 Additional References
GP00002125
Morphology
candidate locus is a small (approx. 70 kb) non-coding region mapping to the Z chromosome near the FST and MOCS2
Erythrura gouldiae
Gouldian finch - (species)
Erythrura gouldiae
Gouldian finch - (species)
FST/MOCS2
Erythrura gouldiae
Gouldian finch - (species)
Published - Accepted by Curator
FW2.2
Fruit size
Cis-regulatory,
Unknown
Solanum lycopersicum
tomato - (species)
Domesticated
Linkage Mapping
Frary A; Nesbitt TC; Grandillo S ; et al. (2000)
fw2.2: a quantitative trait locus key to the evolution of tomato fruit size.
1 Additional References
GP00000383
ORFX
Q9LKV7
Morphology
Not identified
Lycopersicon
(subgenus)
Solanum lycopersicum
tomato - (species)
FW2.2
Solanum lycopersicum
tomato - (species)
Published - Accepted by Curator
GADD45G
Brain development
Cis-regulatory,
Deletion
Pan troglodytes
chimpanzee - (species) D
Interspecific
Association Mapping
McLean CY; Reno PL; Pollen AA ; et al. (2011)
Human-specific loss of regulatory DNA and the evolution of human-specific traits.
GP00000384
GADD45G
O95257
Morphology
Enhancer loss
Homo sapiens
human - (species)
Pan troglodytes
chimpanzee - (species) D
GADD45G
Pan troglodytes
chimpanzee - (species)
Published - Accepted by Curator
GCNF (NR6A1)
Vertebrae number
Coding,
SNP
Sus scrofa domesticus
domestic pig - (subspecies)
Domesticated
Linkage Mapping
Mikawa S; Morozumi T; Shimanuki S ; et al. (2007)
Fine mapping of a swine quantitative trait locus for number of vertebrae and analysis of an orphan n[...]
GP00000386
Nr6a1
Q64249
Morphology
Pro192Leu
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies)
GCNF (NR6A1)
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
GDF5
Body size (height)
Unknown,
Unknown
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Sanna S; Jackson AU; Nagaraja R ; et al. (2008)
Common variants in the GDF5-UQCC region are associated with variation in human height.
1 Additional References
GP00000387
GDF5
P43026
Morphology
unknown
Homo sapiens
human - (species)
Homo sapiens
human - (species)
GDF5
Homo sapiens
human - (species)
Published - Accepted by Curator
GDF6
Dermal bone size (armor plates)
Cis-regulatory,
Unknown
Gasterosteus aculeatus
three-spined stickleback - (species) D
Intraspecific
Linkage Mapping
Indjeian VB; Kingman GA; Jones FC ; et al. (2016)
Evolving New Skeletal Traits by cis-Regulatory Changes in Bone Morphogenetic Proteins.
GP00000388
GDF6
Q6KF10
Morphology
gain of a flank enhancer activity involving a complex repeat region; 1.2kb L2 LINE insertion; 18 small indels and 89 SNPs - the LINE insertion is required but not sufficient, to produce increased flank expression
Gasterosteus aculeatus
three-spined stickleback - (species)
Gasterosteus aculeatus
three-spined stickleback - (species) D
GDF6
Gasterosteus aculeatus
three-spined stickleback - (species)
Published - Accepted by Curator
GDF6
Limb morphology (hindlimb;skeleton)
Cis-regulatory,
Deletion
Homininae
(subfamily) D
Intergeneric or Higher
Candidate Gene
Indjeian VB; Kingman GA; Jones FC ; et al. (2016)
Evolving New Skeletal Traits by cis-Regulatory Changes in Bone Morphogenetic Proteins.
GP00000389
GDF6
Q6KF10
Morphology
Loss of a limb specific enhancer, the deletion is 5.6 kb
Homo sapiens
human - (species)
Homininae
(subfamily) D
GDF6
Homininae
(subfamily)
Published - Accepted by Curator
GDF7
Feathers (loss)
Cis-regulatory,
Insertion
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Mou C; Pitel F; Gourichon D ; et al. (2011)
Cryptic patterning of avian skin confers a developmental facility for loss of neck feathering.
GP00002185
Gdf7
P43029
Morphology
a large insertion approximately 260kb downstream from the BMP12 gene (now known as GFD7) increasing the expression of this gene in embryonic skin
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
GDF7
Gallus gallus
chicken - (species)
Published - Accepted by Curator
GH
Body size (dwarfism)
Coding,
SNP
Bos taurus
cattle - (species) D
Domesticated
Candidate Gene
McCormack BL; Chase CC; Olson TA ; et al. (2009)
A miniature condition in Brahman cattle is associated with a single nucleotide mutation within the g[...]
GP00002037
GH1
P01241
Morphology
g.48768780C>T c.593C>T p.T198M
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
GH
Bos taurus
cattle - (species)
Published - Accepted by Curator
Ghd7
Flowering time
Inflorescence morphology
Unknown,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Xue W; Xing Y; Weng X ; et al. (2008)
Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice.
GP00000393
GHD7
E5RQA1
Physiology
Morphology
unknown
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Ghd7
Oryza sativa
rice - (species)
Published - Accepted by Curator
GHSR
Body size (height)
Unknown,
Unknown
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Lettre G (2011)
Recent progress in the study of the genetics of height.
GP00000394
GHSR
Q92847
Morphology
unknown
Homo sapiens
human - (species)
Homo sapiens
human - (species)
GHSR
Homo sapiens
human - (species)
Published - Accepted by Curator
GIBBERELLIC ACID REQUIRING 1 (GA1)
Flower morphology
Unknown,
Unknown
Arabidopsis thaliana
thale cress - (species)
Intraspecific
Linkage Mapping
Brock MT; Kover PX; Weinig C (2012)
Natural variation in GA1 associates with floral morphology in Arabidopsis thaliana.
GP00000395
GA1
Q38802
Morphology
unknown
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
GIBBERELLIC ACID REQUIRING 1 (GA1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
GL3.1
Grain size
2 Mutations:
Coding
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Qi P; Lin YS; Song XJ ; et al. (2012)
The novel quantitative trait locus GL3.1 controls rice grain size and yield by regulating Cyclin-T1;[...]
GP00000397
GL3
Q9FN69
Morphology
2 mutations
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
GL3.1
Oryza sativa
rice - (species)
Published - Accepted by Curator
GL7
Grain size
Grain quality
Gene Amplification,
Indel
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Wang Y; Xiong G; Hu J ; et al. (2015)
Copy number variation at the GL7 locus contributes to grain size diversity in rice.
GP00001541
LNG1
Q9LF24
Morphology
Physiology
tandem duplication of a 17.1 kb segment containing GL7. Both copies encode exactly the same polypeptide and exhibit similar transcript levels leading to upregulation
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
GL7
Oryza sativa
rice - (species)
Published - Accepted by Curator
GLABROUS1
Trichome (leaves)
Unknown,
Unknown
Arabidopsis
(genus)
Intraspecific
Candidate Gene
Hauser MT; Harr B; Schlötterer C (2001)
Trichome distribution in Arabidopsis thaliana and its close relative Arabidopsis lyrata: molecular a[...]
1 Additional References
GP00000398
GL1
P27900
Morphology
unknown
Arabidopsis
(genus)
Arabidopsis
(genus)
GLABROUS1
Arabidopsis
(genus)
Published - Accepted by Curator
GLABROUS1
Trichome density (leaf)
Gene Loss,
Deletion
N
Arabidopsis thaliana
thale cress - (species)
Intraspecific
Candidate Gene
Hauser MT; Harr B; Schlötterer C (2001)
Trichome distribution in Arabidopsis thaliana and its close relative Arabidopsis lyrata: molecular a[...]
1 Additional References
GP00001238
GL1
P27900
Morphology
gene loss: -4.7KB at position -948bp N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
GLABROUS1
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
GLABROUS1
Trichome density (leaf)
Coding,
SNP
Arabidopsis thaliana
thale cress - (species)
Intraspecific
Candidate Gene
Hauser MT; Harr B; Schlötterer C (2001)
Trichome distribution in Arabidopsis thaliana and its close relative Arabidopsis lyrata: molecular a[...]
1 Additional References
GP00001239
GL1
P27900
Morphology
S92F
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
GLABROUS1
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
GLABROUS1
Trichome density (leaf)
Coding,
Insertion
N
Arabidopsis thaliana
thale cress - (species)
Intraspecific
Candidate Gene
Hauser MT; Harr B; Schlötterer C (2001)
Trichome distribution in Arabidopsis thaliana and its close relative Arabidopsis lyrata: molecular a[...]
1 Additional References
GP00001240
GL1
P27900
Morphology
+1bp at position 352 causing premature stop N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
GLABROUS1
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
GLABROUS1
Trichome density (leaf)
Coding,
Deletion
N
Arabidopsis thaliana
thale cress - (species) D
Intraspecific
Candidate Gene
Hauser MT; Harr B; Schlötterer C (2001)
Trichome distribution in Arabidopsis thaliana and its close relative Arabidopsis lyrata: molecular a[...]
1 Additional References
GP00001241
GL1
P27900
Morphology
-1bp at position 203 causing premature stop N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
GLABROUS1
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
GLABROUS1
Trichome density (leaf)
Unknown,
Unknown
Arabidopsis thaliana
thale cress - (species)
Intraspecific
Association Mapping
Hauser MT; Harr B; Schlötterer C (2001)
Trichome distribution in Arabidopsis thaliana and its close relative Arabidopsis lyrata: molecular a[...]
1 Additional References
GP00001242
GL1
P27900
Morphology
high frequency pattern of polymorphism identified in the third exon and 3' flank
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
GLABROUS1
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
GLO(T)
Flower morphology (anther elevation)
Coding,
Insertion
N
Primula vulgaris
(species) D
Intraspecific
Linkage Mapping
Li J; Cocker JM; Wright J ; et al. (2016)
Genetic architecture and evolution of the S locus supergene in Primula vulgaris.
GP00001393
GLO
Q03378
Morphology
A 2.5 kb retrotransposon in exon 2 severely truncates the protein N
Primula vulgaris
(species)
Primula vulgaris
(species) D
GLO(T)
Primula vulgaris
(species)
Published - Accepted by Curator
goldentouch
Coloration
Cis-regulatory,
Insertion
Amphilophus citrinellus
Midas cichlid - (species)
Intraspecific
Association Mapping
Kratochwil CF; Kautt AF; Nater A ; et al. (2022)
An intronic transposon insertion associates with a trans-species color polymorphism in Midas cichlid[...]
GP00002362
Morphology
"Using a new haplotype-resolved long-read assembly we discover an 8.2 kb, transposon-derived inverted repeat in an intron of an undescribed gene, which we term goldentouch in reference to the Greek myth of King Midas. The gene goldentouch is differentially expressed between morphs, presumably due to structural implications of inverted repeats in both DNA and/or RNA (cruciform and hairpin formation). The near-perfect association of the insertion with the phenotype across independent populations suggests that it likely underlies this trans-specific, stable polymorphism."
Amphilophus citrinellus
Midas cichlid - (species)
Amphilophus citrinellus
Midas cichlid - (species)
goldentouch
Amphilophus citrinellus
Midas cichlid - (species)
Published - Accepted by Curator
GPR133
Body size (height; male-limited)
Unknown,
Unknown
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Tönjes A; Koriath M; Schleinitz D ; et al. (2009)
Genetic variation in GPR133 is associated with height: genome wide association study in the self-con[...]
GP00000412
ADGRD1
Q6QNK2
Morphology
unknown
Homo sapiens
human - (species)
Homo sapiens
human - (species)
GPR133
Homo sapiens
human - (species)
Published - Accepted by Curator
GPR22
Coloration (coat)
Cis-regulatory,
Insertion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Batcher K; Varney S; Affolter VK ; et al. (2022)
An SNN retrocopy insertion upstream of GPR22 is associated with dark red coat color in Poodles.
GP00002389
GPR22
Q99680
Morphology
A SNNL1 retrocopy element is inserted within the intron of COG5 and 2.8kbp upstream of and in the same orientation as GPR22. It is likely disrupting regulation of the CPR22 gene, resulting in higher gene expression and atypical expression in the skin.
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
GPR22
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
GRAIN INCOMPLETE FILLING 1
Grain weight
Cis-regulatory,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Wang E; Wang J; Zhu X ; et al. (2008)
Control of rice grain-filling and yield by a gene with a potential signature of domestication.
GP00000413
CIN2
Q0JDC5
Morphology
unknown
Oryza rufipogon
(species)
Oryza sativa
rice - (species)
GRAIN INCOMPLETE FILLING 1
Oryza sativa
rice - (species)
Published - Accepted by Curator
GRAMD3
Coloration (skin)
Cis-regulatory,
Unknown
Gallus gallus
chicken - (species)
Domesticated
Association Mapping
Xu J; Lin S; Gao X ; et al. (2017)
Mapping of Id locus for dermal shank melanin in a Chinese indigenous chicken breed.
GP00002391
GRAMD3
F1NDM3
Morphology
No coding mutation in GRAMD3. The expression of GRAMD3 gene in the dermis tissues of the shank was significantly (P = 0.010738 < 0.05) higher in 350-day-old Gushi chickens characterized by the dermal shank pigmentation than in one-day-old Gushi chickens. Variation in the flanking region of GRAMD3 probably leads to the abnormal expression of GRAMD3.
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
GRAMD3
Gallus gallus
chicken - (species)
Published - Accepted by Curator
grassy tillers1
Plant architecture (number of ears)
Cis-regulatory,
Unknown
Zea mays
(species)
Domesticated
Linkage Mapping
Wills DM; Whipple CJ; Takuno S ; et al. (2013)
From many, one: genetic control of prolificacy during maize domestication.
GP00000414
gt1
G1AQA5
Morphology
unknown but narrow 2.7kb interval
Zea mays
(species)
Zea mays
(species)
grassy tillers1
Zea mays
(species)
Published - Accepted by Curator
Growth Hormone Receptor (GHR)
Body size (height)
Coding,
SNP
N
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Zoledziewska M; Sidore C; Chiang CWK ; et al. (2015)
Height-reducing variants and selection for short stature in Sardinia.
GP00000415
GHR
P10912
Morphology
Arg61* N
Homo sapiens
human - (species)
Homo sapiens
human - (species)
Growth Hormone Receptor (GHR)
Homo sapiens
human - (species)
Published - Accepted by Curator
growth hormone receptor (GHR)
Body size (weight)
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Rimbault M; Beale HC; Schoenebeck JJ ; et al. (2013)
Derived variants at six genes explain nearly half of size reduction in dog breeds.
GP00001475
GHR
Q9TU69
Morphology
G>A in exon 5 p.E191K in extracellular domain
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
growth hormone receptor (GHR)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
growth hormone receptor (GHR)
Body size (weight)
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Rimbault M; Beale HC; Schoenebeck JJ ; et al. (2013)
Derived variants at six genes explain nearly half of size reduction in dog breeds.
GP00001476
GHR
Q9TU69
Morphology
C>T in exon 5 p.P177L in extracellular domain
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
growth hormone receptor (GHR)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Growth Hormone Receptor (GHR)
Body size (dwarfism)
Coding,
Deletion
N
Gallus gallus
chicken - (species) D
Domesticated
Association Mapping
Agarwal SK; Cogburn LA; Burnside J (1994)
Dysfunctional growth hormone receptor in a strain of sex-linked dwarf chicken: evidence for a mutati[...]
GP00002189
GHR
P10912
Morphology
deletion of 1773 bp in the 3' end of the coding region N
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
Growth Hormone Receptor (GHR)
Gallus gallus
chicken - (species)
Published - Accepted by Curator
GS3
Grain size
Coding,
SNP
N
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Fan C; Xing Y; Mao H ; et al. (2006)
GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, en[...]
1 Additional References
GP00000417
GS3
C6L686
Morphology
C55*;TGC>TGA causing a 178-aa truncation in the C-terminus of the predicted protein N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
GS3
Oryza sativa
rice - (species)
Published - Accepted by Curator
GS5
Grain size
Cis-regulatory,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Li Y; Fan C; Xing Y ; et al. (2011)
Natural variation in GS5 plays an important role in regulating grain size and yield in rice.
GP00000418
GS5
B8AYD6
Morphology
Promoter variation
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
GS5
Oryza sativa
rice - (species)
Published - Accepted by Curator
GSS (glutathione synthetase)
Coloration (skin)
Unknown,
Unknown
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Liu F; Visser M; Duffy DL ; et al. (2015)
Genetics of skin color variation in Europeans: genome-wide association studies with functional follo[...]
GP00001362
GSS
P48637
Morphology
unknown
Homo sapiens
human - (species)
Homo sapiens
human - (species)
GSS (glutathione synthetase)
Homo sapiens
human - (species)
Published - Accepted by Curator
GW2
Grain size
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Song XJ; Huang W; Shi M ; et al. (2007)
A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase.
GP00000424
GW2
A4GWX9
Morphology
1bp deletion resulting in a premature stop codon in exon 4; the premature stop codon led to truncation of 310 amino acid residues N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
GW2
Oryza sativa
rice - (species)
Published - Accepted by Curator
GW2
Grain size
Coding,
Insertion
N
Triticum aestivum
bread wheat - (species) D
Domesticated
Linkage Mapping
Yang Z; Bai Z; Li X ; et al. (2012)
SNP identification and allelic-specific PCR markers development for TaGW2, a gene linked to wheat ke[...]
GP00000425
GW2
A4GWX9
Morphology
1bp insertion resulting in premature stop codon N
Triticum aestivum
bread wheat - (species)
Triticum aestivum
bread wheat - (species) D
GW2
Triticum aestivum
bread wheat - (species)
Published - Accepted by Curator
GW7
Grain shape
Grain quality
Cis-regulatory,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Wang S; Li S; Liu Q ; et al. (2015)
The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and [...]
GP00001540
TON1A
Q9FQ25
Morphology
Physiology
18 SNPs and 9 indels observed in the promoter region and exon 1 and in particular an 11-bp deletion and 18-bp insertion near GTAC motifs which are normally binded by OsSPL16 repressor (reduced binding increasing transcription)
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
GW7
Oryza sativa
rice - (species)
Published - Accepted by Curator
hairy (h)
Bristle number (thorax)
Unknown,
Unknown
Drosophila melanogaster
fruit fly - (species)
Intraspecific
Linkage Mapping
Robin C; Lyman RF; Long AD ; et al. (2002)
hairy: A quantitative trait locus for drosophila sensory bristle number.
GP00000436
h
P14003
Morphology
unknown; complex promoter indel variation shows high-association
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species)
hairy (h)
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
HAO1
Fertility (egg production)
Bird head morphology (male comb)
Cis-regulatory,
Unknown
Gallus gallus
chicken - (species)
Domesticated
Linkage Mapping
Johnsson M; Gustafson I; Rubin CJ ; et al. (2012)
A sexual ornament in chickens is affected by pleiotropic alleles at HAO1 and BMP2, selected during d[...]
1 Additional References
GP00000437
HAO1
E1BRR7
Physiology
Morphology
unknown; but intergenic QTL peak with decomposed effects on expression of BMP2 and HAO1
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
HAO1
Gallus gallus
chicken - (species)
Published - Accepted by Curator
HAS2
Wrinkled skin (Shar-Pei dogs)
Cis-regulatory,
Unknown
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Akey JM; Ruhe AL; Akey DT ; et al. (2010)
Tracking footprints of artificial selection in the dog genome.
GP00000438
HAS2
J9PB16
Morphology
unknown
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
HAS2
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
herfst
Coloration (wing; seasonal)
Cis-regulatory,
Unknown
Junonia coenia
buckeye - (species) D
Experimental Evolution
Association Mapping
van der Burg KRL; Lewis JJ; Brack BJ ; et al. (2020)
Genomic architecture of a genetically assimilated seasonal color pattern.
GP00002422
rk
Q7KTA0
Morphology
No variation in coding region. Strong association with cis-regulatory SNP. CRISPR mutant clones for the herfst gene display light tan scales.
Junonia coenia
buckeye - (species)
Junonia coenia
buckeye - (species) D
herfst
Junonia coenia
buckeye - (species)
Published - Accepted by Curator
HES7
Organ size (tail; short)
Coding,
SNP
Felis catus
domestic cat - (species) D
Domesticated
Candidate Gene
Lyons LA; Creighton EK; Alhaddad H ; et al. (2016)
Whole genome sequencing in cats, identifies new models for blindness in AIPL1 and somite segmentatio[...]
1 Additional References
GP00002190
HES7
Q9BYE0
Morphology
g.2819475A>G c.5A>G p.V2A
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
HES7
Felis catus
domestic cat - (species)
Published - Accepted by Curator
HMGA2
Body size
Unknown,
Unknown
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Akey JM; Ruhe AL; Akey DT ; et al. (2010)
Tracking footprints of artificial selection in the dog genome.
1 Additional References
GP00000484
HMGA2
P52926
Morphology
unknown
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
HMGA2
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
HMGA2
Body size
Unknown,
Unknown
Equus caballus
horse - (species)
Domesticated
Association Mapping
Makvandi-Nejad S; Hoffman GE; Allen JJ ; et al. (2012)
Four loci explain 83% of size variation in the horse.
GP00000485
HMGA2
P52926
Morphology
unknown
Equus caballus
horse - (species)
Equus caballus
horse - (species)
HMGA2
Equus caballus
horse - (species)
Published - Accepted by Curator
HMGA2
Body size (height; bone mineral density)
Unknown,
Unknown
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Weedon MN; Lettre G; Freathy RM ; et al. (2007)
A common variant of HMGA2 is associated with adult and childhood height in the general population.
3 Additional References
GP00000486
HMGA2
P52926
Morphology
unknown
Homo sapiens
human - (species)
Homo sapiens
human - (species)
HMGA2
Homo sapiens
human - (species)
Published - Accepted by Curator
HMGA2
Ear size
Unknown,
Unknown
Sus scrofa domesticus
domestic pig - (subspecies)
Domesticated
Linkage Mapping
Li P; Xiao S; Wei N ; et al. (2012)
Fine mapping of a QTL for ear size on porcine chromosome 5 and identification of high mobility group[...]
GP00000487
HMGA2
P52926
Morphology
unknown
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies)
HMGA2
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
HMGA2
Body size (dwarfism)
Cranio-facial morphology
Coding,
Deletion
N
Oryctolagus cuniculus
rabbit - (species) D
Domesticated
Association Mapping
Carneiro M; Hu D; Archer J ; et al. (2017)
Dwarfism and Altered Craniofacial Development in Rabbits Is Caused by a 12.1 kb Deletion at the HMGA[...]
GP00001675
HMGA2
P52926
Morphology
Morphology
deletion of 12.1 kb overlapping the promoter region and first three exons leading to inactivation of the gene. The 5'-end of this deletion overlaps a CSINE2 element N
Oryctolagus cuniculus
rabbit - (species)
Oryctolagus cuniculus
rabbit - (species) D
HMGA2
Oryctolagus cuniculus
rabbit - (species)
Published - Accepted by Curator
HMX1
Organ size (ear; cropped)
Cis-regulatory,
Insertion
Bos taurus
cattle - (species) D
Domesticated
Association Mapping
Koch CT; Bruggmann R; Tetens J ; et al. (2013)
A non-coding genomic duplication at the HMX1 locus is associated with crop ears in highland cattle.
GP00002191
HMX1
Q9NP08
Morphology
76bp duplication in an ultra-conserved enhancer located 148 kb apart of the coding region of HMX1
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
HMX1
Bos taurus
cattle - (species)
Published - Accepted by Curator
Hooded
Flower morphology
Cis-regulatory,
Insertion
Hordeum vulgare
(species) D
Domesticated
Linkage Mapping
Müller KJ; Romano N; Gerstner O ; et al. (1995)
The barley Hooded mutation caused by a duplication in a homeobox gene intron.
GP00000488
KNOX3
Q43484
Morphology
305bp duplication in intron 4
Hordeum vulgare
(species)
Hordeum vulgare
(species) D
Hooded
Hordeum vulgare
(species)
Published - Accepted by Curator
Hox gene cluster
Body plan (number of segments)
Gene Loss,
Deletion
N
Hypsibius dujardini
(species) D
Paramacrobiotus richtersi
(species) D
Milnesium tardigradum
(species) D
Intergeneric or Higher
Candidate Gene
Smith FW; Boothby TC; Giovannini I ; et al. (2016)
The Compact Body Plan of Tardigrades Evolved by the Loss of a Large Body Region.
GP00001946
Antp
P02833
Morphology
The three genes Antp Ubx AbdA are missing in the genome sequences of the three tardigrades. This loss is ancient so difficult to evaluate whether the three genes were lost due to a single mutational event or due to successive mutations. The Hox cluster is disorganized in the H. dujardini genome. N
Drosophila melanogaster
fruit fly - (species)
Hypsibius dujardini
(species) D
Paramacrobiotus richtersi
(species) D
Milnesium tardigradum
(species) D
Hox gene cluster
Hypsibius dujardini
(species)
Paramacrobiotus richtersi
(species)
Milnesium tardigradum
(species)
Published - Accepted by Curator
Hoxb8
Feather (bird face)
Cis-regulatory,
Insertion
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Guo Y; Gu X; Sheng Z ; et al. (2016)
A Complex Structural Variation on Chromosome 27 Leads to the Ectopic Expression of HOXB8 and the Muf[...]
GP00002193
Hoxb8
P09632
Morphology
Complex Structural Variation with 3 CNVs including a 14.8kb copy of hoxb7 + hoxb8 ; results in ectopic (unrepressed) expression of hoxb8 in feathers especially in the facial region
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
Hoxb8
Gallus gallus
chicken - (species)
Published - Accepted by Curator
HOXC8 - uncertain
Feathers (crest morphology)
Cis-regulatory,
Unknown
Gallus gallus
chicken - (species)
Domesticated
Association Mapping
Wang Y; Gao Y; Imsland F ; et al. (2012)
The crest phenotype in chicken is associated with ectopic expression of HOXC8 in cranial skin.
GP00000489
HOXC8
Q9YH13
Morphology
unknown
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
HOXC8 - uncertain
Gallus gallus
chicken - (species)
Published - Accepted by Curator
Hps4
Coloration (albinism)
Coding,
Deletion
N
Ictalurus punctatus
channel catfish - (species) D
Intraspecific
Association Mapping
Li Y; Geng X; Bao L ; et al. (2017)
A deletion in the Hermansky-Pudlak syndrome 4 (Hps4) gene appears to be responsible for albinism in [...]
GP00002122
Hps4
Q99KG7
Morphology
A 99‐bp deletion was identified spanning intron 2 and exon 3 junction of the Hps4 gene N
Ictalurus punctatus
channel catfish - (species)
Ictalurus punctatus
channel catfish - (species) D
Hps4
Ictalurus punctatus
channel catfish - (species)
Published - Accepted by Curator
HUA2
Flowering time
Shoot morphology
Coding,
SNP
N
Arabidopsis thaliana
thale cress - (species)
Intraspecific
Linkage Mapping
Wang Q; Sajja U; Rosloski S ; et al. (2007)
HUA2 caused natural variation in shoot morphology of A. thaliana.
GP00000491
HUA2
Q9XER9
Physiology
Morphology
K525E N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
HUA2
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
HUA2
Flowering time
Coloration (temperature-dependent)
Coding,
Unknown
N
Arabidopsis thaliana
thale cress - (species) D
Intraspecific
Linkage Mapping
Ilk N; Ding J; Ihnatowicz A ; et al. (2015)
Natural variation for anthocyanin accumulation under high-light and low-temperature stress is attrib[...]
1 Additional References
GP00001230
HUA2
Q9XER9
Physiology
Morphology
Premature stop codon resulting in truncation of 290 C-terminal amino-acids (hua-2-5 Ler allele) N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
HUA2
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
HvbHLH1
Coloration
Coding,
Deletion
N
Hordeum vulgare
(species) D
Domesticated
Association Mapping
Cockram J; White J; Zuluaga DL ; et al. (2010)
Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genom[...]
GP00000493
bHLH1
E5FCX3
Morphology
16bp deletion resulting in premature stop codon N
Hordeum vulgare
(species)
Hordeum vulgare
(species) D
HvbHLH1
Hordeum vulgare
(species)
Published - Accepted by Curator
IGF2BP1
Body size (weight)
Cis-regulatory,
Unknown
Anas platyrhynchos
mallard - (species) D
Domesticated
Linkage Mapping
Zhou Z; Li M; Cheng H ; et al. (2018)
An intercross population study reveals genes associated with body size and plumage color in ducks.
GP00002128
IGF2BP1
O42254
Morphology
We found that the phenotypic values of body size related traits together with IGF2BP1 expression levels were successfully fine-mapped of the causal variation in an ~100-kb region (chr28: 4,413,785-4,513,671) located on the 148 kb upstream of the IGF2BP1 gene
Anas platyrhynchos
mallard - (species)
Anas platyrhynchos
mallard - (species) D
IGF2BP1
Anas platyrhynchos
mallard - (species)
Published - Accepted by Curator
IIL1
Plant growth (pleiotropic growth abnormalities)
Cis-regulatory,
Insertion
Arabidopsis thaliana
thale cress - (species)
Intraspecific
Linkage Mapping
Sureshkumar S; Todesco M; Schneeberger K ; et al. (2009)
A genetic defect caused by a triplet repeat expansion in Arabidopsis thaliana.
1 Additional References
GP00001229
IIL1
Q94AR8
Morphology
expansion of a GAA/TTC trinucleotide repeat in the third intron
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
IIL1
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
Indian hedgehog (IHH)
Limb size (legs)
Gene Loss,
Deletion
N
Gallus gallus
chicken - (species) D
Domesticated
Association Mapping
Jin S; Zhu F; Wang Y ; et al. (2016)
Deletion of Indian hedgehog gene causes dominant semi-lethal Creeper trait in chicken.
GP00002194
IHH
Q98938
Morphology
11,896 bp large deletion region (chr7: 21,798,705-21,810,600) covering the entire Indian hedgehog (IHH) gene N
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
Indian hedgehog (IHH)
Gallus gallus
chicken - (species)
Published - Accepted by Curator
InR
Fertility
Developmental time
Body size
Stress response
Lifespan
Coding,
Indel
Drosophila melanogaster
fruit fly - (species)
Intraspecific
Candidate Gene
Paaby AB; Bergland AO; Behrman EL ; et al. (2014)
A highly pleiotropic amino acid polymorphism in the Drosophila insulin receptor contributes to life-[...]
1 Additional References
GP00002663
InR
P09208
Morphology
Morphology; Physiology
Physiology
Physiology
Physiology
Deletion of 9 nucleotides in the first exon. The two alleles differ by presence/absence of the three amino acids QHH.
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species)
InR
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
Insulin-like growth factor 1 (IGF1)
Body size
Cis-regulatory,
Unknown
Canis lupus familiaris
dog - (subspecies)
Domesticated
Association Mapping
Sutter NB; Bustamante CD; Chase K ; et al. (2007)
A single IGF1 allele is a major determinant of small size in dogs.
1 Additional References
GP00000501
Igf1
P05017
Morphology
Not identified / several haplotypes
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies)
Insulin-like growth factor 1 (IGF1)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Insulin-like growth factor 2 (IGF2)
Muscular mass
Fat deposition
Heart size
Cis-regulatory,
SNP
Sus scrofa domesticus
domestic pig - (subspecies)
Domesticated
Linkage Mapping
Van Laere AS; Nguyen M; Braunschweig M ; et al. (2003)
A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig.
GP00000502
Igf2
P09535
Morphology
Physiology
Morphology
1bp change
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies)
Insulin-like growth factor 2 (IGF2)
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
Insulin-like growth factor receptor 1 (IGF1R)
Body size (height)
Unknown,
Unknown
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Lettre G (2011)
Recent progress in the study of the genetics of height.
GP00000503
IGF1R
P08069
Morphology
unknown
Homo sapiens
human - (species)
Homo sapiens
human - (species)
Insulin-like growth factor receptor 1 (IGF1R)
Homo sapiens
human - (species)
Published - Accepted by Curator
Insulin-like growth factor receptor 1 (IGF1R)
Body size (weight)
Coding,
SNP
Homo sapiens
human - (species) D
Domesticated
Candidate Gene
Rimbault M; Beale HC; Schoenebeck JJ ; et al. (2013)
Derived variants at six genes explain nearly half of size reduction in dog breeds.
GP00001479
IGF1R
P08069
Morphology
G>A p.R204H in exon 2
Canis lupus
gray wolf - (species)
Homo sapiens
human - (species) D
Insulin-like growth factor receptor 1 (IGF1R)
Homo sapiens
human - (species)
Published - Accepted by Curator
IRF2BP2
Hair type (woolly)
Cis-regulatory,
Insertion
Ovis aries
sheep - (species) D
Domesticated
Linkage Mapping
Demars J; Cano M; Drouilhet L ; et al. (2017)
Genome-Wide Identification of the Mutation Underlying Fleece Variation and Discriminating Ancestral [...]
GP00002195
IRF2BP2
Q7Z5L9
Morphology
insertion of an antisense EIF2S2 retrogene (asEIF2S2) into the 3′ UTR of the IRF2BP2 gene ; RNA-RNA hybrid creates a long endogenous double-stranded RNA which alters the expression of both EIF2S2 and IRF2BP2 mRNA
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
IRF2BP2
Ovis aries
sheep - (species)
Published - Accepted by Curator
IRF4
Coloration (skin)
Cis-regulatory,
SNP
Homo sapiens
human - (species) D
Intraspecific
Association Mapping
Praetorius C; Grill C; Stacey SN ; et al. (2013)
A polymorphism in IRF4 affects human pigmentation through a tyrosinase-dependent MITF/TFAP2A pathway[...]
1 Additional References
GP00001364
IRF4
Q15306
Morphology
a C>T substitution in intron4 located within an enhancer
Homo sapiens
human - (species)
Homo sapiens
human - (species) D
IRF4
Homo sapiens
human - (species)
Published - Accepted by Curator
JAZF1
Body size (height)
Unknown,
Unknown
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Johansson A; Marroni F; Hayward C ; et al. (2009)
Common variants in the JAZF1 gene associated with height identified by linkage and genome-wide assoc[...]
1 Additional References
GP00000507
JAZF1
Q86VZ6
Morphology
unknown
Homo sapiens
human - (species)
Homo sapiens
human - (species)
JAZF1
Homo sapiens
human - (species)
Published - Accepted by Curator
Kcnj13
Coloration
Unknown,
Unknown
Danio aesculapii
(species) D
Interspecific
Candidate Gene
Podobnik M; Frohnhöfer HG; Dooley CM ; et al. (2020)
Evolution of the potassium channel gene Kcnj13 underlies colour pattern diversification in Danio fis[...]
GP00002364
Kcnj13
P86046
Morphology
Danio rerio
zebrafish - (species)
Danio aesculapii
(species) D
Kcnj13
Danio aesculapii
(species)
Published - Accepted by Curator
KCNQ1
Body size (height)
Unknown,
Epigenetic Change
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Zoledziewska M; Sidore C; Chiang CWK ; et al. (2015)
Height-reducing variants and selection for short stature in Sardinia.
GP00000511
KCNQ1
P51787
Morphology
unknown causative change in an imprinted region - consistent with maternal inheritance detected by the association
Homo sapiens
human - (species)
Homo sapiens
human - (species)
KCNQ1
Homo sapiens
human - (species)
Published - Accepted by Curator
Kit
Coloration (coat ; white-spotting)
Coding,
Insertion
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Wong AK; Ruhe AL; Robertson KR ; et al. (2013)
A de novo mutation in KIT causes white spotting in a subpopulation of German Shepherd dogs.
GP00002228
Kit
P05532
Morphology
a 1-bp insertion of an adenine 70 bases downstream of the beginning of exon 2 resulting in frameshift N
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
Kit
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Gene Amplification,
Complex Change
Bos taurus
cattle - (species)
Domesticated
Linkage Mapping
Durkin K; Coppieters W; Drögemüller C ; et al. (2012)
Serial translocation by means of circular intermediates underlies colour sidedness in cattle.
GP00000514
Kit
P05532
Morphology
Copy Number Variation of <600kb segments encompassing KIT
Bos taurus
cattle - (species)
Bos taurus
cattle - (species)
Kit (type III receptor protein-tyrosine kinase)
Bos taurus
cattle - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Linkage Mapping
Brooks SA; Bailey E (2005)
Exon skipping in the KIT gene causes a Sabino spotting pattern in horses.
GP00000515
Kit
P05532
Morphology
T->A in intron 16; leads to skipping of exon 17
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
N
Equus caballus
horse - (species) D
Domesticated
Linkage Mapping
Haase B; Brooks SA; Schlumbaum A ; et al. (2007)
Allelic heterogeneity at the equine KIT locus in dominant white (W) horses.
GP00000516
Kit
P05532
Morphology
c.2151C>G pY717* N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Cis-regulatory,
Insertion
Felis catus
domestic cat - (species) D
Domesticated
Association Mapping
David VA; Menotti-Raymond M; Wallace AC ; et al. (2014)
Endogenous retrovirus insertion in the KIT oncogene determines white and white spotting in domestic [...]
GP00000517
Kit
P05532
Morphology
full-length (7125 bp) FERV1 endogenous retrovirus insertion in intron
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
Kit (type III receptor protein-tyrosine kinase)
Felis catus
domestic cat - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
Indel
Felis catus
domestic cat - (species) D
Domesticated
Association Mapping
Montague MJ; Li G; Gandolfi B ; et al. (2014)
Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology[...]
GP00000518
Kit
P05532
Morphology
Two nucleotide changes affecting site 3 of codon 345 and site 1 of codon 346 - resulting in Glu345Asp + His346Asn
c. 1035_1036delinsCA GAGCAY > GACAAY
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
Kit (type III receptor protein-tyrosine kinase)
Felis catus
domestic cat - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Cis-regulatory,
Deletion
Felis catus
domestic cat - (species) D
Domesticated
Association Mapping
David VA; Menotti-Raymond M; Wallace AC ; et al. (2014)
Endogenous retrovirus insertion in the KIT oncogene determines white and white spotting in domestic [...]
GP00000519
Kit
P05532
Morphology
Excision of the full-length FERV1 elevement leaving the two LTR residues
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
Kit (type III receptor protein-tyrosine kinase)
Felis catus
domestic cat - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
2 Mutations:
Sus scrofa domesticus
domestic pig - (subspecies) D
Domesticated
Linkage Mapping
Marklund S; Kijas J; Rodriguez-Martinez H ; et al. (1998)
Molecular basis for the dominant white phenotype in the domestic pig.
3 Additional References
GP00000520
Kit
P05532
Morphology
2 mutations
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies) D
Kit (type III receptor protein-tyrosine kinase)
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Cis-regulatory,
Deletion
Vulpes vulpes
red fox - (species) D
Domesticated
Linkage Mapping
Johnson JL; Kozysa A; Kharlamova AV ; et al. (2015)
Platinum coat color in red fox (Vulpes vulpes) is caused by a mutation in an autosomal copy of KIT.
GP00000521
Kit
P05532
Morphology
splice mutation; G to A substitution in the first nucleotide of intron 17; leads to skipping of exon 17.
Vulpes vulpes
red fox - (species)
Vulpes vulpes
red fox - (species) D
Kit (type III receptor protein-tyrosine kinase)
Vulpes vulpes
red fox - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Cis-regulatory,
Insertion
Sus scrofa domesticus
domestic pig - (subspecies) D
Domesticated
Candidate Gene
Rubin CJ; Megens HJ; Martinez Barrio A ; et al. (2012)
Strong signatures of selection in the domestic pig genome.
1 Additional References
GP00001326
Kit
P05532
Morphology
4.3kb duplication (DUP2) located about 100 kb upstream of KIT
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies) D
Kit (type III receptor protein-tyrosine kinase)
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Unknown,
Unknown
Vulpes vulpes
red fox - (species) D
Domesticated
Association Mapping
Kukekova AV; Johnson JL; Kharlamova AV ; et al. (2016)
Georgian white coat color of red fox (Vulpes vulpes) maps to fox chromosome 2 in the region containi[...]
GP00001328
Kit
P05532
Morphology
unknown
Vulpes vulpes
red fox - (species)
Vulpes vulpes
red fox - (species) D
Kit (type III receptor protein-tyrosine kinase)
Vulpes vulpes
red fox - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (skin; coat)
Coding,
SNP
Equus asinus
ass - (species) D
Domesticated
Candidate Gene
Haase B; Rieder S; Leeb T (2015)
Two variants in the KIT gene as candidate causative mutations for a dominant white and a white spott[...]
GP00001340
Kit
P05532
Morphology
c.662A>C p.Tyr221Ser
Equus asinus
ass - (species)
Equus asinus
ass - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus asinus
ass - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (skin; coat)
Coding,
SNP
Equus asinus
ass - (species) D
Domesticated
Candidate Gene
Haase B; Rieder S; Leeb T (2015)
Two variants in the KIT gene as candidate causative mutations for a dominant white and a white spott[...]
GP00001341
Kit
P05532
Morphology
c.1978+2T>A in splice donor site
Equus asinus
ass - (species)
Equus asinus
ass - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus asinus
ass - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Brooks SA; Tozaki T ; et al. (2009)
Seven novel KIT mutations in horses with white coat colour phenotypes.
GP00001344
Kit
P05532
Morphology
c.1789G>A p.G597R
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Gene Amplification,
Complex Change
Bos taurus
cattle - (species) D
Domesticated
Candidate Gene
Brenig B; Beck J; Floren C ; et al. (2013)
Molecular genetics of coat colour variations in White Galloway and White Park cattle.
GP00001345
Kit
P05532
Morphology
duplication and aberrant insertion on chromosome 29
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Kit (type III receptor protein-tyrosine kinase)
Bos taurus
cattle - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Other,
SNP
Vulpes lagopus
Arctic fox - (species) D
Domesticated
Candidate Gene
Yan SQ; Hou JN; Bai CY ; et al. (2014)
A base substitution in the donor site of intron 12 of KIT gene is responsible for the dominant white[...]
GP00002192
Kit
P05532
Morphology
dominant white coat colour of blue fox results from an exon 12 skipping caused by a c.1867+1G>T substitution in the first nucleotide of intron 12 of the KIT gene
Vulpes lagopus
Arctic fox - (species)
Vulpes lagopus
Arctic fox - (species) D
Kit (type III receptor protein-tyrosine kinase)
Vulpes lagopus
Arctic fox - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Cis-regulatory,
Insertion
Sus scrofa domesticus
domestic pig - (subspecies) D
Domesticated
Candidate Gene
Rubin CJ; Megens HJ; Martinez Barrio A ; et al. (2012)
Strong signatures of selection in the domestic pig genome.
1 Additional References
GP00002196
Kit
P05532
Morphology
the patch allele comprises a 450kb duplication that includes KIT (roughly in the middle)
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies) D
Kit (type III receptor protein-tyrosine kinase)
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Gene Amplification,
Complex Change
Bos taurus
cattle - (species) D
Domesticated
Candidate Gene
Küttel L; Letko A; Häfliger IM ; et al. (2019)
A complex structural variant at the KIT locus in cattle with the Pinzgauer spotting pattern.
1 Additional References
GP00002197
Kit
P05532
Morphology
Complex chromosomal rearragements including a ~310-kb duplication
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Kit (type III receptor protein-tyrosine kinase)
Bos taurus
cattle - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
N
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Brooks SA; Schlumbaum A ; et al. (2007)
Allelic heterogeneity at the equine KIT locus in dominant white (W) horses.
GP00002198
Kit
P05532
Morphology
c.706A>T p.K236* N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Brooks SA; Schlumbaum A ; et al. (2007)
Allelic heterogeneity at the equine KIT locus in dominant white (W) horses.
GP00002199
Kit
P05532
Morphology
c.1805C>T p.A602V
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Brooks SA; Schlumbaum A ; et al. (2007)
Allelic heterogeneity at the equine KIT locus in dominant white (W) horses.
GP00002200
Kit
P05532
Morphology
c.1960G>A p.G654R
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Brooks SA; Tozaki T ; et al. (2009)
Seven novel KIT mutations in horses with white coat colour phenotypes.
GP00002201
Kit
P05532
Morphology
c.2222-1G>A (putative splicing site)
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
Deletion
N
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Brooks SA; Tozaki T ; et al. (2009)
Seven novel KIT mutations in horses with white coat colour phenotypes.
GP00002202
Kit
P05532
Morphology
c.1126_1129delGAAC p.E376FfsX3 N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Brooks SA; Tozaki T ; et al. (2009)
Seven novel KIT mutations in horses with white coat colour phenotypes.
GP00002203
Kit
P05532
Morphology
c.2684+1G>A (putative splicing site)
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Brooks SA; Tozaki T ; et al. (2009)
Seven novel KIT mutations in horses with white coat colour phenotypes.
GP00002204
Kit
P05532
Morphology
c.338-1G>C (putative splicing site)
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
Deletion
N
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Brooks SA; Tozaki T ; et al. (2009)
Seven novel KIT mutations in horses with white coat colour phenotypes.
GP00002205
Kit
P05532
Morphology
c.2193delG p.T732QfsX9 N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Brooks SA; Tozaki T ; et al. (2009)
Seven novel KIT mutations in horses with white coat colour phenotypes.
GP00002206
Kit
P05532
Morphology
c.856G>A p.G286R
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Rieder S; Tozaki T ; et al. (2011)
Five novel KIT mutations in horses with white coat colour phenotypes.
GP00002207
Kit
P05532
Morphology
c.1597T>C p.C533R
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Rieder S; Tozaki T ; et al. (2011)
Five novel KIT mutations in horses with white coat colour phenotypes.
GP00002208
Kit
P05532
Morphology
c.2021T>C p.L674P
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Rieder S; Tozaki T ; et al. (2011)
Five novel KIT mutations in horses with white coat colour phenotypes.
GP00002209
Kit
P05532
Morphology
c.2001A>T p.E667D
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Rieder S; Tozaki T ; et al. (2011)
Five novel KIT mutations in horses with white coat colour phenotypes.
GP00002210
Kit
P05532
Morphology
c.2472+5G>C (putative splicing mutation)
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Rieder S; Tozaki T ; et al. (2011)
Five novel KIT mutations in horses with white coat colour phenotypes.
GP00002211
Kit
P05532
Morphology
c.2489A>T p.K830I
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
Deletion
N
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Rieder S; Tozaki T ; et al. (2011)
Five novel KIT mutations in horses with white coat colour phenotypes.
GP00002212
Kit
P05532
Morphology
c.2392_2445del p.H798_N815del N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Hauswirth R; Jude R; Haase B ; et al. (2013)
Novel variants in the KIT and PAX3 genes in horses with white-spotted coat colour phenotypes.
GP00002213
Kit
P05532
Morphology
c.2045G>A p.R682H
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Hauswirth R; Jude R; Haase B ; et al. (2013)
Novel variants in the KIT and PAX3 genes in horses with white-spotted coat colour phenotypes.
GP00002214
Kit
P05532
Morphology
c.1322A>G p.Y441C
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Hauswirth R; Jude R; Haase B ; et al. (2013)
Novel variants in the KIT and PAX3 genes in horses with white-spotted coat colour phenotypes.
GP00002215
Kit
P05532
Morphology
c.1346 + 1G>A (putative splicing mutation)
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
Deletion
N
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Jagannathan V; Rieder S ; et al. (2015)
A novel KIT variant in an Icelandic horse with white-spotted coat colour.
GP00002216
Kit
P05532
Morphology
c.2369delC p.Ala790Glufs*20 N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Cis-regulatory,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Holl HM; Brooks SA; Carpenter ML ; et al. (2017)
A novel splice mutation within equine KIT and the W15 allele in the homozygous state lead to all whi[...]
GP00002217
Kit
P05532
Morphology
c.756+1G>C (putative splicing mutation)
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Cis-regulatory,
Deletion
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Capomaccio S; Milanesi M; Nocelli C ; et al. (2017)
Splicing site disruption in the KIT gene as strong candidate for white dominant phenotype in an Ital[...]
GP00002218
Kit
P05532
Morphology
g.77736559C>T (putative splicing mutation)
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
Deletion
N
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Dürig N; Jude R; Holl H ; et al. (2017)
Whole genome sequencing reveals a novel deletion variant in the KIT gene in horses with white spotte[...]
GP00002219
Kit
P05532
Morphology
g.77;740;239_77;742;136del1898insTATAT ~1.9-kb deletion N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Hoban R; Castle K; Hamilton N ; et al. (2018)
Novel KIT variants for dominant white in the Australian horse population.
GP00002220
Kit
P05532
Morphology
c.1473T>G p.Cys491Trp
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
Deletion
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Hoban R; Castle K; Hamilton N ; et al. (2018)
Novel KIT variants for dominant white in the Australian horse population.
GP00002221
Kit
P05532
Morphology
c.2536delA p.Ser846Valfs*15
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Hoban R; Castle K; Hamilton N ; et al. (2018)
Novel KIT variants for dominant white in the Australian horse population.
GP00002222
Kit
P05532
Morphology
c.668T>C p.Leu223Pro
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
Deletion
N
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Hug P; Jude R; Henkel J ; et al. (2019)
A novel KIT deletion variant in a German Riding Pony with white-spotting coat colour phenotype.
GP00002223
Kit
P05532
Morphology
g.79;579;925-79;581;197del 1273bp deletion N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Cis-regulatory,
Deletion
Sus scrofa domesticus
domestic pig - (subspecies) D
Domesticated
Linkage Mapping
Lim HT; Zhong T; Cho IC ; et al. (2011)
Novel alternative splicing by exon skipping in KIT associated with whole-body roan in an intercrosse[...]
1 Additional References
GP00002227
Kit
P05532
Morphology
U(26) repeat in intron 5 of the KIT gene with a single G interruption likely to mediate skipping of exon 5 of the gene in some tissues including skin ; the WT allele has an U(27) repeat interrupted by 5 G
Sus scrofa domesticus
domestic pig - (subspecies)
Sus scrofa domesticus
domestic pig - (subspecies) D
Kit (type III receptor protein-tyrosine kinase)
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat ; white-spotting)
Coding,
Deletion
N
Camelus dromedarius
Arabian camel - (species) D
Domesticated
Candidate Gene
Holl H; Isaza R; Mohamoud Y ; et al. (2017)
A Frameshift Mutation in KIT is Associated with White Spotting in the Arabian Camel.
GP00002229
Kit
P05532
Morphology
c.1842delG p.M614IfsX5 N
Camelus dromedarius
Arabian camel - (species)
Camelus dromedarius
Arabian camel - (species) D
Kit (type III receptor protein-tyrosine kinase)
Camelus dromedarius
Arabian camel - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase) [pseudoreplicate with two Bos taurus KIT entries]
Coloration (coat)
Gene Amplification,
Complex Change
Bos grunniens
domestic yak - (species) D
Domesticated
Candidate Gene
Zhang MQ; Xu X; Luo SJ (2014)
The genetics of brown coat color and white spotting in domestic yaks (Bos grunniens).
GP00001342
Kit
P05532
Morphology
serial translocations Cs6 and Cs29
Bos grunniens
domestic yak - (species)
Bos grunniens
domestic yak - (species) D
Kit (type III receptor protein-tyrosine kinase) [pseudoreplicate with two Bos taurus KIT entries]
Bos grunniens
domestic yak - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase) [pseudoreplicate with two Bos taurus KIT entries]
Coloration (coat)
Unknown,
Complex Change
Bos grunniens
domestic yak - (species) D
Domesticated
Candidate Gene
Zhang MQ; Xu X; Luo SJ (2014)
The genetics of brown coat color and white spotting in domestic yaks (Bos grunniens).
GP00001343
Kit
P05532
Morphology
haplotype Swf (indels and SNP)
Bos grunniens
domestic yak - (species)
Bos grunniens
domestic yak - (species) D
Kit (type III receptor protein-tyrosine kinase) [pseudoreplicate with two Bos taurus KIT entries]
Bos grunniens
domestic yak - (species)
Published - Accepted by Curator
Kit ligand
Coloration (coat)
Coding,
SNP
N
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Seitz JJ; Schmutz SM; Thue TD ; et al. (1999)
A missense mutation in the bovine MGF gene is associated with the roan phenotype in Belgian Blue and[...]
1 Additional References
GP00000101
KITLG
P21583
Morphology
Ala193Asp ; missense mutation at position 654 - according to OMIA: c.572C>A p.A191N N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Kit ligand
Bos taurus
cattle - (species)
Published - Accepted by Curator
Kit ligand
Coloration (coat)
Cis-regulatory,
Unknown
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Miller CT; Beleza S; Pollen AA ; et al. (2007)
cis-Regulatory changes in Kit ligand expression and parallel evolution of pigmentation in sticklebac[...]
1 Additional References
GP00000522
KITLG
P21583
Morphology
unknown
Homo sapiens
human - (species)
Homo sapiens
human - (species)
Kit ligand
Homo sapiens
human - (species)
Published - Accepted by Curator
Kit ligand
Coloration (gills; ventrum)
Cis-regulatory,
Unknown
Gasterosteus aculeatus
three-spined stickleback - (species)
Intraspecific
Linkage Mapping
Miller CT; Beleza S; Pollen AA ; et al. (2007)
cis-Regulatory changes in Kit ligand expression and parallel evolution of pigmentation in sticklebac[...]
GP00000523
KITLG
P21583
Morphology
Not identified
Gasterosteus aculeatus
three-spined stickleback - (species)
Gasterosteus aculeatus
three-spined stickleback - (species)
Kit ligand
Gasterosteus aculeatus
three-spined stickleback - (species)
Published - Accepted by Curator
Kit ligand
Coloration (hair)
Cis-regulatory,
SNP
Homo sapiens
human - (species) D
Intraspecific
Association Mapping
Guenther CA; Tasic B; Luo L ; et al. (2014)
A molecular basis for classic blond hair color in Europeans.
GP00001349
KITLG
P21583
Morphology
A>G SNP(rs12821256) 350kb upstream of transcription start
Homo sapiens
human - (species)
Homo sapiens
human - (species) D
Kit ligand
Homo sapiens
human - (species)
Published - Accepted by Curator
KRT25
Hair type (curly)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Association Mapping
Morgenthaler C; Diribarne M; Capitan A ; et al. (2017)
A missense variant in the coil1A domain of the keratin 25 gene is associated with the dominant curly[...]
1 Additional References
GP00002230
Krt25
Q8VCW2
Morphology
c.266G>A p.Arg89His
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
KRT25
Equus caballus
horse - (species)
Published - Accepted by Curator
KRT25
Hair type (curly)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Association Mapping
Thomer A; Gottschalk M; Christmann A ; et al. (2018)
An epistatic effect of KRT25 on SP6 is involved in curly coat in horses.
GP00002288
Sp6
Q9ESX2
Morphology
c.1090G>A p.Asp364Asn
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
KRT25
Equus caballus
horse - (species)
Published - Accepted by Curator
KRT27
Hair type (curly)
Coding,
SNP
Bos taurus
cattle - (species) D
Domesticated
Association Mapping
Daetwyler HD; Capitan A; Pausch H ; et al. (2014)
Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle.
GP00002026
KRT27
Q0P5J6
Morphology
g.41636961C>G c.276C>G p.Asn92Lys
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
KRT27
Bos taurus
cattle - (species)
Published - Accepted by Curator
KRT6A
Feathers
Coding,
Deletion
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Ng CS; Wu P; Foley J ; et al. (2012)
The chicken frizzle feather is due to an α-keratin (KRT75) mutation that causes a defective rachis.
GP00000527
Krt6a
P50446
Morphology
69bp deletion partially overlapping with exon 5
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
KRT6A
Gallus gallus
chicken - (species)
Published - Accepted by Curator
KRT71
Hair type (curly)
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Cadieu E; Neff MW; Quignon P ; et al. (2009)
Coat variation in the domestic dog is governed by variants in three genes.
GP00000524
Krt71
Q9R0H5
Morphology
c.451A>T in exon 2 - Arg151Trp
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
KRT71
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
KRT71
Hair type (curly and hairless)
2 Mutations:
Coding
Felis catus
domestic cat - (species) D
Domesticated
Candidate Gene
Gandolfi B; Outerbridge CA; Beresford LG ; et al. (2010)
The naked truth: Sphynx and Devon Rex cat breed mutations in KRT71.
GP00000525
Krt71
Q9R0H5
Morphology
2 mutations
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
KRT71
Felis catus
domestic cat - (species)
Published - Accepted by Curator
KRT71
Hair type (curly and hairless)
Coding,
Deletion
N
Rattus norvegicus
Norway rat - (species) D
Domesticated
Linkage Mapping
Kuramoto T; Hirano R; Kuwamura M ; et al. (2010)
Identification of the rat Rex mutation as a 7-bp deletion at splicing acceptor site of the Krt71 gen[...]
GP00001729
Krt71
Q9R0H5
Morphology
a 7-bp deletion at the splicing acceptor site of intron 1. The deletion provoked a 6-amino acid in-frame deletion (p.Val149_Gln154del) in the alpha-helical rod domain of KRT71 protein N
Rattus norvegicus
Norway rat - (species)
Rattus norvegicus
Norway rat - (species) D
KRT71
Rattus norvegicus
Norway rat - (species)
Published - Accepted by Curator
KRT71
Hair type (curly and hairless)
Coding,
Deletion
N
Bos taurus
cattle - (species) D
Domesticated
Association Mapping
Gandolfi B; Outerbridge CA; Beresford LG ; et al. (2010)
The naked truth: Sphynx and Devon Rex cat breed mutations in KRT71.
GP00001730
Krt71
Q9R0H5
Morphology
eight base pair deletion mutation in exon one of the keratin 71 (KRT71) c.334delTGTGCCCA p.Met93AsnfsX14 N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
KRT71
Bos taurus
cattle - (species)
Published - Accepted by Curator
KRT71
Hair type (curly)
Coding,
Indel
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Bauer A; Hadji Rasouliha S; Brunner MT ; et al. (2019)
A second KRT71 allele in curly coated dogs.
1 Additional References
GP00002231
Krt71
Q9R0H5
Morphology
c.1266_1273delinsACA p.Ser422ArgfsTer?
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
KRT71
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
KRT71
Hair type (curly)
Coding,
SNP
N
Felis catus
domestic cat - (species) D
Domesticated
Candidate Gene
Gandolfi B; Alhaddad H; Joslin SE ; et al. (2013)
A splice variant in KRT71 is associated with curly coat phenotype of Selkirk Rex cats.
GP00002232
Krt71
Q9R0H5
Morphology
c.445-1G>C in splice site likely disrupts the highly conserved acceptor splicing site of intron one. Sequence of the complete RNA transcript revealed that an alternative downstream acceptor was employed N
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
KRT71
Felis catus
domestic cat - (species)
Published - Accepted by Curator
KRT75L4
Feathers
Coding,
Deletion
Gallus gallus
chicken - (species) D
Domesticated
Association Mapping
Guo X; Li YQ; Wang MS ; et al. (2018)
A parallel mechanism underlying frizzle in domestic chickens.
GP00002334
KRT75L4
A0A1L1RKR4
Morphology
15bp deletion resulting in loss of 5 conserved amino-acids
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
KRT75L4
Gallus gallus
chicken - (species)
Published - Accepted by Curator
KUK
Root development
2 Mutations:
Unknown
Arabidopsis thaliana
thale cress - (species)
Intraspecific
Association Mapping
Meijón M; Satbhai SB; Tsuchimatsu T ; et al. (2014)
Genome-wide association study using cellular traits identifies a new regulator of root development i[...]
GP00001233
At1g60370
O80758
Morphology
2 mutations
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
KUK
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
Latexin (Lxn)
Stem cell number (hematopoietic precursors)
Cis-regulatory,
Unknown
Mus musculus
house mouse - (species)
Intraspecific
Linkage Mapping
Liang Y; Jansen M; Aronow B ; et al. (2007)
The quantitative trait gene latexin influences the size of the hematopoietic stem cell population in[...]
GP00000534
Lxn
P70202
Morphology
Not identified
Mus musculus
house mouse - (species)
Mus musculus
house mouse - (species)
Latexin (Lxn)
Mus musculus
house mouse - (species)
Published - Accepted by Curator
lbh (limb bud and heart homolog)
Cranio-facial morphology (mandible)
Coding,
SNP
Labeotropheus fuelleborni
blue mbuna - (species) D
Interspecific
Linkage Mapping
Powder KE; Cousin H; McLinden GP ; et al. (2014)
A nonsynonymous mutation in the transcriptional regulator lbh is associated with cichlid craniofacia[...]
GP00001387
LBH
Q53QV2
Morphology
G>A p.R17Q
Maylandia zebra
zebra mbuna - (species)
Labeotropheus fuelleborni
blue mbuna - (species) D
lbh (limb bud and heart homolog)
Labeotropheus fuelleborni
blue mbuna - (species)
Published - Accepted by Curator
LCORL
Body size
Unknown,
Unknown
Bos taurus
cattle - (species)
Domesticated
Linkage Mapping
Lindholm-Perry AK; Sexten AK; Kuehn LA ; et al. (2011)
Association, effects and validation of polymorphisms within the NCAPG - LCORL locus located on BTA6 [...]
GP00000535
LCORL
Q8N3X6
Morphology
Not identified
Bos taurus
cattle - (species)
Bos taurus
cattle - (species)
LCORL
Bos taurus
cattle - (species)
Published - Accepted by Curator
LCORL
Body size
Unknown,
Unknown
Equus caballus
horse - (species)
Domesticated
Linkage Mapping
Makvandi-Nejad S; Hoffman GE; Allen JJ ; et al. (2012)
Four loci explain 83% of size variation in the horse.
3 Additional References
GP00000536
LCORL
Q8N3X6
Morphology
Not identified
Equus caballus
horse - (species)
Equus caballus
horse - (species)
LCORL
Equus caballus
horse - (species)
Published - Accepted by Curator
LCORL
Body size
Unknown,
Unknown
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Horikoshi M; Yaghootkar H; Mook-Kanamori DO ; et al. (2013)
New loci associated with birth weight identify genetic links between intrauterine growth[...]
GP00000537
LCORL
Q8N3X6
Morphology
Not identified
Homo sapiens
human - (species)
Homo sapiens
human - (species)
LCORL
Homo sapiens
human - (species)
Published - Accepted by Curator
Ldia2 - Diaphanous-related formin
Shell chirality (coiling)
Coding,
Deletion
N
Lymnaea stagnalis
great pond snail - (species) D
Intraspecific
Association Mapping
Davison A; McDowell GS; Holden JM ; et al. (2016)
Formin Is Associated with Left-Right Asymmetry in the Pond Snail and the Frog.
GP00000538
DIAPH1
O60610
Morphology
1bp deletion resulting in frame-shift (pseudogenization) N
Lymnaea stagnalis
great pond snail - (species)
Lymnaea stagnalis
great pond snail - (species) D
Ldia2 - Diaphanous-related formin
Lymnaea stagnalis
great pond snail - (species)
Published - Accepted by Curator
LIGHT AREAS1 (LAR1)
Coloration (flowers)
Cis-regulatory,
Unknown
Erythranthe lewisii
(species)
Interspecific
Linkage Mapping
Yuan YW; Rebocho AB; Sagawa JM ; et al. (2016)
Competition between anthocyanin and flavonol biosynthesis produces spatial pattern variation of flor[...]
GP00000543
LAR1
A0A0S2T0F2
Morphology
unknown
Erythranthe lewisii
(species)
Erythranthe lewisii
(species)
LIGHT AREAS1 (LAR1)
Erythranthe lewisii
(species)
Published - Accepted by Curator
lin-48
Excretory duct position
4 Mutations:
Cis-regulatory
Unknown
Caenorhabditis elegans
(species) D
Interspecific
Candidate Gene
Wang X; Chamberlin HM (2002)
Multiple regulatory changes contribute to the evolution of the Caenorhabditis lin-48 ovo gene.
1 Additional References
GP00000544
lin-48
G5EDU6
Morphology
4 mutations
Caenorhabditis briggsae
(species)
Caenorhabditis remanei
(species)
Caenorhabditis japonica
(species)
Caenorhabditis elegans
(species) D
lin-48
Caenorhabditis elegans
(species)
Published - Accepted by Curator
LIN28B
Body size (height)
Unknown,
Unknown
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Lettre G (2011)
Recent progress in the study of the genetics of height.
GP00000548
LIN28B
Q6ZN17
Morphology
unknown
Homo sapiens
human - (species)
Homo sapiens
human - (species)
LIN28B
Homo sapiens
human - (species)
Published - Accepted by Curator
LIPH
Hair length
Coding,
Deletion
N
Oryctolagus cuniculus
rabbit - (species) D
Domesticated
Linkage Mapping
Diribarne M; Mata X; Chantry-Darmon C ; et al. (2011)
A deletion in exon 9 of the LIPH gene is responsible for the rex hair coat phenotype in rabbits (Ory[...]
GP00000550
Liph
Q8CIV3
Morphology
1bp deletion resulting in frameshift N
Oryctolagus cuniculus
rabbit - (species)
Oryctolagus cuniculus
rabbit - (species) D
LIPH
Oryctolagus cuniculus
rabbit - (species)
Published - Accepted by Curator
Low-density lipoprotein receptor-related protein 2
Organ size (eye; enlarged)
3 Mutations:
Coding
N
Carassius auratus
goldfish - (species) D
Domesticated
Association Mapping
Kon T; Omori Y; Fukuta K ; et al. (2020)
The Genetic Basis of Morphological Diversity in Domesticated Goldfish.
GP00002349
LRP2
P98164
Morphology
3 mutations
Carassius auratus
goldfish - (species)
Carassius auratus
goldfish - (species) D
Low-density lipoprotein receptor-related protein 2
Carassius auratus
goldfish - (species)
Published - Accepted by Curator
mab-23
Male genitalia
Coding,
SNP
N
Caenorhabditis elegans
(species) D
Intraspecific
Linkage Mapping
Lints R; Emmons SW (2002)
Regulation of sex-specific differentiation and mating behavior in C. elegans by a new member of the [...]
1 Additional References
GP00001323
mab-23
G5ECK3
Morphology
TGC>TTC - cysteine of the DM motif transformed into phenylalanine; so is likely to disrupt DNA-binding function N
Caenorhabditis elegans
(species)
Caenorhabditis elegans
(species) D
mab-23
Caenorhabditis elegans
(species)
Published - Accepted by Curator
MaMyb2
Coloration (flowers)
Cis-regulatory,
Unknown
Diplacus aurantiacus
(species)
Intraspecific
Linkage Mapping
Streisfeld MA; Young WN; Sobel JM (2013)
Divergent selection drives genetic differentiation in an R2R3-MYB transcription factor that contribu[...]
GP00000563
Myb2
M9QXG2
Morphology
unknown expression-phenotype co-vary
Diplacus aurantiacus
(species)
Diplacus aurantiacus
(species)
MaMyb2
Diplacus aurantiacus
(species)
Published - Accepted by Curator
MC1R
Coloration (albinism)
Coding,
Deletion
N
Astyanax mexicanus
Mexican tetra - (species) D
Intraspecific
Linkage Mapping
Gross JB; Borowsky R; Tabin CJ (2009)
A novel role for Mc1r in the parallel evolution of depigmentation in independent populations of the [...]
GP00000567
MC1R
Q01726
Morphology
2bp deletion resulting in frameshift N
Astyanax mexicanus
Mexican tetra - (species)
Astyanax mexicanus
Mexican tetra - (species) D
MC1R
Astyanax mexicanus
Mexican tetra - (species)
Published - Accepted by Curator
MC1R
Coloration (albinism)
Coding,
SNP
Astyanax mexicanus
Mexican tetra - (species) D
Intraspecific
Linkage Mapping
Gross JB; Borowsky R; Tabin CJ (2009)
A novel role for Mc1r in the parallel evolution of depigmentation in independent populations of the [...]
GP00000568
MC1R
Q01726
Morphology
Arg164Cys (position 160 in human; so this mutation resembles the human R160W hypomorphic human mutation)
Astyanax mexicanus
Mexican tetra - (species)
Astyanax mexicanus
Mexican tetra - (species) D
MC1R
Astyanax mexicanus
Mexican tetra - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
2 Mutations:
Coding
SNP
Vulpes lagopus
Arctic fox - (species)
Interspecific
Candidate Gene
Våge DI; Fuglei E; Snipstad K ; et al. (2005)
Two cysteine substitutions in the MC1R generate the blue variant of the Arctic fox (Alopex lagopus) [...]
1 Additional References
GP00000569
MC1R
Q01726
Morphology
2 mutations
Vulpes vulpes
red fox - (species)
Vulpes lagopus
Arctic fox - (species)
MC1R
Vulpes lagopus
Arctic fox - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
Deletion
N
Bos taurus
cattle - (species) D
Domesticated
Candidate Gene
Klungland H; Våge DI; Gomez-Raya L ; et al. (1995)
The role of melanocyte-stimulating hormone (MSH) receptor in bovine coat color determination.
1 Additional References
GP00000571
MC1R
Q01726
Morphology
1 bp deletion at 104: frameshift and premature stop at amino acid 156 N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
MC1R
Bos taurus
cattle - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Bos taurus
cattle - (species) D
Domesticated
Candidate Gene
Klungland H; Våge DI; Gomez-Raya L ; et al. (1995)
The role of melanocyte-stimulating hormone (MSH) receptor in bovine coat color determination.
GP00000572
MC1R
Q01726
Morphology
L99P ; presumably constitutively active - g.14757910T>C c.296T>C p.L99P
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
MC1R
Bos taurus
cattle - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Newton JM; Wilkie AL; He L ; et al. (2000)
Melanocortin 1 receptor variation in the domestic dog.
1 Additional References
GP00000573
MC1R
Q01726
Morphology
R306ter; deletes 12 of 17 a.a. from C-terminus
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
MC1R
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Schmutz SM; Berryere TG; Ellinwood NM ; et al. (2003 Jan-Feb)
MC1R studies in dogs with melanistic mask or brindle patterns.
GP00000574
MC1R
Q01726
Morphology
M264V
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
MC1R
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
MC1R
Coloration (coat)
Gene Loss,
Complex Change
N
Cavia porcellus
domestic guinea pig - (species) D
Domesticated
Candidate Gene
Cone RD; Lu D; Koppula S ; et al. (1996)
The melanocortin receptors: agonists, antagonists, and the hormonal control of pigmentation.
GP00000575
MC1R
Q01726
Morphology
Deletion of part or all of gene N
Cavia porcellus
domestic guinea pig - (species)
Cavia porcellus
domestic guinea pig - (species) D
MC1R
Cavia porcellus
domestic guinea pig - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Chaetodipus intermedius
rock pocket mouse - (species) D
Intraspecific
Candidate Gene
Nachman MW; Hoekstra HE; D'Agostino SL (2003)
The genetic basis of adaptive melanism in pocket mice.
GP00000576
MC1R
Q01726
Morphology
R18C
Chaetodipus intermedius
rock pocket mouse - (species)
Chaetodipus intermedius
rock pocket mouse - (species) D
MC1R
Chaetodipus intermedius
rock pocket mouse - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Chaetodipus intermedius
rock pocket mouse - (species) D
Intraspecific
Candidate Gene
Nachman MW; Hoekstra HE; D'Agostino SL (2003)
The genetic basis of adaptive melanism in pocket mice.
GP00000577
MC1R
Q01726
Morphology
R109W
Chaetodipus intermedius
rock pocket mouse - (species)
Chaetodipus intermedius
rock pocket mouse - (species) D
MC1R
Chaetodipus intermedius
rock pocket mouse - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Chaetodipus intermedius
rock pocket mouse - (species) D
Intraspecific
Candidate Gene
Nachman MW; Hoekstra HE; D'Agostino SL (2003)
The genetic basis of adaptive melanism in pocket mice.
GP00000578
MC1R
Q01726
Morphology
R160W
Chaetodipus intermedius
rock pocket mouse - (species)
Chaetodipus intermedius
rock pocket mouse - (species) D
MC1R
Chaetodipus intermedius
rock pocket mouse - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Chaetodipus intermedius
rock pocket mouse - (species) D
Intraspecific
Candidate Gene
Nachman MW; Hoekstra HE; D'Agostino SL (2003)
The genetic basis of adaptive melanism in pocket mice.
GP00000579
MC1R
Q01726
Morphology
Q233H
Chaetodipus intermedius
rock pocket mouse - (species)
Chaetodipus intermedius
rock pocket mouse - (species) D
MC1R
Chaetodipus intermedius
rock pocket mouse - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species)
Intraspecific
Candidate Gene
Marklund L; Moller MJ; Sandberg K ; et al. (1996)
A missense mutation in the gene for melanocyte-stimulating hormone receptor (MC1R) is associated wit[...]
1 Additional References
GP00000580
MC1R
Q01726
Morphology
S83F
Equus caballus
horse - (species)
Equus caballus
horse - (species)
MC1R
Equus caballus
horse - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
Deletion
Puma yagouaroundi
jaguarundi - (species) D
Intraspecific
Candidate Gene
Eizirik E; Yuhki N; Johnson WE ; et al. (2003)
Molecular genetics and evolution of melanism in the cat family.
GP00000581
MC1R
Q01726
Morphology
Deletion of aa 95-102
Puma yagouaroundi
jaguarundi - (species)
Puma yagouaroundi
jaguarundi - (species) D
MC1R
Puma yagouaroundi
jaguarundi - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
Deletion
N
Mus musculus
house mouse - (species) D
Domesticated
Candidate Gene
Robbins LS; Nadeau JH; Johnson KR ; et al. (1993)
Pigmentation phenotypes of variant extension locus alleles result from point mutations that alter MS[...]
GP00000582
MC1R
Q01726
Morphology
1bp deletion at 183; frameshift & premature stop N
Mus musculus
house mouse - (species)
Mus musculus
house mouse - (species) D
MC1R
Mus musculus
house mouse - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Mus poschiavinus
(species)
Interspecific
Candidate Gene
Robbins LS; Nadeau JH; Johnson KR ; et al. (1993)
Pigmentation phenotypes of variant extension locus alleles result from point mutations that alter MS[...]
GP00000583
MC1R
Q01726
Morphology
S69L
Mus musculus
house mouse - (species)
Mus poschiavinus
(species)
MC1R
Mus poschiavinus
(species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Mus musculus
house mouse - (species)
Domesticated
Candidate Gene
Robbins LS; Nadeau JH; Johnson KR ; et al. (1993)
Pigmentation phenotypes of variant extension locus alleles result from point mutations that alter MS[...]
GP00000584
MC1R
Q01726
Morphology
E92K
Mus musculus
house mouse - (species)
Mus musculus
house mouse - (species)
MC1R
Mus musculus
house mouse - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Mus musculus
house mouse - (species)
Domesticated
Candidate Gene
Robbins LS; Nadeau JH; Johnson KR ; et al. (1993)
Pigmentation phenotypes of variant extension locus alleles result from point mutations that alter MS[...]
GP00000585
MC1R
Q01726
Morphology
L98P
Mus musculus
house mouse - (species)
Mus musculus
house mouse - (species)
MC1R
Mus musculus
house mouse - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Mus musculus
house mouse - (species)
Intraspecific
Candidate Gene
Wada A; Kunieda T; Nishimura M ; et al. (2005 Mar-Apr)
A nucleotide substitution responsible for the tawny coat color mutation carried by the MSKR inbred s[...]
GP00000586
MC1R
Q01726
Morphology
W252C
Mus musculus
house mouse - (species)
Mus musculus
house mouse - (species)
MC1R
Mus musculus
house mouse - (species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
Coding,
Deletion
Numida meleagris
helmeted guineafowl - (species) D
Domesticated
Candidate Gene
Vidal O; Araguas RM; Fernández E ; et al. (2010)
Melanism in guinea fowl (Numida meleagris) is associated with a deletion of Phenylalanine-256 in the[...]
GP00000587
MC1R
Q01726
Morphology
Phe256del
Numida meleagris
helmeted guineafowl - (species)
Numida meleagris
helmeted guineafowl - (species) D
MC1R
Numida meleagris
helmeted guineafowl - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
Deletion
Oryctolagus cuniculus
rabbit - (species) D
Domesticated
Candidate Gene
Fontanesi L; Tazzoli M; Beretti F ; et al. (2006)
Mutations in the melanocortin 1 receptor (MC1R) gene are associated with coat colours in the domesti[...]
GP00000588
MC1R
Q01726
Morphology
6bp in-frame del of 94-95
Oryctolagus cuniculus
rabbit - (species)
Oryctolagus cuniculus
rabbit - (species) D
MC1R
Oryctolagus cuniculus
rabbit - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
Deletion
Oryctolagus cuniculus
rabbit - (species) D
Domesticated
Candidate Gene
Fontanesi L; Tazzoli M; Beretti F ; et al. (2006)
Mutations in the melanocortin 1 receptor (MC1R) gene are associated with coat colours in the domesti[...]
GP00000589
MC1R
Q01726
Morphology
30bp in-frame del of 102-111
Oryctolagus cuniculus
rabbit - (species)
Oryctolagus cuniculus
rabbit - (species) D
MC1R
Oryctolagus cuniculus
rabbit - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
Deletion
Oryctolagus cuniculus
rabbit - (species) D
Domesticated
Candidate Gene
Fontanesi L; Scotti E; Colombo M ; et al. (2010)
A composite six bp in-frame deletion in the melanocortin 1 receptor (MC1R) gene is associated with t[...]
GP00000590
MC1R
Q01726
Morphology
6bp in frame deletion c.[124G>A;125_130del6] + L44T (homozygous state in Japanese, Rhinelander and Dutch tricolour rabbits )
Oryctolagus cuniculus
rabbit - (species)
Oryctolagus cuniculus
rabbit - (species) D
MC1R
Oryctolagus cuniculus
rabbit - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Ovis aries
sheep - (species)
Domesticated
Candidate Gene
Våge DI; Klungland H; Lu D ; et al. (1999)
Molecular and pharmacological characterization of dominant black coat color in sheep.
1 Additional References
GP00000591
MC1R
Q01726
Morphology
D121N
Ovis aries
sheep - (species)
Ovis aries
sheep - (species)
MC1R
Ovis aries
sheep - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Ovis aries
sheep - (species)
Domesticated
Candidate Gene
Våge DI; Klungland H; Lu D ; et al. (1999)
Molecular and pharmacological characterization of dominant black coat color in sheep.
1 Additional References
GP00000592
MC1R
Q01726
Morphology
M73K
Ovis aries
sheep - (species)
Ovis aries
sheep - (species)
MC1R
Ovis aries
sheep - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
Deletion
Panthera onca
jaguar - (species) D
Intraspecific
Candidate Gene
Eizirik E; Yuhki N; Johnson WE ; et al. (2003)
Molecular genetics and evolution of melanism in the cat family.
GP00000593
MC1R
Q01726
Morphology
Deletion of aa 101-105 and L106T
Panthera onca
jaguar - (species)
Panthera onca
jaguar - (species) D
MC1R
Panthera onca
jaguar - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Peromyscus polionotus
oldfield mouse - (species)
Intraspecific
Linkage Mapping
Hoekstra HE; Hirschmann RJ; Bundey RA ; et al. (2006)
A single amino acid mutation contributes to adaptive beach mouse color pattern.
GP00000594
MC1R
Q01726
Morphology
R65C
Peromyscus polionotus
oldfield mouse - (species)
Peromyscus polionotus
oldfield mouse - (species)
MC1R
Peromyscus polionotus
oldfield mouse - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Rattus rattus
black rat - (species)
Interspecific
Candidate Gene
Kambe Y; Tanikawa T; Matsumoto Y ; et al. (2011)
Origin of agouti-melanistic polymorphism in Wild Black Rats (Rattus rattus) inferred from Mc1r gene [...]
GP00000595
MC1R
Q01726
Morphology
Glu93Lys
Rattus tanezumi
Oriental house rat - (species)
Rattus rattus
black rat - (species)
MC1R
Rattus rattus
black rat - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
Deletion
Sciurus carolinensis
gray squirrel - (species) D
Sciurus niger
fox squirrel - (species) D
Intraspecific
Candidate Gene
McRobie H; Thomas A; Kelly J (2009 Nov-Dec)
The genetic basis of melanism in the gray squirrel (Sciurus carolinensis).
1 Additional References
GP00000596
MC1R
Q01726
Morphology
Deletion of 8 a.a.
Sciurus carolinensis
gray squirrel - (species)
Sciurus niger
fox squirrel - (species)
Sciurus carolinensis
gray squirrel - (species) D
Sciurus niger
fox squirrel - (species) D
MC1R
Sciurus carolinensis
gray squirrel - (species)
Sciurus niger
fox squirrel - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Ursus americanus
American black bear - (species)
Intraspecific
Candidate Gene
Ritland K; Newton C; Marshall HD (2001)
Inheritance and population structure of the white-phased "Kermode" black bear.
GP00000597
MC1R
Q01726
Morphology
Y298C
Ursus americanus
American black bear - (species)
Ursus americanus
American black bear - (species)
MC1R
Ursus americanus
American black bear - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Vulpes vulpes
red fox - (species)
Domesticated
Candidate Gene
Våge DI; Lu D; Klungland H ; et al. (1997)
A non-epistatic interaction of agouti and extension in the fox, Vulpes vulpes.
1 Additional References
GP00000598
MC1R
Q01726
Morphology
C125R; constitutively active receptor
Vulpes vulpes
red fox - (species)
Vulpes vulpes
red fox - (species)
MC1R
Vulpes vulpes
red fox - (species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
Coding,
SNP
Anser caerulescens
snow goose - (species)
Intraspecific
Candidate Gene
Mundy NI; Badcock NS; Hart T ; et al. (2004)
Conserved genetic basis of a quantitative plumage trait involved in mate choice.
GP00000599
MC1R
Q01726
Morphology
V85M
Anser caerulescens
snow goose - (species)
Anser caerulescens
snow goose - (species)
MC1R
Anser caerulescens
snow goose - (species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
Coding,
SNP
Coereba flaveola
Bananaquit - (species) D
Intraspecific
Candidate Gene
Theron E; Hawkins K; Bermingham E ; et al. (2001)
The molecular basis of an avian plumage polymorphism in the wild: a melanocortin-1-receptor point mu[...]
GP00000600
MC1R
Q01726
Morphology
E92K
Coereba flaveola
Bananaquit - (species)
Coereba flaveola
Bananaquit - (species) D
MC1R
Coereba flaveola
Bananaquit - (species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
Coding,
SNP
Columba livia
rock pigeon - (species)
Domesticated
Candidate Gene
Guernsey MW; Ritscher L; Miller MA ; et al. (2013)
A Val85Met mutation in melanocortin-1 receptor is associated with reductions in eumelanic pigmentati[...]
GP00000601
MC1R
Q01726
Morphology
Val85Met (G253A)
Columba livia
rock pigeon - (species)
Columba livia
rock pigeon - (species)
MC1R
Columba livia
rock pigeon - (species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
Coding,
SNP
Coturnix japonica
Japanese quail - (species)
Domesticated
Linkage Mapping
Nadeau NJ; Minvielle F; Mundy NI (2006)
Association of a Glu92Lys substitution in MC1R with extended brown in Japanese quail (Coturnix japon[...]
GP00000602
MC1R
Q01726
Morphology
E92K
Coturnix japonica
Japanese quail - (species)
Coturnix japonica
Japanese quail - (species)
MC1R
Coturnix japonica
Japanese quail - (species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
Coding,
Deletion
Falco eleonorae
(species) D
Intraspecific
Candidate Gene
Gangoso L; Grande JM; Ducrest AL ; et al. (2011)
MC1R-dependent, melanin-based colour polymorphism is associated with cell-mediated response in the E[...]
GP00000603
MC1R
Q01726
Morphology
Deletion of 3 a.a.
Falco eleonorae
(species)
Falco eleonorae
(species) D
MC1R
Falco eleonorae
(species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
Coding,
SNP
Falco rusticolus
gyrfalcon - (species)
Intraspecific
Candidate Gene
Johnson JA; Ambers AD; Burnham KK (2012 May-Jun)
Genetics of plumage color in the Gyrfalcon (Falco rusticolus): analysis of the melanocortin-1 recept[...]
GP00000604
MC1R
Q01726
Morphology
Val128Ile
Falco rusticolus
gyrfalcon - (species)
Falco rusticolus
gyrfalcon - (species)
MC1R
Falco rusticolus
gyrfalcon - (species)
Published - Accepted by Curator
MC1R
Coloration (feathers; eyes)
Coding,
SNP
Gallus gallus
chicken - (species)
Domesticated
Linkage Mapping
Takeuchi S; Suzuki H; Yabuuchi M ; et al. (1996)
A possible involvement of melanocortin 1-receptor in regulating feather color pigmentation in the ch[...]
2 Additional References
GP00000605
MC1R
Q01726
Morphology
E92K; constitutive activation
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
MC1R
Gallus gallus
chicken - (species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
Coding,
SNP
Gallus gallus
chicken - (species)
Domesticated
Candidate Gene
Takeuchi S; Suzuki H; Yabuuchi M ; et al. (1996)
A possible involvement of melanocortin 1-receptor in regulating feather color pigmentation in the ch[...]
GP00000606
MC1R
Q01726
Morphology
C33W
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
MC1R
Gallus gallus
chicken - (species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
Coding,
SNP
Gallus gallus
chicken - (species)
Domesticated
Candidate Gene
Takeuchi S; Suzuki H; Yabuuchi M ; et al. (1996)
A possible involvement of melanocortin 1-receptor in regulating feather color pigmentation in the ch[...]
GP00000607
MC1R
Q01726
Morphology
D37G
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
MC1R
Gallus gallus
chicken - (species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
Coding,
SNP
Gallus gallus
chicken - (species)
Domesticated
Candidate Gene
Takeuchi S; Suzuki H; Yabuuchi M ; et al. (1996)
A possible involvement of melanocortin 1-receptor in regulating feather color pigmentation in the ch[...]
GP00000608
MC1R
Q01726
Morphology
L244P
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
MC1R
Gallus gallus
chicken - (species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
Coding,
SNP
Gallus gallus
chicken - (species)
Domesticated
Candidate Gene
Kerje S; Lind J; Schütz K ; et al. (2003)
Melanocortin 1-receptor (MC1R) mutations are associated with plumage colour in chicken.
1 Additional References
GP00000609
MC1R
Q01726
Morphology
H215P
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
MC1R
Gallus gallus
chicken - (species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
Coding,
SNP
Malurus leucopterus
white-winged fairy-wren - (species)
Intraspecific
Candidate Gene
Doucet SM; Shawkey MD; Rathburn MK ; et al. (2004)
Concordant evolution of plumage colour, feather microstructure and a melanocortin receptor gene betw[...]
GP00000610
MC1R
Q01726
Morphology
A16T caused by guanine-to-adenine (G_A) transition at site 46; and/or I38N cause by a tyrosine-to-adenine (T_A) transition at site 113; and/or V11N caused by a G_A transition at site 331; and/or Q157R caused by an A_G substitution at site 470; Val166Ileu - exact causing amino acid change(s) unknown
Malurus leucopterus
white-winged fairy-wren - (species)
Malurus leucopterus
white-winged fairy-wren - (species)
MC1R
Malurus leucopterus
white-winged fairy-wren - (species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
Coding,
SNP
Stercorarius parasiticus
(species)
Intraspecific
Candidate Gene
Mundy NI; Badcock NS; Hart T ; et al. (2004)
Conserved genetic basis of a quantitative plumage trait involved in mate choice.
GP00000611
MC1R
Q01726
Morphology
R230H
Stercorarius parasiticus
(species)
Stercorarius parasiticus
(species)
MC1R
Stercorarius parasiticus
(species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
Coding,
SNP
Sula leucogaster
(species)
Intraspecific
Candidate Gene
Baião PC; Parker PG (2012 May-Jun)
Evolution of the melanocortin-1 receptor (MC1R) in Boobies and Gannets (Aves, Suliformes).
GP00000612
MC1R
Q01726
Morphology
R112H
Sula leucogaster
(species)
Sula leucogaster
(species)
MC1R
Sula leucogaster
(species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
Coding,
SNP
Sula sula
red-footed booby - (species)
Intraspecific
Candidate Gene
Baião PC; Schreiber E; Parker PG (2007 Jul-Aug)
The genetic basis of the plumage polymorphism in red-footed boobies (Sula sula): a melanocortin-1 re[...]
GP00000613
MC1R
Q01726
Morphology
V85M and/or H207R; current data cannot determine which one or if both these substitutions are underlying the phenotypic variation
Sula sula
red-footed booby - (species)
Sula sula
red-footed booby - (species)
MC1R
Sula sula
red-footed booby - (species)
Published - Accepted by Curator
MC1R
Coloration (red hair)
Coding,
SNP
Homo sapiens
human - (species) D
Intraspecific
Candidate Gene
Smith R; Healy E; Siddiqui S ; et al. (1998)
Melanocortin 1 receptor variants in an Irish population.
1 Additional References
GP00000615
MC1R
Q01726
Morphology
R151C
Homo sapiens
human - (species)
Homo sapiens
human - (species) D
MC1R
Homo sapiens
human - (species)
Published - Accepted by Curator
MC1R
Coloration (red hair)
Coding,
SNP
Homo sapiens
human - (species) D
Intraspecific
Candidate Gene
Smith R; Healy E; Siddiqui S ; et al. (1998)
Melanocortin 1 receptor variants in an Irish population.
1 Additional References
GP00000616
MC1R
Q01726
Morphology
D294H
Homo sapiens
human - (species)
Homo sapiens
human - (species) D
MC1R
Homo sapiens
human - (species)
Published - Accepted by Curator
MC1R
Coloration (red hair)
Coding,
SNP
Homo sapiens
human - (species) D
Intraspecific
Candidate Gene
Smith R; Healy E; Siddiqui S ; et al. (1998)
Melanocortin 1 receptor variants in an Irish population.
1 Additional References
GP00000617
MC1R
Q01726
Morphology
R160W
Homo sapiens
human - (species)
Homo sapiens
human - (species) D
MC1R
Homo sapiens
human - (species)
Published - Accepted by Curator
MC1R
Coloration (red hair)
Coding,
SNP
Homo sapiens
human - (species) D
Intraspecific
Association Mapping
Box NF; Wyeth JR; O'Gorman LE ; et al. (1997)
Characterization of melanocyte stimulating hormone receptor variant alleles in twins with red hair.
3 Additional References
GP00000618
MC1R
Q01726
Morphology
Val60Leu
Homo sapiens
human - (species)
Homo sapiens
human - (species) D
MC1R
Homo sapiens
human - (species)
Published - Accepted by Curator
MC1R
Coloration (red hair)
Coding,
SNP
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Sulem P; Gudbjartsson DF; Stacey SN ; et al. (2007)
Genetic determinants of hair, eye and skin pigmentation in Europeans.
1 Additional References
GP00000619
MC1R
Q01726
Morphology
Asp84Glu
Homo sapiens
human - (species)
Homo sapiens
human - (species)
MC1R
Homo sapiens
human - (species)
Published - Accepted by Curator
MC1R
Coloration (red hair)
Coding,
SNP
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Sulem P; Gudbjartsson DF; Stacey SN ; et al. (2007)
Genetic determinants of hair, eye and skin pigmentation in Europeans.
1 Additional References
GP00000620
MC1R
Q01726
Morphology
Val92Met
Homo sapiens
human - (species)
Homo sapiens
human - (species)
MC1R
Homo sapiens
human - (species)
Published - Accepted by Curator
MC1R
Coloration (red hair)
Coding,
SNP
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Sulem P; Gudbjartsson DF; Stacey SN ; et al. (2007)
Genetic determinants of hair, eye and skin pigmentation in Europeans.
1 Additional References
GP00000621
MC1R
Q01726
Morphology
Arg142His
Homo sapiens
human - (species)
Homo sapiens
human - (species)
MC1R
Homo sapiens
human - (species)
Published - Accepted by Curator
MC1R
Coloration (red hair)
Coding,
SNP
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Sulem P; Gudbjartsson DF; Stacey SN ; et al. (2007)
Genetic determinants of hair, eye and skin pigmentation in Europeans.
1 Additional References
GP00000622
MC1R
Q01726
Morphology
Arg151Cys
Homo sapiens
human - (species)
Homo sapiens
human - (species)
MC1R
Homo sapiens
human - (species)
Published - Accepted by Curator
MC1R
Coloration (red hair)
Coding,
SNP
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Sulem P; Gudbjartsson DF; Stacey SN ; et al. (2007)
Genetic determinants of hair, eye and skin pigmentation in Europeans.
1 Additional References
GP00000623
MC1R
Q01726
Morphology
Ile155Thr
Homo sapiens
human - (species)
Homo sapiens
human - (species)
MC1R
Homo sapiens
human - (species)
Published - Accepted by Curator
MC1R
Coloration (red hair)
Coding,
SNP
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Sulem P; Gudbjartsson DF; Stacey SN ; et al. (2007)
Genetic determinants of hair, eye and skin pigmentation in Europeans.
1 Additional References
GP00000624
MC1R
Q01726
Morphology
Arg160Trp
Homo sapiens
human - (species)
Homo sapiens
human - (species)
MC1R
Homo sapiens
human - (species)
Published - Accepted by Curator
MC1R
Coloration (red hair)
Coding,
SNP
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Sulem P; Gudbjartsson DF; Stacey SN ; et al. (2007)
Genetic determinants of hair, eye and skin pigmentation in Europeans.
1 Additional References
GP00000625
MC1R
Q01726
Morphology
Arg163Gln
Homo sapiens
human - (species)
Homo sapiens
human - (species)
MC1R
Homo sapiens
human - (species)
Published - Accepted by Curator
MC1R
Coloration (red hair)
Coding,
SNP
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Sulem P; Gudbjartsson DF; Stacey SN ; et al. (2007)
Genetic determinants of hair, eye and skin pigmentation in Europeans.
1 Additional References
GP00000626
MC1R
Q01726
Morphology
Asp294His
Homo sapiens
human - (species)
Homo sapiens
human - (species)
MC1R
Homo sapiens
human - (species)
Published - Accepted by Curator
MC1R
Coloration (scales)
Coding,
SNP
Aspidoscelis inornatus
Little striped whiptail - (species)
Intraspecific
Candidate Gene
Rosenblum EB; Hoekstra HE; Nachman MW (2004)
Adaptive reptile color variation and the evolution of the Mc1r gene.
1 Additional References
GP00000627
MC1R
Q01726
Morphology
I170T
Aspidoscelis inornatus
Little striped whiptail - (species)
Aspidoscelis inornatus
Little striped whiptail - (species)
MC1R
Aspidoscelis inornatus
Little striped whiptail - (species)
Published - Accepted by Curator
MC1R
Coloration (scales)
Coding,
SNP
Holbrookia maculata
lesser earless lizard - (species)
Intraspecific
Candidate Gene
Rosenblum EB; Hoekstra HE; Nachman MW (2004)
Adaptive reptile color variation and the evolution of the Mc1r gene.
1 Additional References
GP00000628
MC1R
Q01726
Morphology
V168I; but failed functional validation in Rosenblum et al. 2010
Holbrookia maculata
lesser earless lizard - (species)
Holbrookia maculata
lesser earless lizard - (species)
MC1R
Holbrookia maculata
lesser earless lizard - (species)
Published - Accepted by Curator
MC1R
Coloration (scales)
Coding,
SNP
Sceloporus undulatus
fence lizard - (species)
Intraspecific
Candidate Gene
Rosenblum EB; Römpler H; Schöneberg T ; et al. (2010)
Molecular and functional basis of phenotypic convergence in white lizards at White Sands.
GP00000629
MC1R
Q01726
Morphology
H208Y
Sceloporus undulatus
fence lizard - (species)
Sceloporus undulatus
fence lizard - (species)
MC1R
Sceloporus undulatus
fence lizard - (species)
Published - Accepted by Curator
MC1R
Coloration (skin)
Coding,
SNP
Homo sapiens
human - (species)
Intraspecific
Candidate Gene
Lalueza-Fox C; Römpler H; Caramelli D ; et al. (2007)
A melanocortin 1 receptor allele suggests varying pigmentation among Neanderthals.
GP00000630
MC1R
Q01726
Morphology
Arg307Gly
Homo sapiens
human - (species)
Homo sapiens
human - (species)
MC1R
Homo sapiens
human - (species)
Published - Accepted by Curator
MC1R
Coloration (skin)
Coding,
Insertion
N
Sus scrofa domesticus
domestic pig - (subspecies) D
Domesticated
Linkage Mapping
Kijas JM; Moller M; Plastow G ; et al. (2001)
A frameshift mutation in MC1R and a high frequency of somatic reversions cause black spotting in pig[...]
1 Additional References
GP00000631
MC1R
Q01726
Morphology
2bp insertion at 23 generates early stop @ 56 & D"121"N ? N
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies) D
MC1R
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
MC1R
Coloration (skin)
Coding,
SNP
Sus scrofa domesticus
domestic pig - (subspecies)
Domesticated
Candidate Gene
Kijas JM; Wales R; Törnsten A ; et al. (1998)
Melanocortin receptor 1 (MC1R) mutations and coat color in pigs.
1 Additional References
GP00000632
MC1R
Q01726
Morphology
V"92"M actually at 95
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies)
MC1R
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
MC1R
Coloration (skin)
Coding,
SNP
Sus scrofa domesticus
domestic pig - (subspecies)
Domesticated
Candidate Gene
Kijas JM; Wales R; Törnsten A ; et al. (1998)
Melanocortin receptor 1 (MC1R) mutations and coat color in pigs.
1 Additional References
GP00000633
MC1R
Q01726
Morphology
D"121"N Actually 124
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies)
MC1R
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
MC1R
Coloration (skin)
Coding,
SNP
Sus scrofa domesticus
domestic pig - (subspecies)
Domesticated
Candidate Gene
Kijas JM; Wales R; Törnsten A ; et al. (1998)
Melanocortin receptor 1 (MC1R) mutations and coat color in pigs.
1 Additional References
GP00000634
MC1R
Q01726
Morphology
A"161"V actually 164
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies)
MC1R
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
MC1R
Coloration (skin)
Coding,
SNP
Sus scrofa domesticus
domestic pig - (subspecies)
Domesticated
Candidate Gene
Kijas JM; Wales R; Törnsten A ; et al. (1998)
Melanocortin receptor 1 (MC1R) mutations and coat color in pigs.
1 Additional References
GP00000635
MC1R
Q01726
Morphology
L"99" P Actually 102
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies)
MC1R
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
MC1R
Coloration (skin)
Coding,
SNP
Sus scrofa domesticus
domestic pig - (subspecies)
Domesticated
Candidate Gene
Kijas JM; Wales R; Törnsten A ; et al. (1998)
Melanocortin receptor 1 (MC1R) mutations and coat color in pigs.
1 Additional References
GP00000636
MC1R
Q01726
Morphology
A"240"T actually 243
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies)
MC1R
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
Deletion
Felis catus
domestic cat - (species) D
Domesticated
Candidate Gene
Gustafson NA; Gandolfi B; Lyons LA (2017)
Not another type of potato: MC1R and the russet coloration of Burmese cats.
GP00001330
MC1R
Q01726
Morphology
3bp deletion at c.439-441del (p.Phe146del)
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
MC1R
Felis catus
domestic cat - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Monarcha castaneiventris
Makira monarch - (species) D
Intraspecific
Association Mapping
Uy JA; Cooper EA; Cutie S ; et al. (2016)
Mutations in different pigmentation genes are associated with parallel melanism in island flycatcher[...]
GP00001333
MC1R
Q01726
Morphology
Asp119Asn
Monarcha castaneiventris
Makira monarch - (species)
Monarcha castaneiventris
Makira monarch - (species) D
MC1R
Monarcha castaneiventris
Makira monarch - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Sus scrofa domesticus
domestic pig - (subspecies) D
Domesticated
Candidate Gene
Rubin CJ; Megens HJ; Martinez Barrio A ; et al. (2012)
Strong signatures of selection in the domestic pig genome.
1 Additional References
GP00001337
MC1R
Q01726
Morphology
c.G>A p.Asp124Asn
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies) D
MC1R
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Arctocephalus gazella
antarctic fur seal - (species) D
Intraspecific
Candidate Gene
Norris BJ; Whan VA (2008)
A gene duplication affecting expression of the ovine ASIP gene is responsible for white and black sh[...]
GP00001338
MC1R
Q01726
Morphology
c.C>T p.Ser291Phe
Arctocephalus gazella
antarctic fur seal - (species)
Arctocephalus gazella
antarctic fur seal - (species) D
MC1R
Arctocephalus gazella
antarctic fur seal - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Tyto alba
Barn owl - (species) D
Intraspecific
Candidate Gene
San-Jose LM; Ducrest AL; Ducret V ; et al. (2015)
Effect of the MC1R gene on sexual dimorphism in melanin-based colorations.
3 Additional References
GP00001339
MC1R
Q01726
Morphology
p.Val126Ile
Tyto alba
Barn owl - (species)
Tyto alba
Barn owl - (species) D
R
MC1R
Tyto alba
Barn owl - (species)
Reviewed
September 26, 2019 17:00
MC1R
Coloration (coat)
2 Mutations:
Coding
SNP
Rangifer tarandus
reindeer - (species) D
Domesticated
Candidate Gene
Våge DI; Nieminen M; Anderson DG ; et al. (2014)
Two missense mutations in melanocortin 1 receptor (MC1R) are strongly associated with dark ventral c[...]
GP00001350
Mc1r
Q01727
Morphology
2 mutations
Rangifer tarandus
reindeer - (species)
Rangifer tarandus
reindeer - (species) D
MC1R
Rangifer tarandus
reindeer - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Equus asinus
ass - (species) D
Domesticated
Candidate Gene
Abitbol M; Legrand R; Tiret L (2014)
A missense mutation in melanocortin 1 receptor is associated with the red coat colour in donkeys.
GP00001351
Mc1r
Q01727
Morphology
c.629T>C p.Met210Thr
Equus asinus
ass - (species)
Equus asinus
ass - (species) D
MC1R
Equus asinus
ass - (species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
Coding,
SNP
Anas platyrhynchos
mallard - (species) D
Domesticated
Candidate Gene
Yu W; Wang C; Xin Q ; et al. (2013)
Non-synonymous SNPs in MC1R gene are associated with the extended black variant in domestic ducks (A[...]
GP00001352
Mc1r
Q01727
Morphology
c.52G>A p.Glu18Lys
Anas platyrhynchos
mallard - (species)
Anas platyrhynchos
mallard - (species) D
MC1R
Anas platyrhynchos
mallard - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Capra hircus
goat - (species) D
Domesticated
Candidate Gene
Fontanesi L; Beretti F; Riggio V ; et al. (2009)
Missense and nonsense mutations in melanocortin 1 receptor (MC1R) gene of different goat breeds: ass[...]
GP00001353
Mc1r
Q01727
Morphology
c.801C>G p.Cys267Trp
Capra hircus
goat - (species)
Capra hircus
goat - (species) D
MC1R
Capra hircus
goat - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
N
Bos grunniens
domestic yak - (species) D
Domesticated
Candidate Gene
Zhang MQ; Xu X; Luo SJ (2014)
The genetics of brown coat color and white spotting in domestic yaks (Bos grunniens).
GP00001354
Mc1r
Q01727
Morphology
p.Gln34* and p.Met73Leu and p.Arg142Pro - p.Met73Leu and p.Arg142Pro were only found in heterozygous and their association with phenotype is supposed but not sure N
Bos grunniens
domestic yak - (species)
Bos grunniens
domestic yak - (species) D
MC1R
Bos grunniens
domestic yak - (species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
Coding,
SNP
Stercorarius parasiticus
(species)
Intraspecific
Candidate Gene
Janssen K; Mundy NI (2013)
Molecular population genetics of the melanic plumage polymorphism in Arctic skuas (Stercorarius para[...]
GP00001355
Mc1r
Q01727
Morphology
Melanic and nonmelanic haplotypes in the Arctic skua are defined by three amino acid changes: nonmelanic: His8-Glu12-Arg230; melanic: Arg8-Lys12-His230. The effect of each single amino acid change has not been tested
Stercorarius parasiticus
(species)
Stercorarius parasiticus
(species)
MC1R
Stercorarius parasiticus
(species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
3 Mutations:
Coding
SNP
Ramphastos dicolorus
(species) D
Ramphastos vitellinus
(species) D
Ramphastos tucanus
(species) D
Ramphastos toco
(species) D
Interspecific
Candidate Gene
Corso J; Mundy NI; Fagundes NJ ; et al. (2016)
Evolution of dark colour in toucans (Ramphastidae): a case of molecular adaptation?
GP00001367
Mc1r
Q01727
Morphology
3 mutations
Ramphastidae
(family)
Ramphastos dicolorus
(species) D
Ramphastos vitellinus
(species) D
Ramphastos tucanus
(species) D
Ramphastos toco
(species) D
MC1R
Ramphastos dicolorus
(species)
Ramphastos vitellinus
(species)
Ramphastos tucanus
(species)
Ramphastos toco
(species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
Coding,
SNP
Calidris pugnax
ruff - (species) D
Intraspecific
Association Mapping
Lamichhaney S; Fan G; Widemo F ; et al. (2016)
Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pug[...]
1 Additional References
GP00001466
MC1R
Q01726
Morphology
Several amino acid changes. The His207Arg substitution most likely has functional consequences because the same variant is associated with light color in the red-footed booby.
Calidris pugnax
ruff - (species)
Calidris pugnax
ruff - (species) D
MC1R
Calidris pugnax
ruff - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Leopardus geoffroyi
Geoffroy's cat - (species) D
Intraspecific
Candidate Gene
Schneider A; Henegar C; Day K ; et al. (2015)
Recurrent evolution of melanism in South American felids.
GP00001733
MC1R
Q01726
Morphology
All melanistic individuals were heterozygous for four variants that predicted three nonsynonymous substitutions, p.C125R, p.T177I, and p.G194S - In the laboratory mouse a Cys to Arg substitution at the site homologous to felid residue 125 causes constitutive activation of the receptor and the exact same change is thought to be responsible for melanism in the Alaska silver fox - therefore C125R is considered to be the likely causative alteration in the Geoffroy’s cat.
Leopardus geoffroyi
Geoffroy's cat - (species)
Leopardus geoffroyi
Geoffroy's cat - (species) D
MC1R
Leopardus geoffroyi
Geoffroy's cat - (species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
Coding,
SNP
Meleagris gallopavo mexicana
(subspecies) D
Domesticated
Candidate Gene
Vidal O; Viñas J; Pla C (2010)
Variability of the melanocortin 1 receptor (MC1R) gene explains the segregation of the bronze locus [...]
GP00002299
MC1R
Q01726
Morphology
c.364A>T p.I122F
Meleagris gallopavo mexicana
(subspecies)
Meleagris gallopavo mexicana
(subspecies) D
MC1R
Meleagris gallopavo mexicana
(subspecies)
Published - Accepted by Curator
MC1R
Coloration (feathers)
2 Mutations:
Coding
SNP
Meleagris gallopavo mexicana
(subspecies) D
Domesticated
Candidate Gene
Vidal O; Viñas J; Pla C (2010)
Variability of the melanocortin 1 receptor (MC1R) gene explains the segregation of the bronze locus [...]
GP00002300
MC1R
Q01726
Morphology
2 mutations
Meleagris gallopavo mexicana
(subspecies)
Meleagris gallopavo mexicana
(subspecies) D
MC1R
Meleagris gallopavo mexicana
(subspecies)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
Deletion
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Dürig N; Letko A; Lepori V ; et al. (2018)
Two MC1R loss-of-function alleles in cream-coloured Australian Cattle Dogs and white Huskies.
GP00002301
MC1R
Q01726
Morphology
2-bp deletion in the coding sequence c.816_817delCT N
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
MC1R
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
MC1R
Coloration (coat)
Cis-regulatory,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Dürig N; Letko A; Lepori V ; et al. (2018)
Two MC1R loss-of-function alleles in cream-coloured Australian Cattle Dogs and white Huskies.
GP00002302
MC1R
Q01726
Morphology
single nucleotide variant within the MITF binding site of the canine MC1R promoter
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
MC1R
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Dreger DL; Schmutz SM (2010 Sep-Oct)
A new mutation in MC1R explains a coat color phenotype in 2 "old" breeds: Saluki and Afghan hound.
GP00002303
MC1R
Q01726
Morphology
c.233G>T p.G78V N
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
MC1R
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
MC1R
Coloration (feathers; eyes)
Coding,
SNP
Gallus gallus
chicken - (species)
Domesticated
Candidate Gene
Dávila SG; Gil MG; Resino-Talaván P ; et al. (2014)
Association between polymorphism in the melanocortin 1 receptor gene and E locus plumage color pheno[...]
GP00002390
MC1R
Q01726
Morphology
the Arg213Cys mutation may be the cause of the loss or the decrease of function of the receptor to produce eumelanin
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
MC1R
Gallus gallus
chicken - (species)
Published - Accepted by Curator
MdMYB10
Coloration (fruit flesh; foliage)
Cis-regulatory,
Unknown
Malus domestica
apple - (species)
Domesticated
Linkage Mapping
Chagné D; Carlisle CM; Blond C ; et al. (2007)
Mapping a candidate gene (MdMYB10) for red flesh and foliage colour in apple.
1 Additional References
GP00000639
MYB1
A0SQ35
Morphology
unknown
Malus domestica
apple - (species)
Malus domestica
apple - (species)
MdMYB10
Malus domestica
apple - (species)
Published - Accepted by Curator
MdMYB110a
Coloration (fruit flesh)
Cis-regulatory,
Unknown
Malus domestica
apple - (species)
Domesticated
Linkage Mapping
Chagné D; Lin-Wang K; Espley RV ; et al. (2013)
An ancient duplication of apple MYB transcription factors is responsible for novel red fruit-flesh p[...]
GP00000640
K4FA06
Morphology
unknown
Malus domestica
apple - (species)
Malus domestica
apple - (species)
MdMYB110a
Malus domestica
apple - (species)
Published - Accepted by Curator
Melanophilin (MLPH)
Coloration (coat)
Coding,
Deletion
N
Bos taurus
cattle - (species) D
Domesticated
Candidate Gene
Li W; Sartelet A; Tamma N ; et al. (2016)
Reverse genetic screen for loss-of-function mutations uncovers a frameshifting deletion in the melan[...]
GP00000642
Mlph
Q91V27
Morphology
10bp deletion in exon1 ; c.87_96del p.Glu32Aspfs*1 N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Melanophilin (MLPH)
Bos taurus
cattle - (species)
Published - Accepted by Curator
Melanophilin (MLPH)
Coloration (coat)
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Bauer A; Kehl A; Jagannathan V ; et al. (2018)
A novel MLPH variant in dogs with coat colour dilution.
GP00000643
Mlph
Q91V27
Morphology
c.705G>C p.Gln235His
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
Melanophilin (MLPH)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Melanophilin (MLPH)
Coloration (coat)
Coding,
Deletion
N
Felis catus
domestic cat - (species) D
Domesticated
Linkage Mapping
Ishida Y; David VA; Eizirik E ; et al. (2006)
A homozygous single-base deletion in MLPH causes the dilute coat color phenotype in the domestic cat[...]
GP00000644
Mlph
Q91V27
Morphology
1bp deletion resulting in frameshift c.83delT N
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
Melanophilin (MLPH)
Felis catus
domestic cat - (species)
Published - Accepted by Curator
Melanophilin (MLPH)
Coloration (coat)
Coding,
SNP
Gallus gallus
chicken - (species) D
Domesticated
Candidate Gene
Vaez M; Follett SA; Bed'hom B ; et al. (2008)
A single point-mutation within the melanophilin gene causes the lavender plumage colour dilution phe[...]
GP00000645
Mlph
Q91V27
Morphology
c.103C>T p.R35W
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
Melanophilin (MLPH)
Gallus gallus
chicken - (species)
Published - Accepted by Curator
Melanophilin (MLPH)
Coloration (coat)
Coding,
Deletion
N
Neovison vison
American mink - (species) D
Domesticated
Candidate Gene
Cirera S; Markakis MN; Christensen K ; et al. (2013)
New insights into the melanophilin (MLPH) gene controlling coat color phenotypes in American mink.
GP00000646
Mlph
Q91V27
Morphology
deletion including intron 7 and exon 8 N
Neovison vison
American mink - (species)
Neovison vison
American mink - (species) D
Melanophilin (MLPH)
Neovison vison
American mink - (species)
Published - Accepted by Curator
Melanophilin (MLPH)
Coloration (coat)
Coding,
SNP
Neovison vison
American mink - (species) D
Domesticated
Candidate Gene
Cirera S; Markakis MN; Christensen K ; et al. (2013)
New insights into the melanophilin (MLPH) gene controlling coat color phenotypes in American mink.
1 Additional References
GP00000647
Mlph
Q91V27
Morphology
Splice donor site variation in exon 8 resulting in a premature stop codon c.901+1G>A
Neovison vison
American mink - (species)
Neovison vison
American mink - (species) D
Melanophilin (MLPH)
Neovison vison
American mink - (species)
Published - Accepted by Curator
Melanophilin (MLPH)
Coloration (coat)
Coding,
Deletion
N
Oryctolagus
(genus) D
Domesticated
Candidate Gene
Fontanesi L; Scotti E; Allain D ; et al. (2014)
A frameshift mutation in the melanophilin gene causes the dilute coat colour in rabbit (Oryctolagus [...]
GP00000648
Mlph
Q91V27
Morphology
1bp deletion resulting in frameshift N
Oryctolagus
(genus)
Oryctolagus
(genus) D
Melanophilin (MLPH)
Oryctolagus
(genus)
Published - Accepted by Curator
Melanophilin (MLPH)
Coloration (coat)
Coding,
SNP
Oryctolagus
(genus) D
Domesticated
Candidate Gene
Lehner S; Gähle M; Dierks C ; et al. (2013)
Two-exon skipping within MLPH is associated with coat color dilution in rabbits.
GP00000649
Mlph
Q91V27
Morphology
c.111-5C>A (exon skipping resulting in frameshift and truncated protein)
Oryctolagus
(genus)
Oryctolagus
(genus) D
Melanophilin (MLPH)
Oryctolagus
(genus)
Published - Accepted by Curator
Melanophilin (MLPH)
Coloration (feathers)
Unknown,
Complex Change
Coturnix japonica
Japanese quail - (species)
Domesticated
Linkage Mapping
Minvielle F; Cecchi T; Passamonti P ; et al. (2009)
Plumage colour mutations and melanins in the feathers of the Japanese quail: a first comparison.
1 Additional References
GP00000650
Mlph
Q91V27
Morphology
Large deletions and rearrangement with pseudogenization of MLPH and loss of two other genes
Coturnix japonica
Japanese quail - (species)
Coturnix japonica
Japanese quail - (species)
Melanophilin (MLPH)
Coturnix japonica
Japanese quail - (species)
Published - Accepted by Curator
Melanophilin (MLPH)
Coloration (coat)
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Linkage Mapping
Drögemüller C; Philipp U; Haase B ; et al. (2007)
A noncoding melanophilin gene (MLPH) SNP at the splice donor of exon 1 represents a candidate causal[...]
GP00002330
Mlph
Q91V27
Morphology
GA substitution at splice donor site causing Splicing defect
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
Melanophilin (MLPH)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Melanophilin (MLPH)
Coloration (coat)
Coding,
Insertion
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Van Buren SL; Minor KM; Grahn RA ; et al. (2020)
A Third MLPH Variant Causing Coat Color Dilution in Dogs.
GP00002331
Mlph
Q91V27
Morphology
c.667_668insC p.(His223Profs*41) N
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
Melanophilin (MLPH)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Melanophilin (MLPH)
Coloration (coat)
Coding,
Deletion
N
Oryctolagus cuniculus
rabbit - (species) D
Domesticated
Candidate Gene
Lehner S; Gähle M; Dierks C ; et al. (2013)
Two-exon skipping within MLPH is associated with coat color dilution in rabbits.
GP00002332
Mlph
Q91V27
Morphology
c.585delG p.L195LfsX123* N
Oryctolagus cuniculus
rabbit - (species)
Oryctolagus cuniculus
rabbit - (species) D
Melanophilin (MLPH)
Oryctolagus cuniculus
rabbit - (species)
Published - Accepted by Curator
MFSD12
Coloration (coat)
Coding,
Insertion
N
Equus caballus
horse - (species) D
Domesticated
Association Mapping
Tanaka J; Leeb T; Rushton J ; et al. (2019)
Frameshift Variant in MFSD12 Explains the Mushroom Coat Color Dilution in Shetland Ponies.
GP00002243
MFSD12
Q6NUT3
Morphology
p.(Asp201fs) due to c.600Cins N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
MFSD12
Equus caballus
horse - (species)
Published - Accepted by Curator
MFSD12
Coloration (coat)
Coding,
SNP
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Hédan B; Cadieu E; Botherel N ; et al. (2019)
Identification of a Missense Variant in MFSD12 Involved in Dilution of Phaeomelanin Leading to White[...]
GP00002244
MFSD12
Q6NUT3
Morphology
c.151C>T p.Arg51Cys N
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
MFSD12
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
MFSD12
Coloration (skin)
Coding,
SNP
N
Homo sapiens
human - (species) D
Intraspecific
Association Mapping
Adhikari K; Mendoza-Revilla J; Sohail A ; et al. (2019)
A GWAS in Latin Americans highlights the convergent evolution of lighter skin pigmentation in Eurasi[...]
1 Additional References
GP00002245
MFSD12
Q6NUT3
Morphology
Y182H N
Homo sapiens
human - (species)
Homo sapiens
human - (species) D
MFSD12
Homo sapiens
human - (species)
Published - Accepted by Curator
MFSD12
Coloration (skin)
Cis-regulatory,
Complex Change
N
Homo sapiens
human - (species) D
Intraspecific
Association Mapping
Crawford NG; Kelly DE; Hansen MEB ; et al. (2017)
Loci associated with skin pigmentation identified in African populations.
GP00002246
MFSD12
Q6NUT3
Morphology
eight potentially causal SNPs cluster in two regions: one within MFSD12 (intronic SNP and synonymous SNP in exon 9) and the other ~7600 to 9000 base pairs (bp) upstream of MFSD12 ; many SNPs are in predicted regulatory regions active in melanocytes and/or keratinocytes show enhancer activity in luciferase expression assays N
Homo sapiens
human - (species)
Homo sapiens
human - (species) D
MFSD12
Homo sapiens
human - (species)
Published - Accepted by Curator
Microphtalmia-associated transcription factor
Coloration (coat)
Unknown,
Unknown
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Fontanesi L; Scotti E; Russo V (2012)
Haplotype variability in the bovine MITF gene and association with piebaldism in Holstein and Simmen[...]
2 Additional References
GP00000656
Mitf
Q08874
Morphology
unknown but association with intronic variant
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Microphtalmia-associated transcription factor
Bos taurus
cattle - (species)
Published - Accepted by Curator
Microphtalmia-associated transcription factor
Coloration (coat)
Cis-regulatory,
Deletion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Karlsson EK; Baranowska I; Wade CM ; et al. (2007)
Efficient mapping of mendelian traits in dogs through genome-wide association.
1 Additional References
GP00000657
Mitf
Q08874
Morphology
g.21836232_21836427ins>del - this SINE-insertion variant is the first of three possible regulatory variants described by Karlsson et al. (2007). Its genomic location and description were kindly provided by Professor Claire Wade in August 2018. OMIA 000214-9615
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
Microphtalmia-associated transcription factor
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Microphtalmia-associated transcription factor
Coloration (coat)
Cis-regulatory,
Insertion
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Hauswirth R; Haase B; Blatter M ; et al. (2012)
Mutations in MITF and PAX3 cause "splashed white" and other white spotting phenotypes in horses.
GP00000658
Mitf
Q08874
Morphology
11bp insertion in melanocyte-specific promoter; disrupting PAX3 binding site
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Microphtalmia-associated transcription factor
Equus caballus
horse - (species)
Published - Accepted by Curator
Microphtalmia-associated transcription factor
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Hauswirth R; Haase B; Blatter M ; et al. (2012)
Mutations in MITF and PAX3 cause "splashed white" and other white spotting phenotypes in horses.
GP00000659
Mitf
Q08874
Morphology
c.629A>G N310S yielding defective DNA-binding
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Microphtalmia-associated transcription factor
Equus caballus
horse - (species)
Published - Accepted by Curator
Microphtalmia-associated transcription factor
Coloration (feathers)
Coding,
Deletion
N
Coturnix japonica
Japanese quail - (species) D
Domesticated
Candidate Gene
Minvielle F; Bed'hom B; Coville JL ; et al. (2010)
The "silver" Japanese quail and the MITF gene: causal mutation, associated traits and homology with [...]
1 Additional References
GP00000660
Mitf
Q08874
Morphology
2bp deletion N
Coturnix japonica
Japanese quail - (species)
Coturnix japonica
Japanese quail - (species) D
Microphtalmia-associated transcription factor
Coturnix japonica
Japanese quail - (species)
Published - Accepted by Curator
Microphtalmia-associated transcription factor
Coloration (feathers)
Cis-regulatory,
Insertion
Anas platyrhynchos
mallard - (species) D
Domesticated
Linkage Mapping
Zhou Z; Li M; Cheng H ; et al. (2018)
An intercross population study reveals genes associated with body size and plumage color in ducks.
GP00002127
Mitf
Q08874
Morphology
6.6kb insertion between exon 1M and exon 2, leads to lower expression of isoform MITF M in pekin white ducks
Anas platyrhynchos
mallard - (species)
Anas platyrhynchos
mallard - (species) D
Microphtalmia-associated transcription factor
Anas platyrhynchos
mallard - (species)
Published - Accepted by Curator
Microphtalmia-associated transcription factor
Coloration (coat)
Coding,
Deletion
N
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Hauswirth R; Haase B; Blatter M ; et al. (2012)
Mutations in MITF and PAX3 cause "splashed white" and other white spotting phenotypes in horses.
GP00002322
Mitf
Q08874
Morphology
c.519_523delGTGTC p.C174Sfs*20 N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Microphtalmia-associated transcription factor
Equus caballus
horse - (species)
Published - Accepted by Curator
Microphtalmia-associated transcription factor
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Dürig N; Jude R; Jagannathan V ; et al. (2017)
A novel MITF variant in a white American Standardbred foal.
GP00002323
Mitf
Q08874
Morphology
c.731G>A p.G244E
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Microphtalmia-associated transcription factor
Equus caballus
horse - (species)
Published - Accepted by Curator
Microphtalmia-associated transcription factor
Coloration (coat)
Coding,
Deletion
N
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Henkel J; Lafayette C; Brooks SA ; et al. (2019)
Whole-genome sequencing reveals a large deletion in the MITF gene in horses with white spotted coat [...]
GP00002324
Mitf
Q08874
Morphology
~63-kb deletion spanning exons 6-9 N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Microphtalmia-associated transcription factor
Equus caballus
horse - (species)
Published - Accepted by Curator
Microphtalmia-associated transcription factor
Coloration (coat)
Coding,
Deletion
N
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Magdesian KG; Tanaka J; Bellone RR (2020)
A De Novo MITF Deletion Explains a Novel Splashed White Phenotype in an American Paint Horse.
GP00002325
Mitf
Q08874
Morphology
8.7 kb deletion N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Microphtalmia-associated transcription factor
Equus caballus
horse - (species)
Published - Accepted by Curator
Microphtalmia-associated transcription factor
Coloration (coat)
Unknown,
Unknown
Bos taurus
cattle - (species) D
Domesticated
Association Mapping
Hofstetter S; Seefried F; Häfliger IM ; et al. (2019)
A non-coding regulatory variant in the 5'-region of the MITF gene is associated with white-spotted c[...]
GP00002326
Mitf
Q08874
Morphology
unknown based SNP association
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Microphtalmia-associated transcription factor
Bos taurus
cattle - (species)
Published - Accepted by Curator
Microphtalmia-associated transcription factor
Coloration (coat)
Coding,
SNP
N
Bubalus bubalis
water buffalo - (species) D
Domesticated
Candidate Gene
Yusnizar Y; Wilbe M; Herlino AO ; et al. (2015)
Microphthalmia-associated transcription factor mutations are associated with white-spotted coat colo[...]
GP00002327
Mitf
Q08874
Morphology
c.328C>T p.R110* N
Bubalus bubalis
water buffalo - (species)
Bubalus bubalis
water buffalo - (species) D
Microphtalmia-associated transcription factor
Bubalus bubalis
water buffalo - (species)
Published - Accepted by Curator
Microphtalmia-associated transcription factor
Coloration (coat)
Coding,
SNP
N
Bubalus bubalis
water buffalo - (species) D
Domesticated
Candidate Gene
Yusnizar Y; Wilbe M; Herlino AO ; et al. (2015)
Microphthalmia-associated transcription factor mutations are associated with white-spotted coat colo[...]
GP00002328
Mitf
Q08874
Morphology
donor splice-site mutation leads to aberrant splicing of exon 8 that encodes part of a highly conserved region of MITF N
Bubalus bubalis
water buffalo - (species)
Bubalus bubalis
water buffalo - (species) D
Microphtalmia-associated transcription factor
Bubalus bubalis
water buffalo - (species)
Published - Accepted by Curator
Microphtalmia-associated transcription factor a (MITFA)
Coloration (amelanism)
Cis-regulatory,
Deletion
Betta splendens
Siamese fighting fish - (species) D
Domesticated
Linkage Mapping
Wang L; Sun F; Wan ZY ; et al. (2021)
Genomic Basis of Striking Fin Shapes and Colors in the Fighting Fish.
GP00002379
Q6P0E9NULL
Morphology
"Comparison between homozygous albino and wild-type pigmented fish revealed a cluster of indels and SNPs about 25 kb upstream of mitfa, including a 366-bp deletion in the albino mutant. Genotyping this deletion in ∼1,000 fish revealed that this deletion was strictly correlated with the albino phenotype (supplementary fig. S14 and table S9, Supplementary Material online). These data suggest that the 366-bp deletion is a distant cis-regulatory element and could underlie the albino phenotype."
Betta splendens
Siamese fighting fish - (species)
Betta splendens
Siamese fighting fish - (species) D
Microphtalmia-associated transcription factor a (MITFA)
Betta splendens
Siamese fighting fish - (species)
Published - Accepted by Curator
miR-15a-16
Body size (weight)
Cis-regulatory,
Insertion
N
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Jia X; Lin H; Nie Q ; et al. (2016)
A short insertion mutation disrupts genesis of miR-16 and causes increased body weight in domesticat[...]
GP00002247
Morphology
54-bp insertion introducing splicing site that affect the mature transcript N
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
miR-15a-16
Gallus gallus
chicken - (species)
Published - Accepted by Curator
mir-92a
Trichome pattern (leg)
Cis-regulatory,
Unknown
Drosophila melanogaster
fruit fly - (species)
Intraspecific
Linkage Mapping
Arif S; Murat S; Almudi I ; et al. (2013)
Evolution of mir-92a underlies natural morphological variation in Drosophila melanogaster.
GP00000661
Morphology
Not identified
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species)
mir-92a
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
Mlana
Coloration (feathers ; white-spotting)
Gene Amplification,
Complex Change
Columba livia
rock pigeon - (species) D
Domesticated
Association Mapping
Bruders R; Van Hollebeke H; Osborne EJ ; et al. (2020)
A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Col[...]
GP00002342
MLANA
Q16655
Morphology
CNV with 7 copies of the outer 77-kb segment and 14 copies of the inner 25-kb segment in the genomes of female (ZStW) Almond pigeons
Columba livia
rock pigeon - (species)
Columba livia
rock pigeon - (species) D
Mlana
Columba livia
rock pigeon - (species)
Published - Accepted by Curator
MNR2
Bird head comb
Fertility (sperm motility)
Gene Amplification,
Inversion
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Imsland F; Feng C; Boije H ; et al. (2012)
The Rose-comb mutation in chickens constitutes a structural rearrangement causing both altered comb [...]
GP00000675
MNR2
Q9YHY8
Morphology
Physiology
7.4Mb inversion (and secondary structural re-arrangement in some individuals)
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
MNR2
Gallus gallus
chicken - (species)
Published - Accepted by Curator
MRC2
Muscular mass
Tail shape (crooked ; defect)
Coding,
Deletion
N
Bos taurus
cattle - (species) D
Domesticated
Association Mapping
Fasquelle C; Sartelet A; Li W ; et al. (2009)
Balancing selection of a frame-shift mutation in the MRC2 gene accounts for the outbreak of the Croo[...]
2 Additional References
GP00002264
MRC2
Q9UBG0
Physiology
Morphology
c.2904-2905delAG p.Gly934X N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
MRC2
Bos taurus
cattle - (species)
Published - Accepted by Curator
MRC2
Muscular mass
Tail shape (crooked ; defect)
Coding,
SNP
Bos taurus
cattle - (species) D
Domesticated
Association Mapping
Fasquelle C; Sartelet A; Li W ; et al. (2009)
Balancing selection of a frame-shift mutation in the MRC2 gene accounts for the outbreak of the Croo[...]
2 Additional References
GP00002265
MRC2
Q9UBG0
Physiology
Morphology
c.1906T>G p.C636G
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
MRC2
Bos taurus
cattle - (species)
Published - Accepted by Curator
MuPKS
Coloration (psittacofulvin; feathers)
Coding,
SNP
Melopsittacus undulatus
budgerigar - (species) D
Domesticated
Association Mapping
Cooke TF; Fischer CR; Wu P ; et al. (2017)
Genetic Mapping and Biochemical Basis of Yellow Feather Pigmentation in Budgerigars.
GP00002121
PKS15
A0A218V6J0
Morphology
Melopsittacus undulatus
budgerigar - (species)
Melopsittacus undulatus
budgerigar - (species) D
MuPKS
Melopsittacus undulatus
budgerigar - (species)
Published - Accepted by Curator
MYB-FL
Coloration (flower ; UV absorbance)
Cis-regulatory,
Insertion
Petunia axillaris
(species) D
Interspecific
Linkage Mapping
Sheehan H; Moser M; Klahre U ; et al. (2016)
MYB-FL controls gain and loss of floral UV absorbance, a key trait affecting pollinator preference a[...]
GP00001589
MYB-FL
A0A0S3CVD3
Morphology
A 977-kb insertion 12 bp upstream of the predicted TATA-binding box is causing upregulation of the promoter
Petunia integrifolia
(species)
Petunia axillaris
(species) D
MYB-FL
Petunia axillaris
(species)
Published - Accepted by Curator
MYB-FL
Coloration (flower ; UV absorbance)
Coding,
Deletion
N
Petunia exserta
(species) D
Interspecific
Linkage Mapping
Sheehan H; Moser M; Klahre U ; et al. (2016)
MYB-FL controls gain and loss of floral UV absorbance, a key trait affecting pollinator preference a[...]
GP00001590
MYB-FL
A0A0S3CVC7
Morphology
A 1-bp deletion in exon 3 causing a frameshift resulting in a truncated protein N
Petunia axillaris
(species)
Petunia exserta
(species) D
MYB-FL
Petunia exserta
(species)
Published - Accepted by Curator
MYB1
Coloration (flower)
Coding,
Deletion
N
Ipomoea purpurea
common morning-glory - (species) D
Intraspecific
Candidate Gene
Chang SM; Lu Y; Rausher MD (2005)
Neutral evolution of the nonbinding region of the anthocyanin regulatory gene Ipmyb1 in Ipomoea.
GP00001458
myb1
Q4QS21
Morphology
2 deletions; 6-bp and 19-bp long; the larger produces a frameshift and a premature stop N
Ipomoea purpurea
common morning-glory - (species)
Ipomoea purpurea
common morning-glory - (species) D
MYB1
Ipomoea purpurea
common morning-glory - (species)
Published - Accepted by Curator
MYB1
Coloration (flowers; seeds; stems)
Coding,
Deletion
N
Ipomoea nil
Japanese morning glory - (species) D
Domesticated
Candidate Gene
Morita Y; Saitoh M; Hoshino A ; et al. (2006)
Isolation of cDNAs for R2R3-MYB, bHLH and WDR transcriptional regulators and identification of c and[...]
GP00002089
myb1
Q4QS21
Morphology
frameshift mutation caused by a 2 bp deletion N
Ipomoea nil
Japanese morning glory - (species)
Ipomoea nil
Japanese morning glory - (species) D
MYB1
Ipomoea nil
Japanese morning glory - (species)
Published - Accepted by Curator
Myogenic factor 5 (Myf5)
Rib morphology (skeleton)
Cis-regulatory,
SNP
Pantherophis guttatus guttatus
(subspecies) D
Malayopython reticulatus
reticulated python - (species) D
Boa constrictor
boa - (species) D
Intergeneric or Higher
Candidate Gene
Guerreiro I; Nunes A; Woltering JM ; et al. (2013)
Role of a polymorphism in a Hox/Pax-responsive enhancer in the evolution of the vertebrate spine.
GP00001716
Myf5
P24699
Morphology
one nucleotide change at a Hox binding site (CTAATTG to CCAATTG) - mouse transgenics and protein-DNA binding assay
Squamata
squamates - (order)
Pantherophis guttatus guttatus
(subspecies) D
Malayopython reticulatus
reticulated python - (species) D
Boa constrictor
boa - (species) D
Myogenic factor 5 (Myf5)
Pantherophis guttatus guttatus
(subspecies)
Malayopython reticulatus
reticulated python - (species)
Boa constrictor
boa - (species)
Published - Accepted by Curator
Myogenic factor 5 (Myf5)
Rib morphology (skeleton)
Cis-regulatory,
SNP
Trichechus manatus
West Indian manatee - (species) D
Procavia capensis
Cape rock hyrax - (species) D
Loxodonta africana
African savanna elephant - (species) D
Intergeneric or Higher
Candidate Gene
Guerreiro I; Nunes A; Woltering JM ; et al. (2013)
Role of a polymorphism in a Hox/Pax-responsive enhancer in the evolution of the vertebrate spine.
GP00001717
Myf5
P24699
Morphology
one nucleotide change at a Hox binding site (CTAATTG to CCAATTG) - mouse transgenics and protein-DNA binding assay
Eutheria
placentals - (no rank)
Trichechus manatus
West Indian manatee - (species) D
Procavia capensis
Cape rock hyrax - (species) D
Loxodonta africana
African savanna elephant - (species) D
Myogenic factor 5 (Myf5)
Trichechus manatus
West Indian manatee - (species)
Procavia capensis
Cape rock hyrax - (species)
Loxodonta africana
African savanna elephant - (species)
Published - Accepted by Curator
myosin heavy chain 16 (MYH16)
Masticatory muscles
Coding,
Deletion
N
Homo sapiens
human - (species) D
Intergeneric or Higher
Candidate Gene
Stedman HH; Kozyak BW; Nelson A ; et al. (2004)
Myosin gene mutation correlates with anatomical changes in the human lineage.
GP00000683
MYH16
Q9H6N6
Morphology
2bp deletion at codon 660 N
Pan troglodytes
chimpanzee - (species)
Homo sapiens
human - (species) D
myosin heavy chain 16 (MYH16)
Homo sapiens
human - (species)
Published - Accepted by Curator
Myostatin (MSTN = GDF8)
Muscular mass (double muscling)
Coding,
Deletion
N
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Grobet L; Martin LJ; Poncelet D ; et al. (1997)
A deletion in the bovine myostatin gene causes the double-muscled phenotype in cattle.
2 Additional References
GP00000685
MSTN
O14793
Morphology
nt821 11bp deletion c.821-831delTGAACACTCCA p.Glu275ArgfsX14 N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Myostatin (MSTN = GDF8)
Bos taurus
cattle - (species)
Published - Accepted by Curator
Myostatin (MSTN = GDF8)
Muscular mass (double muscling)
Coding,
Indel
N
Bos taurus
cattle - (species) D
Domesticated
Candidate Gene
Grobet L; Poncelet D; Royo LJ ; et al. (1998)
Molecular definition of an allelic series of mutations disrupting the myostatin function and causing[...]
GP00000686
MSTN
O14793
Morphology
nt419 7bp deletion and 10bp insertion; leading to a premature stop codon at position 140 c.419_425del7, c418_426ins10 N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Myostatin (MSTN = GDF8)
Bos taurus
cattle - (species)
Published - Accepted by Curator
Myostatin (MSTN = GDF8)
Muscular mass (double muscling)
Coding,
SNP
N
Bos taurus
cattle - (species) D
Domesticated
Candidate Gene
Grobet L; Poncelet D; Royo LJ ; et al. (1998)
Molecular definition of an allelic series of mutations disrupting the myostatin function and causing[...]
GP00000687
MSTN
O14793
Morphology
c.610C>T p.Q204* N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Myostatin (MSTN = GDF8)
Bos taurus
cattle - (species)
Published - Accepted by Curator
Myostatin (MSTN = GDF8)
Muscular mass (double muscling)
Coding,
SNP
N
Bos taurus
cattle - (species) D
Domesticated
Candidate Gene
Grobet L; Poncelet D; Royo LJ ; et al. (1998)
Molecular definition of an allelic series of mutations disrupting the myostatin function and causing[...]
GP00000688
MSTN
O14793
Morphology
E226* caused by G676T N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Myostatin (MSTN = GDF8)
Bos taurus
cattle - (species)
Published - Accepted by Curator
Myostatin (MSTN = GDF8)
Muscular mass (double muscling)
Coding,
SNP
Bos taurus
cattle - (species) D
Domesticated
Candidate Gene
McPherron AC; Lee SJ (1997)
Double muscling in cattle due to mutations in the myostatin gene.
2 Additional References
GP00000689
MSTN
O14793
Morphology
C313Y caused by G938A; disrupts disulphide bond
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Myostatin (MSTN = GDF8)
Bos taurus
cattle - (species)
Published - Accepted by Curator
Myostatin (MSTN = GDF8)
Muscular mass (double muscling)
Coding,
SNP
N
Bos taurus
cattle - (species) D
Domesticated
Candidate Gene
Marchitelli C; Savarese MC; Crisà A ; et al. (2003)
Double muscling in Marchigiana beef breed is caused by a stop codon in the third exon of myostatin g[...]
GP00000690
MSTN
O14793
Morphology
E291* caused by G>T N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Myostatin (MSTN = GDF8)
Bos taurus
cattle - (species)
Published - Accepted by Curator
Myostatin (MSTN = GDF8)
Muscular mass (double muscling)
Coding,
SNP
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Alexander LJ; Kuehn LA; Smith TP ; et al. (2009)
A Limousin specific myostatin allele affects longissimus muscle area and fatty acid profiles in a Wa[...]
GP00000692
MSTN
O14793
Morphology
c.282C>A p.Phe94Leu
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Myostatin (MSTN = GDF8)
Bos taurus
cattle - (species)
Published - Accepted by Curator
Myostatin (MSTN = GDF8)
Muscular mass (double muscling)
Coding,
Deletion
N
Ovis aries
sheep - (species) D
Domesticated
Candidate Gene
Boman IA; Klemetsdal G; Blichfeldt T ; et al. (2009)
A frameshift mutation in the coding region of the myostatin gene (MSTN) affects carcass conformation[...]
GP00000693
MSTN
O14793
Morphology
1bp deletion resulting in a premature stop codon at position 320 N
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
Myostatin (MSTN = GDF8)
Ovis aries
sheep - (species)
Published - Accepted by Curator
Myostatin (MSTN = GDF8)
Muscular mass (double muscling)
Coding,
Insertion
N
Ovis aries
sheep - (species) D
Domesticated
Candidate Gene
Boman IA; Våge DI (2009)
An insertion in the coding region of the myostatin (MSTN) gene affects carcass conformation and fatn[...]
GP00000694
MSTN
O14793
Morphology
1bp insertion resulting in premature stop codon at position 49 N
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
Myostatin (MSTN = GDF8)
Ovis aries
sheep - (species)
Published - Accepted by Curator
Myostatin (MSTN = GDF8)
Muscular mass (double muscling)
Cis-regulatory,
SNP
Ovis aries
sheep - (species)
Domesticated
Linkage Mapping
Clop A; Marcq F; Takeda H ; et al. (2006)
A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects musc[...]
GP00000695
MSTN
O14793
Morphology
1bp change; generates binding site for two muscle-expressed miRNAs; causing mRNA degradation and lower levels of circulating myostatin
G to A transition in the 3' UTR that creates a target site for mir1 and mir206 microRNAs
Ovis aries
sheep - (species)
Ovis aries
sheep - (species)
Myostatin (MSTN = GDF8)
Ovis aries
sheep - (species)
Published - Accepted by Curator
Myostatin (MSTN = GDF8)
Muscular mass (double muscling)
Cis-regulatory,
SNP
Sus scrofa domesticus
domestic pig - (subspecies)
Domesticated
Candidate Gene
Stinckens A; Luyten T; Bijttebier J ; et al. (2008)
Characterization of the complete porcine MSTN gene and expression levels in pig breeds differing in [...]
GP00000696
MSTN
O14793
Morphology
Possible promoter disruption ; changes the G nucleotide at position 8 of the MEF3 binding site into an A nucleotide, thus disrupting the MEF3 binding site
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies)
Myostatin (MSTN = GDF8)
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
Myostatin (MSTN = GDF8)
Muscular mass (double muscling)
Coding,
SNP
Bos taurus
cattle - (species) D
Domesticated
Candidate Gene
Dierks C; Eder J; Glatzer S ; et al. (2015)
A novel myostatin mutation in double-muscled German Gelbvieh.
GP00002248
MSTN
O14793
Morphology
c.191T>C p.L64P
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Myostatin (MSTN = GDF8)
Bos taurus
cattle - (species)
Published - Accepted by Curator
nath-10
Fertility (sperm number; egg laying rate)
Coding,
SNP
Caenorhabditis elegans
(species)
Intraspecific
Linkage Mapping
Duveau F; Félix MA (2012)
Role of pleiotropy in the evolution of a cryptic developmental variation in Caenorhabditis elegans.
GP00000718
nath-10
O01757
Morphology
Met746Ile (according to Table S2 C>T but it should be G>A - Needs curation)
Caenorhabditis elegans
(species)
Caenorhabditis elegans
(species)
nath-10
Caenorhabditis elegans
(species)
Published - Accepted by Curator
natriuretic peptide precursor type C (NPPC)
Body size (height)
Unknown,
Unknown
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Estrada K; Krawczak M; Schreiber S ; et al. (2009)
A genome-wide association study of northwestern Europeans involves the C-type natriuretic peptide si[...]
GP00000719
Nppc
Q61839
Morphology
unknown
Homo sapiens
human - (species)
Homo sapiens
human - (species)
natriuretic peptide precursor type C (NPPC)
Homo sapiens
human - (species)
Published - Accepted by Curator
natriuretic peptide receptor 3 (NPR3)
Body size (height)
Unknown,
Unknown
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Estrada K; Krawczak M; Schreiber S ; et al. (2009)
A genome-wide association study of northwestern Europeans involves the C-type natriuretic peptide si[...]
1 Additional References
GP00000720
NPR3
Q8L746
Morphology
unknown
Homo sapiens
human - (species)
Homo sapiens
human - (species)
natriuretic peptide receptor 3 (NPR3)
Homo sapiens
human - (species)
Published - Accepted by Curator
ndp (norrin)
Coloration (plumage)
Cis-regulatory,
Insertion
Corvus cornix
hooded crow - (species) D
Intraspecific
Association Mapping
Knief U; Bossu CM; Saino N ; et al. (2019)
Epistatic mutations under divergent selection govern phenotypic variation in the crow hybrid zone.
2 Additional References
GP00002148
Ndp
P48744
Morphology
2.25-kb LTR retrotransposon insertion reducing expression of the NDP gene and candidate gene LRP6 and a large LD haplotype in chr.18 also show a signal
Corvus corone corone
(subspecies)
Corvus cornix
hooded crow - (species) D
ndp (norrin)
Corvus cornix
hooded crow - (species)
Published - Accepted by Curator
ndp (norrin)
Coloration (plumage)
Coding,
SNP
N
Columba livia
rock pigeon - (species) D
Domesticated
Association Mapping
Vickrey AI; Bruders R; Kronenberg Z ; et al. (2018)
Introgression of regulatory alleles and a missense coding mutation drive plumage pattern diversity i[...]
GP00002250
Ndp
P48744
Morphology
Start-codon change predicted to truncate the amino terminus of the NDP protein by 11 amino acids thereby disrupting the 24-amino acid signal peptide sequence N
Columba livia
rock pigeon - (species)
Columba livia
rock pigeon - (species) D
ndp (norrin)
Columba livia
rock pigeon - (species)
Published - Accepted by Curator
ndp (norrin)
Coloration (plumage)
Cis-regulatory,
Insertion
N
Columba livia
rock pigeon - (species) D
Columba guinea
speckled pigeon - (species) D
Intraspecific
Association Mapping
Vickrey AI; Bruders R; Kronenberg Z ; et al. (2018)
Introgression of regulatory alleles and a missense coding mutation drive plumage pattern diversity i[...]
GP00002251
Ndp
P48744
Morphology
CNV driven by tandem repeats with one (bar) two (checker) or four (T-checker) copies per chromosome between approximative positions 1790000 and 1805600 N
Columba livia
rock pigeon - (species)
Columba livia
rock pigeon - (species) D
Columba guinea
speckled pigeon - (species) D
ndp (norrin)
Columba livia
rock pigeon - (species)
Columba guinea
speckled pigeon - (species)
Published - Accepted by Curator
Oca2
Coloration (albinism)
Catecholamine metabolism
Coding,
Deletion
N
Astyanax mexicanus
Mexican tetra - (species) D
Intraspecific
Linkage Mapping
Protas ME; Hersey C; Kochanek D ; et al. (2006)
Genetic analysis of cavefish reveals molecular convergence in the evolution of albinism.
2 Additional References
GP00000745
Oca2
Q62052
Morphology
Physiology
Deletion of exon 21 N
Astyanax mexicanus
Mexican tetra - (species)
Astyanax mexicanus
Mexican tetra - (species) D
Oca2
Astyanax mexicanus
Mexican tetra - (species)
Published - Accepted by Curator
Oca2
Coloration (albinism)
Catecholamine metabolism
Coding,
Deletion
N
Astyanax mexicanus
Mexican tetra - (species) D
Intraspecific
Linkage Mapping
Protas ME; Hersey C; Kochanek D ; et al. (2006)
Genetic analysis of cavefish reveals molecular convergence in the evolution of albinism.
2 Additional References
GP00000746
Oca2
Q62052
Morphology
Physiology
Almost complete deletion of exon 24; + 2 a.a subsitutions at conserved positions - the two point mutations do not drastically affect the function of OCA2 in cell lines suggesting that the exon 24 deletion is the mutation that causes albinism in the Pachón population N
Astyanax mexicanus
Mexican tetra - (species)
Astyanax mexicanus
Mexican tetra - (species) D
Oca2
Astyanax mexicanus
Mexican tetra - (species)
Published - Accepted by Curator
Oca2
Coloration (eyes; skin, hair)
Cis-regulatory,
SNP
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Eiberg H; Troelsen J; Nielsen M ; et al. (2008)
Blue eye color in humans may be caused by a perfectly associated founder mutation in a regulatory el[...]
5 Additional References
GP00000747
Oca2
Q62052
Morphology
Causative SNP in enhancer localized in intron of neighbor gene HERC2 : likely rs12913832 within HERC2 which influences on OCA2 expression in eye hair and skin pigmentation
Homo sapiens
human - (species)
Homo sapiens
human - (species)
Oca2
Homo sapiens
human - (species)
Published - Accepted by Curator
Oca2
Coloration (skin)
Coding,
SNP
Homo sapiens
human - (species) D
Intraspecific
Association Mapping
Edwards M; Bigham A; Tan J ; et al. (2010)
Association of the OCA2 polymorphism His615Arg with melanin content in east Asian populations: furth[...]
1 Additional References
GP00000748
Oca2
Q62052
Morphology
His615Arg
Homo sapiens
human - (species)
Homo sapiens
human - (species) D
Oca2
Homo sapiens
human - (species)
Published - Accepted by Curator
Oca2
Coloration (albinism)
Coding,
Insertion
N
Pantherophis guttatus
(species) D
Intraspecific
Linkage Mapping
Saenko SV; Lamichhaney S; Martinez Barrio A ; et al. (2015)
Amelanism in the corn snake is associated with the insertion of an LTR-retrotransposon in the OCA2 g[...]
GP00001619
OCA2
Q04671
Morphology
insertion of an LTR-retrotransposon (5832-bp) in the 11th intron resulting after splicing in an additional 397-bp fragment constituted of 3 new exons inserted between exons 11 and 12. Generates truncated protein with two stop codons N
Pantherophis guttatus
(species)
Pantherophis guttatus
(species) D
Oca2
Pantherophis guttatus
(species)
Published - Accepted by Curator
Oca2
Coloration (albinism)
Coding,
Deletion
N
Melanochromis auratus
(species) D
Intraspecific
Candidate Gene
Kratochwil CF; Urban S; Meyer A (2019)
Genome of the Malawi golden cichlid fish (Melanochromis auratus) reveals exon loss of oca2 in an ame[...]
GP00001955
Oca2
Q62052
Morphology
deletion covering a total of 5.4kb including exon 2 and parts of the flanking introns 1 and 2 N
Melanochromis auratus
(species)
Melanochromis auratus
(species) D
Oca2
Melanochromis auratus
(species)
Published - Accepted by Curator
Oca2
Coloration (albinism)
Coding,
Insertion
N
Carassius auratus
goldfish - (species) D
Domesticated
Candidate Gene
Kon T; Omori Y; Fukuta K ; et al. (2020)
The Genetic Basis of Morphological Diversity in Domesticated Goldfish.
GP00002351
Oca2
Q62052
Morphology
1-bp insert creating a frameshift and a truncated protein (470 amino acids instead of 805). In oca2L ohnolog on chromosome LG6. N
Carassius auratus
goldfish - (species)
Carassius auratus
goldfish - (species) D
Oca2
Carassius auratus
goldfish - (species)
Published - Accepted by Curator
Oca2
Coloration (albinism)
Coding,
Deletion
N
Carassius auratus
goldfish - (species) D
Domesticated
Candidate Gene
Kon T; Omori Y; Fukuta K ; et al. (2020)
The Genetic Basis of Morphological Diversity in Domesticated Goldfish.
GP00002352
Oca2
Q62052
Morphology
1-bp deletion creating a frameshift and a truncated protein (519 amino acids instead of 805). In oca2S ohnolog on chromosome LG31. N
Carassius auratus
goldfish - (species)
Carassius auratus
goldfish - (species) D
Oca2
Carassius auratus
goldfish - (species)
Published - Accepted by Curator
OPRM1
Coloration (skin)
Unknown,
Unknown
Homo sapiens
human - (species) D
Intraspecific
Association Mapping
Quillen EE; Bauchet M; Bigham AW ; et al. (2012)
OPRM1 and EGFR contribute to skin pigmentation differences between Indigenous Americans and European[...]
GP00001536
OPRM1
P35372
Morphology
C>T associated SNP
Homo sapiens
human - (species)
Homo sapiens
human - (species) D
OPRM1
Homo sapiens
human - (species)
Published - Accepted by Curator
Optix
Coloration (wing, Mullerian mimicry)
Cis-regulatory,
Unknown
Heliconius pachinus
(species)
Intraspecific
Linkage Mapping
Reed RD; Papa R; Martin A ; et al. (2011)
optix drives the repeated convergent evolution of butterfly wing pattern mimicry.
1 Additional References
GP00000795
Optix
Q95RW8
Morphology
Not identified
Heliconius cydno
(species)
Heliconius pachinus
(species)
Optix
Heliconius pachinus
(species)
Published - Accepted by Curator
Optix
Coloration (wing, Mullerian mimicry)
Cis-regulatory,
Unknown
Heliconius himera
(species)
Intraspecific
Linkage Mapping
Reed RD; Papa R; Martin A ; et al. (2011)
optix drives the repeated convergent evolution of butterfly wing pattern mimicry.
1 Additional References
GP00000796
Optix
Q95RW8
Morphology
Not identified
Heliconius erato
crimson-patched longwing - (species)
Heliconius himera
(species)
Optix
Heliconius himera
(species)
Published - Accepted by Curator
Optix
Coloration (wing, Mullerian mimicry)
Cis-regulatory,
Unknown
Heliconius erato
crimson-patched longwing - (species)
Intraspecific
Linkage Mapping
Reed RD; Papa R; Martin A ; et al. (2011)
optix drives the repeated convergent evolution of butterfly wing pattern mimicry.
1 Additional References
GP00000797
Optix
Q95RW8
Morphology
Not identified
Heliconius erato
crimson-patched longwing - (species)
Heliconius erato
crimson-patched longwing - (species)
Optix
Heliconius erato
crimson-patched longwing - (species)
Published - Accepted by Curator
Optix
Coloration (wing, Mullerian mimicry)
Cis-regulatory,
Unknown
Heliconius melpomene
postman butterfly - (species)
Intraspecific
Linkage Mapping
Reed RD; Papa R; Martin A ; et al. (2011)
optix drives the repeated convergent evolution of butterfly wing pattern mimicry.
1 Additional References
GP00000798
Optix
Q95RW8
Morphology
Not identified
Heliconius melpomene
postman butterfly - (species)
Heliconius melpomene
postman butterfly - (species)
Optix
Heliconius melpomene
postman butterfly - (species)
Published - Accepted by Curator
Os07g0603400
Grain size
Grain quality
2 Mutations:
Coding
SNP
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Wang Y; Xiong G; Hu J ; et al. (2015)
Copy number variation at the GL7 locus contributes to grain size diversity in rice.
GP00001542
Os07g0603400
A3BLY4
Morphology
Physiology
2 mutations
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
Os07g0603400
Oryza sativa
rice - (species)
Published - Accepted by Curator
OsC1
Coloration (loss of apiculus color)
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Saitoh K; Onishi K; Mikami I ; et al. (2004)
Allelic diversification at the C (OsC1) locus of wild and cultivated rice: nucleotide changes associ[...]
2 Additional References
GP00000805
C
Q76B79
Morphology
10bp deletion N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
OsC1
Oryza sativa
rice - (species)
Published - Accepted by Curator
OsC1
Coloration (loss of apiculus color)
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Saitoh K; Onishi K; Mikami I ; et al. (2004)
Allelic diversification at the C (OsC1) locus of wild and cultivated rice: nucleotide changes associ[...]
2 Additional References
GP00000806
C
Q76B79
Morphology
2bp deletion N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
OsC1
Oryza sativa
rice - (species)
Published - Accepted by Curator
OsCKX2=Gn1a
Grain yield
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Ashikari M; Sakakibara H; Lin S ; et al. (2005)
Cytokinin oxidase regulates rice grain production.
GP00000807
CKX2
Q4ADV8
Morphology
11bp deletion causing premature stop codon N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
OsCKX2=Gn1a
Oryza sativa
rice - (species)
Published - Accepted by Curator
OsCKX2=Gn1a
Grain yield
Cis-regulatory,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Ashikari M; Sakakibara H; Lin S ; et al. (2005)
Cytokinin oxidase regulates rice grain production.
GP00000808
CKX2
Q4ADV8
Morphology
Not identified
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
OsCKX2=Gn1a
Oryza sativa
rice - (species)
Published - Accepted by Curator
OsCKX2=Gn1a
Grain yield
Cis-regulatory,
Unknown
Triticum aestivum
bread wheat - (species)
Domesticated
Linkage Mapping
Zhang L; Zhao YL; Gao LF ; et al. (2012)
TaCKX6-D1, the ortholog of rice OsCKX2, is associated with grain weight in hexaploid wheat.
GP00000809
CKX2
Q4ADV8
Morphology
unknown
Triticum aestivum
bread wheat - (species)
Triticum aestivum
bread wheat - (species)
OsCKX2=Gn1a
Triticum aestivum
bread wheat - (species)
Published - Accepted by Curator
OsLG1
Seed shattering (panicle shape)
Cis-regulatory,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Ishii T; Numaguchi K; Miura K ; et al. (2013)
OsLG1 regulates a closed panicle trait in domesticated rice.
GP00000811
SPL8
Q7XPY1
Morphology
unknown but fine-mapped 9.3kb region
Oryza rufipogon
(species)
Oryza sativa
rice - (species)
OsLG1
Oryza sativa
rice - (species)
Published - Accepted by Curator
OsPPKL1/qGL3
Grain size
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Zhang X; Wang J; Huang J ; et al. (2012)
Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield[...]
GP00000812
qLTG-3-1
B3IWI0
Morphology
Asp364Glu
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
OsPPKL1/qGL3
Oryza sativa
rice - (species)
Published - Accepted by Curator
OsSPL13
Grain size
Cis-regulatory,
Insertion
Oryza sativa Japonica Group
Japanese rice - (no rank) D
Domesticated
Association Mapping
Si L; Chen J; Huang X ; et al. (2016)
OsSPL13 controls grain size in cultivated rice.
GP00001572
SPL13
Q6Z461
Morphology
a CACTTC tandem repeat sequence in the 5' UTR is causing reduced expression
Oryza sativa
rice - (species)
Oryza sativa Japonica Group
Japanese rice - (no rank) D
OsSPL13
Oryza sativa Japonica Group
Japanese rice - (no rank)
Published - Accepted by Curator
OsSPL14 / WFP
Grain yield
Cis-regulatory,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Jiao Y; Wang Y; Xue D ; et al. (2010)
Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice.
1 Additional References
GP00000813
IPA1
D8WJ58
Morphology
Point mutation resulting in altered binding of a micro-RNA
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
OsSPL14 / WFP
Oryza sativa
rice - (species)
Published - Accepted by Curator
OsSPL16
Grain size
Grain shape
Cis-regulatory,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Wang S; Wu K; Yuan Q ; et al. (2012)
Control of grain size, shape and quality by OsSPL16 in rice.
1 Additional References
GP00000814
SPL16
L0AP48
Morphology
Morphology
Promoter variation
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
OsSPL16
Oryza sativa
rice - (species)
Published - Accepted by Curator
OVATE
Fruit shape
Coding,
SNP
N
Solanum lycopersicum
tomato - (species)
Domesticated
Linkage Mapping
Liu J; Van Eck J; Cong B ; et al. (2002)
A new class of regulatory genes underlying the cause of pear-shaped tomato fruit.
GP00000815
Q8GSM4
Morphology
V164* caused by G>T; which leads to a 75-aa truncation in the C terminus of the predicted protein N
Solanum lycopersicum
tomato - (species)
Solanum lycopersicum
tomato - (species)
OVATE
Solanum lycopersicum
tomato - (species)
Published - Accepted by Curator
P2RY5
Hair type (woolly)
Coding,
Insertion
N
Homo sapiens
human - (species) D
Intraspecific
Association Mapping
Shimomura Y; Wajid M; Ishii Y ; et al. (2008)
Disruption of P2RY5, an orphan G protein-coupled receptor, underlies autosomal recessive woolly hair[...]
GP00000817
LPAR6
P43657
Morphology
at position 69 insertion of 4bp CATG - causes frameshift at codon 24 (PTC +29) N
Homo sapiens
human - (species)
Homo sapiens
human - (species) D
P2RY5
Homo sapiens
human - (species)
Published - Accepted by Curator
P2RY5
Hair type (woolly)
Coding,
Deletion
N
Homo sapiens
human - (species) D
Intraspecific
Association Mapping
Shimomura Y; Wajid M; Ishii Y ; et al. (2008)
Disruption of P2RY5, an orphan G protein-coupled receptor, underlies autosomal recessive woolly hair[...]
GP00001734
LPAR6
P43657
Morphology
2 deletions - one at position 172-175 delAACT and one at position 177 delG - cause frameshift at codon 58 (PTC +31) N
Homo sapiens
human - (species)
Homo sapiens
human - (species) D
P2RY5
Homo sapiens
human - (species)
Published - Accepted by Curator
P2RY5
Hair type (woolly)
Coding,
SNP
N
Homo sapiens
human - (species) D
Intraspecific
Association Mapping
Shimomura Y; Wajid M; Ishii Y ; et al. (2008)
Disruption of P2RY5, an orphan G protein-coupled receptor, underlies autosomal recessive woolly hair[...]
GP00001735
LPAR6
P43657
Morphology
188A>T which causes D63V N
Homo sapiens
human - (species)
Homo sapiens
human - (species) D
P2RY5
Homo sapiens
human - (species)
Published - Accepted by Curator
P2RY5
Hair type (woolly)
Coding,
SNP
N
Homo sapiens
human - (species) D
Intraspecific
Association Mapping
Shimomura Y; Wajid M; Ishii Y ; et al. (2008)
Disruption of P2RY5, an orphan G protein-coupled receptor, underlies autosomal recessive woolly hair[...]
GP00001736
LPAR6
P43657
Morphology
562A>T which causes I188F N
Homo sapiens
human - (species)
Homo sapiens
human - (species) D
P2RY5
Homo sapiens
human - (species)
Published - Accepted by Curator
P2RY5
Hair type (woolly)
Coding,
SNP
N
Homo sapiens
human - (species) D
Intraspecific
Association Mapping
Shimomura Y; Wajid M; Ishii Y ; et al. (2008)
Disruption of P2RY5, an orphan G protein-coupled receptor, underlies autosomal recessive woolly hair[...]
GP00001737
LPAR6
P43657
Morphology
565G>A which causes E189K N
Homo sapiens
human - (species)
Homo sapiens
human - (species) D
P2RY5
Homo sapiens
human - (species)
Published - Accepted by Curator
pannier
Coloration (elytra)
Cis-regulatory,
Unknown
Harmonia axyridis
(species)
Intraspecific
Association Mapping
Ando T; Niimi T (2019)
Development and evolution of color patterns in ladybird beetles: A case study in Harmonia axyridis.
2 Additional References
GP00001705
pnr
P52168
Morphology
exact mutation(s) unknown
Harmonia axyridis
(species)
Harmonia axyridis
(species)
pannier
Harmonia axyridis
(species)
Published - Accepted by Curator
pannier
Coloration (elytra)
Cis-regulatory,
Unknown
Harmonia axyridis
(species)
Intraspecific
Association Mapping
Ando T; Niimi T (2019)
Development and evolution of color patterns in ladybird beetles: A case study in Harmonia axyridis.
2 Additional References
GP00001706
pnr
P52168
Morphology
exact mutation(s) unknown
Harmonia axyridis
(species)
Harmonia axyridis
(species)
pannier
Harmonia axyridis
(species)
Published - Accepted by Curator
pannier
Coloration (elytra)
Cis-regulatory,
Unknown
Harmonia axyridis
(species)
Intraspecific
Association Mapping
Ando T; Niimi T (2019)
Development and evolution of color patterns in ladybird beetles: A case study in Harmonia axyridis.
2 Additional References
GP00001707
pnr
P52168
Morphology
exact mutation(s) unknown
Harmonia axyridis
(species)
Harmonia axyridis
(species)
pannier
Harmonia axyridis
(species)
Published - Accepted by Curator
Patched1 (Ptc1)
Body size (height)
Unknown,
Unknown
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Lettre G (2011)
Recent progress in the study of the genetics of height.
GP00000855
ptch1
Q98864
Morphology
unknown
Homo sapiens
human - (species)
Homo sapiens
human - (species)
Patched1 (Ptc1)
Homo sapiens
human - (species)
Published - Accepted by Curator
Patched1 (Ptc1)
Cranio-facial morphology
Cis-regulatory,
Unknown
Maylandia mbenjii
(species) D
Interspecific
Linkage Mapping
Roberts RB; Hu Y; Albertson RC ; et al. (2011)
Craniofacial divergence and ongoing adaptation via the hedgehog pathway.
1 Additional References
GP00000856
ptch1
Q98864
Morphology
Uncharacterized cis-regulatory change - with ancestral Labeotropheus (LF) allele exhibiting relatively higher levels of expression
Labeotropheus fuelleborni
blue mbuna - (species)
Maylandia mbenjii
(species) D
Patched1 (Ptc1)
Maylandia mbenjii
(species)
Published - Accepted by Curator
Pax3
Coloration (white-spotting ; leucism)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Linkage Mapping
Hauswirth R; Haase B; Blatter M ; et al. (2012)
Mutations in MITF and PAX3 cause "splashed white" and other white spotting phenotypes in horses.
GP00002252
PAX3
P23760
Morphology
c.209G>A p.C70Y
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Pax3
Equus caballus
horse - (species)
Published - Accepted by Curator
Pax3
Coloration (white-spotting ; leucism)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Hauswirth R; Jude R; Haase B ; et al. (2013)
Novel variants in the KIT and PAX3 genes in horses with white-spotted coat colour phenotypes.
GP00002253
PAX3
P23760
Morphology
c.95C>G p.Pro32Arg
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Pax3
Equus caballus
horse - (species)
Published - Accepted by Curator
pax3a
Coloration (scales)
Cis-regulatory,
SNP
Tropheops sp. 'red cheek'
(species)
Interspecific
Linkage Mapping
Albertson RC; Powder KE; Hu Y ; et al. (2014)
Genetic basis of continuous variation in the levels and modular inheritance of pigmentation in cichl[...]
GP00001417
pax3a
Q6DHA7
Morphology
C>T SNP within 5UTR
Labeotropheus fuelleborni
blue mbuna - (species)
Tropheops sp. 'red cheek'
(species)
pax3a
Tropheops sp. 'red cheek'
(species)
Published - Accepted by Curator
pax3b
Coloration (scales)
Unknown,
Unknown
Tropheops sp. 'red cheek'
(species)
Interspecific
Linkage Mapping
Albertson RC; Powder KE; Hu Y ; et al. (2014)
Genetic basis of continuous variation in the levels and modular inheritance of pigmentation in cichl[...]
GP00001419
pax3-b
Q0IH87
Morphology
unknown
Labeotropheus fuelleborni
blue mbuna - (species)
Tropheops sp. 'red cheek'
(species)
pax3b
Tropheops sp. 'red cheek'
(species)
Published - Accepted by Curator
Pax7
Coloration (scales)
Cis-regulatory,
Unknown
Maylandia zebra
zebra mbuna - (species)
Interspecific
Linkage Mapping
Roberts RB; Ser JR; Kocher TD (2009)
Sexual conflict resolved by invasion of a novel sex determiner in Lake Malawi cichlid fishes.
GP00000857
Pax7
P47239
Morphology
Not identified
Labeotropheus fuelleborni
blue mbuna - (species)
Maylandia zebra
zebra mbuna - (species)
Pax7
Maylandia zebra
zebra mbuna - (species)
Published - Accepted by Curator
pax7a
Coloration (scales)
Cis-regulatory,
Unknown
Labeotropheus trewavasae
(species)
Intraspecific
Candidate Gene
Roberts RB; Moore EC; Kocher TD (2017)
An allelic series at pax7a is associated with colour polymorphism diversity in Lake Malawi cichlid f[...]
GP00001422
Pax7
P47239
Morphology
unknown
Labeotropheus trewavasae
(species)
Labeotropheus trewavasae
(species)
pax7a
Labeotropheus trewavasae
(species)
Published - Accepted by Curator
pax7a
Coloration (scales)
Cis-regulatory,
Unknown
Labeotropheus trewavasae
(species)
Intraspecific
Candidate Gene
Roberts RB; Moore EC; Kocher TD (2017)
An allelic series at pax7a is associated with colour polymorphism diversity in Lake Malawi cichlid f[...]
GP00001423
Pax7
P47239
Morphology
unknown
Labeotropheus trewavasae
(species)
Labeotropheus trewavasae
(species)
pax7a
Labeotropheus trewavasae
(species)
Published - Accepted by Curator
pax7a
Coloration (scales)
Cis-regulatory,
Unknown
Labeotropheus trewavasae
(species)
Intraspecific
Candidate Gene
Roberts RB; Moore EC; Kocher TD (2017)
An allelic series at pax7a is associated with colour polymorphism diversity in Lake Malawi cichlid f[...]
GP00001424
Pax7
P47239
Morphology
unknown
Labeotropheus trewavasae
(species)
Labeotropheus trewavasae
(species)
pax7a
Labeotropheus trewavasae
(species)
Published - Accepted by Curator
pdm3
Coloration (female abdomen)
Cis-regulatory,
Complex Change
Drosophila serrata
(species) D
Intraspecific
Linkage Mapping
Yassin A; Delaney EK; Reddiex AJ ; et al. (2016)
The pdm3 Locus Is a Hotspot for Recurrent Evolution of Female-Limited Color Dimorphism in Drosophila[...]
GP00001400
pdm3
A0A0B4LEG2
Morphology
1st intron variant divergent in length and sequence. Dark haplotype contains four tandem sets of three motifs.
Drosophila serrata
(species)
Drosophila serrata
(species) D
pdm3
Drosophila serrata
(species)
Published - Accepted by Curator
pdm3
Coloration (female abdomen)
Cis-regulatory,
Unknown
Drosophila kikkawai
(species)
Intraspecific
Linkage Mapping
Yassin A; Delaney EK; Reddiex AJ ; et al. (2016)
The pdm3 Locus Is a Hotspot for Recurrent Evolution of Female-Limited Color Dimorphism in Drosophila[...]
GP00001401
pdm3
A0A0B4LEG2
Morphology
associated SNPs occur in the intergenic upstream region except one in the second intron
Drosophila kikkawai
(species)
Drosophila kikkawai
(species)
pdm3
Drosophila kikkawai
(species)
Published - Accepted by Curator
pdm3
Coloration (female abdomen)
Unknown,
Unknown
Drosophila burlai
(species)
Intraspecific
Linkage Mapping
Yassin A; Delaney EK; Reddiex AJ ; et al. (2016)
The pdm3 Locus Is a Hotspot for Recurrent Evolution of Female-Limited Color Dimorphism in Drosophila[...]
GP00001402
pdm3
A0A0B4LEG2
Morphology
unknown
Drosophila burlai
(species)
Drosophila burlai
(species)
pdm3
Drosophila burlai
(species)
Published - Accepted by Curator
pdm3
Coloration (abdomen; male)
Cis-regulatory,
Unknown
Drosophila santomea
(species) D
Interspecific
Linkage Mapping
Liu Y; Ramos-Womack M; Han C ; et al. (2019)
Changes throughout a Genetic Network Mask the Contribution of Hox Gene Evolution.
GP00002022
pdm3
A0A0B4LEG2
Morphology
change in a cis-regulatory region - exact causing mutation(s) unknown - increased pdm3 abdominal expression associated with lighter color
Drosophila yakuba
(species)
Drosophila santomea
(species) D
pdm3
Drosophila santomea
(species)
Published - Accepted by Curator
PDSS2
Feather
Cis-regulatory,
SNP
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Feng C; Gao Y; Dorshorst B ; et al. (2014)
A cis-regulatory mutation of PDSS2 causes silky-feather in chickens.
GP00002254
Q86YH6NULL
Morphology
Only variant explaining homozygous phenotype is c.-103C>G and shown to reduce PDSS2 promoter activity in vitro
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
PDSS2
Gallus gallus
chicken - (species)
Published - Accepted by Curator
pericarp color1 (P1)
Coloration (seed)
Cis-regulatory,
Insertion
Zea mays
(species) D
Domesticated
Linkage Mapping
Lechelt C; Peterson T; Laird A ; et al. (1989)
Isolation and molecular analysis of the maize P locus.
GP00000859
P1
O24579
Morphology
insertion of transposable element Ac within a large intron; affecting transcripts. The five transcripts found in P-RR plants are absent in P-VV. A chimeric transcript containing part of Ac sequence is found.
Zea mays
(species)
Zea mays
(species) D
pericarp color1 (P1)
Zea mays
(species)
Published - Accepted by Curator
PH4/GmMYB-G20-1
Coloration (flowers)
Coding,
SNP
N
Glycine max
soybean - (species)
Domesticated
Linkage Mapping
Takahashi R; Benitez ER; Oyoo ME ; et al. (2011 Jul-Aug)
Nonsense mutation of an MYB transcription factor is associated with purple-blue flower color in soyb[...]
GP00000862
PH4
Q2TCH0
Morphology
Substitution creating premature Stop (codon 158) N
Glycine max
soybean - (species)
Glycine max
soybean - (species)
PH4/GmMYB-G20-1
Glycine max
soybean - (species)
Published - Accepted by Curator
Phosphate transporter PHO1
Root growth (allometry of lateral roots)
Coding,
SNP
Arabidopsis thaliana
thale cress - (species)
Intraspecific
Association Mapping
Rosas U; Cibrian-Jaramillo A; Ristova D ; et al. (2013)
Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling [...]
GP00001284
PHO1
Q8S403
Morphology
histidine to tyrosine @position 8388425 in chromosome III
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
Phosphate transporter PHO1
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
phytochrome D (PHYD)
Leaf morphology (increased petiole length)
Cotyledon morphology (reduced cotyledon area)
Coloration (anthocyanin accumulation in seedling stems)
Plant size (diminished effect of end-of-day pulse of far red light on hypocotyl elongation)
Plant architecture (decrease in number of rosette leaves at onset of flowering)
Coding,
Deletion
N
Arabidopsis thaliana
thale cress - (species) D
Intraspecific
Candidate Gene
Aukerman MJ; Hirschfeld M; Wester L ; et al. (1997)
A deletion in the PHYD gene of the Arabidopsis Wassilewskija ecotype defines a role for phytochrome [...]
GP00000874
PHYD
P42497
Morphology
Morphology
Morphology
Physiology
Morphology
14bp deletion causing premature stop codon N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
phytochrome D (PHYD)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
Pitx1
Limb Identity (feathered feet)
Cis-regulatory,
Deletion
Columba livia
rock pigeon - (species) D
Domesticated
Linkage Mapping
Domyan ET; Kronenberg Z; Infante CR ; et al. (2016)
Molecular shifts in limb identity underlie development of feathered feet in two domestic avian speci[...]
GP00000885
PITX1
P56673
Morphology
44kb deletion
Columba livia
rock pigeon - (species)
Columba livia
rock pigeon - (species) D
Pitx1
Columba livia
rock pigeon - (species)
Published - Accepted by Curator
pitx1
Pelvis morphology (loss of ventral spines)
Cis-regulatory,
Deletion
Gasterosteus aculeatus
three-spined stickleback - (species) D
Intraspecific
Linkage Mapping
Shapiro MD; Marks ME; Peichel CL ; et al. (2004)
Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks.
1 Additional References
GP00000886
Pitx1
P70314
Morphology
488bp promoter region : deletion 1 ; 5 kb deletion
Gasterosteus aculeatus
three-spined stickleback - (species)
Gasterosteus aculeatus
three-spined stickleback - (species) D
pitx1
Gasterosteus aculeatus
three-spined stickleback - (species)
Published - Accepted by Curator
pitx1
Pelvis morphology (loss of ventral spines)
Cis-regulatory,
Deletion
Gasterosteus aculeatus
three-spined stickleback - (species) D
Intraspecific
Linkage Mapping
Shapiro MD; Marks ME; Peichel CL ; et al. (2004)
Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks.
1 Additional References
GP00000887
Pitx1
P70314
Morphology
488bp promoter region : deletion 2 ; 757bp deletion present in the pelvic-reduced BEPA population from Alaska
Gasterosteus aculeatus
three-spined stickleback - (species)
Gasterosteus aculeatus
three-spined stickleback - (species) D
pitx1
Gasterosteus aculeatus
three-spined stickleback - (species)
Published - Accepted by Curator
pitx1
Pelvis morphology (loss of ventral spines)
Cis-regulatory,
Deletion
Gasterosteus aculeatus
three-spined stickleback - (species) D
Intraspecific
Linkage Mapping
Shapiro MD; Marks ME; Peichel CL ; et al. (2004)
Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks.
1 Additional References
GP00000888
Pitx1
P70314
Morphology
488bp promoter region : deletion 3 ; 3.5 kb deletion
Gasterosteus aculeatus
three-spined stickleback - (species)
Gasterosteus aculeatus
three-spined stickleback - (species) D
pitx1
Gasterosteus aculeatus
three-spined stickleback - (species)
Published - Accepted by Curator
pitx1
Pelvis morphology (loss of ventral spines)
Cis-regulatory,
Deletion
Gasterosteus aculeatus
three-spined stickleback - (species) D
Intraspecific
Linkage Mapping
Shapiro MD; Marks ME; Peichel CL ; et al. (2004)
Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks.
1 Additional References
GP00000889
Pitx1
P70314
Morphology
488bp promoter region : deletion 4 ; 757 bp deletion
Gasterosteus aculeatus
three-spined stickleback - (species)
Gasterosteus aculeatus
three-spined stickleback - (species) D
pitx1
Gasterosteus aculeatus
three-spined stickleback - (species)
Published - Accepted by Curator
pitx1
Pelvis morphology (loss of ventral spines)
Cis-regulatory,
Deletion
Gasterosteus aculeatus
three-spined stickleback - (species) D
Intraspecific
Linkage Mapping
Shapiro MD; Marks ME; Peichel CL ; et al. (2004)
Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks.
1 Additional References
GP00000890
Pitx1
P70314
Morphology
488bp promoter region : deletion 5 ; 2 kb deletion
Gasterosteus aculeatus
three-spined stickleback - (species)
Gasterosteus aculeatus
three-spined stickleback - (species) D
pitx1
Gasterosteus aculeatus
three-spined stickleback - (species)
Published - Accepted by Curator
pitx1
Pelvis morphology (loss of ventral spines)
Cis-regulatory,
Deletion
Gasterosteus aculeatus
three-spined stickleback - (species) D
Intraspecific
Linkage Mapping
Shapiro MD; Marks ME; Peichel CL ; et al. (2004)
Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks.
1 Additional References
GP00000891
Pitx1
P70314
Morphology
488bp promoter region : deletion 6 ; 973bp deletion present in the Hump Lake AK pelvic-reduced population (HUMP)
Gasterosteus aculeatus
three-spined stickleback - (species)
Gasterosteus aculeatus
three-spined stickleback - (species) D
pitx1
Gasterosteus aculeatus
three-spined stickleback - (species)
Published - Accepted by Curator
pitx1
Pelvis morphology (loss of ventral spines)
Cis-regulatory,
Deletion
Gasterosteus aculeatus
three-spined stickleback - (species) D
Intraspecific
Linkage Mapping
Shapiro MD; Marks ME; Peichel CL ; et al. (2004)
Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks.
1 Additional References
GP00000892
Pitx1
P70314
Morphology
488bp promoter region : deletion 7 ; 1868bp deletion
Gasterosteus aculeatus
three-spined stickleback - (species)
Gasterosteus aculeatus
three-spined stickleback - (species) D
pitx1
Gasterosteus aculeatus
three-spined stickleback - (species)
Published - Accepted by Curator
pitx1
Pelvis morphology (loss of ventral spines)
Cis-regulatory,
Deletion
Gasterosteus aculeatus
three-spined stickleback - (species) D
Intraspecific
Linkage Mapping
Shapiro MD; Marks ME; Peichel CL ; et al. (2004)
Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks.
1 Additional References
GP00000893
Pitx1
P70314
Morphology
488bp promoter region : deletion 8 ; 8 kb deletion
Gasterosteus aculeatus
three-spined stickleback - (species)
Gasterosteus aculeatus
three-spined stickleback - (species) D
pitx1
Gasterosteus aculeatus
three-spined stickleback - (species)
Published - Accepted by Curator
pitx1
Pelvis morphology (loss of ventral spines)
Cis-regulatory,
Deletion
Gasterosteus aculeatus
three-spined stickleback - (species) D
Intraspecific
Linkage Mapping
Shapiro MD; Marks ME; Peichel CL ; et al. (2004)
Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks.
1 Additional References
GP00000894
Pitx1
P70314
Morphology
488bp promoter region : deletion 9 ; 8 kb deletion
Gasterosteus aculeatus
three-spined stickleback - (species)
Gasterosteus aculeatus
three-spined stickleback - (species) D
pitx1
Gasterosteus aculeatus
three-spined stickleback - (species)
Published - Accepted by Curator
PLAG1
Body size (height; weight)
Cis-regulatory,
Insertion
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Karim L; Takeda H; Lin L ; et al. (2011)
Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine statur[...]
GP00001569
PLAG1
E1BEA5
Morphology
a (CCG)n trinucleotide repeat with 9> 11 copies and a SNP A>G immediately upstream of PLAG1 transcriptional start site
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
PLAG1
Bos taurus
cattle - (species)
Published - Accepted by Curator
PMEL17
Coloration (feathers)
Coding,
Deletion
Gallus gallus
chicken - (species) D
Domesticated
Candidate Gene
Kerje S; Sharma P; Gunnarsson U ; et al. (2004)
The Dominant white, Dun and Smoky color variants in chicken are associated with insertion/deletion p[...]
GP00000911
PMEL
Q98917
Morphology
deletion of amino acids 731-735
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
PMEL17
Gallus gallus
chicken - (species)
Published - Accepted by Curator
PMEL17
Coloration (feathers)
Coding,
Deletion
Gallus gallus
chicken - (species) D
Domesticated
Candidate Gene
Kerje S; Sharma P; Gunnarsson U ; et al. (2004)
The Dominant white, Dun and Smoky color variants in chicken are associated with insertion/deletion p[...]
GP00000912
PMEL
Q98917
Morphology
deletion of amino acids 280-284
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
PMEL17
Gallus gallus
chicken - (species)
Published - Accepted by Curator
PMEL17
Coloration (feathers)
Coding,
Insertion
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Kerje S; Sharma P; Gunnarsson U ; et al. (2004)
The Dominant white, Dun and Smoky color variants in chicken are associated with insertion/deletion p[...]
GP00000913
PMEL
Q98917
Morphology
insertion of amino acid 723-725 due to a 9bp-insert in exon 10
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
PMEL17
Gallus gallus
chicken - (species)
Published - Accepted by Curator
PMEL17
Coloration (coat)
Coding,
Deletion
Bos grunniens
domestic yak - (species) D
Domesticated
Candidate Gene
Zhang MQ; Xu X; Luo SJ (2014)
The genetics of brown coat color and white spotting in domestic yaks (Bos grunniens).
GP00001365
PMEL
P40967
Morphology
c.50_52del p.Leu18del in signal peptide
Bos grunniens
domestic yak - (species)
Bos grunniens
domestic yak - (species) D
PMEL17
Bos grunniens
domestic yak - (species)
Published - Accepted by Curator
PMEL17
Coloration (coat)
Coding,
SNP
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Gutiérrez-Gil B; Wiener P; Williams JL (2007)
Genetic effects on coat colour in cattle: dilution of eumelanin and phaeomelanin pigments in an F2-B[...]
GP00002027
PMEL
Q06154
Morphology
g.57669926G>A c.64G>A p.Gly22Arg
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
PMEL17
Bos taurus
cattle - (species)
Published - Accepted by Curator
PMEL17
Coloration (coat)
Coding,
Deletion
Bos taurus
cattle - (species) D
Bos grunniens
domestic yak - (species) D
Domesticated
Candidate Gene
Jolly RD; Wills JL; Kenny JE ; et al. (2008)
Coat-colour dilution and hypotrichosis in Hereford crossbred calves.
GP00002028
PMEL
Q06154
Morphology
3bp deletion - g.57669913_57669915delTTC - c.50_52delTTC - p.Leu19del
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Bos grunniens
domestic yak - (species) D
PMEL17
Bos taurus
cattle - (species)
Bos grunniens
domestic yak - (species)
Published - Accepted by Curator
PMEL17
Coloration (coat)
Cis-regulatory,
Insertion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Clark LA; Wahl JM; Rees CA ; et al. (2006)
Retrotransposon insertion in SILV is responsible for merle patterning of the domestic dog.
GP00002072
Pmel
Q60696
Morphology
due to a short interspersed element (SINE) insertion at the intron 10/exon 11 boundary. The SINE segregates with the merle phenotype in multiple breeds (Collie, Border Collie, Australian Shepherd, Cardigan Welsh Corgi, Dachshund, and Great Dane) and is absent from dogs representing breeds that do not have merle patterning. All examined harlequin Great Danes harbored the insertion in either a heterozygous or homozygous state.
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
PMEL17
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
PMEL17
Coloration (coat)
Coding,
Insertion
Mus musculus
house mouse - (species) D
Domesticated
Linkage Mapping
Kwon BS; Halaban R; Ponnazhagan S ; et al. (1995)
Mouse silver mutation is caused by a single base insertion in the putative cytoplasmic domain of Pme[...]
GP00002101
Pmel
Q60696
Morphology
single nucleotide (A) insertion in the putative cytoplasmic tail of the si/si Pmel 17 cDNA clone. This insertion is predicted to alter the last 24 amino acids at the C-terminus. Also predicted is the extension of the Pmel 17 protein by 12 residues because a new termination signal is created downstream from the wild-type reading frame. The silver pmel 17 protein has a major defect at the carboxyl terminus.
Mus musculus
house mouse - (species)
Mus musculus
house mouse - (species) D
PMEL17
Mus musculus
house mouse - (species)
Published - Accepted by Curator
PMEL17
Coloration (coat)
Cis-regulatory,
Insertion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Langevin M; Synkova H; Jancuskova T ; et al. (2018)
Merle phenotypes in dogs - SILV SINE insertions from Mc to Mh.
1 Additional References
GP00002266
Pmel
Q60696
Morphology
Allele of the Merle SINE insertaiion : Mc (208-230bp)
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
PMEL17
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
PMEL17
Coloration (coat)
Cis-regulatory,
Insertion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Langevin M; Synkova H; Jancuskova T ; et al. (2018)
Merle phenotypes in dogs - SILV SINE insertions from Mc to Mh.
1 Additional References
GP00002267
Pmel
Q60696
Morphology
Allele of the Merle SINE insertion : Mc+ (231-245bp)
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
PMEL17
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
PMEL17
Coloration (coat)
Cis-regulatory,
Insertion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Langevin M; Synkova H; Jancuskova T ; et al. (2018)
Merle phenotypes in dogs - SILV SINE insertions from Mc to Mh.
1 Additional References
GP00002268
Pmel
Q60696
Morphology
Allele of the Merle SINE insertion : Ma (247-254bp)
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
PMEL17
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
PMEL17
Coloration (coat)
Cis-regulatory,
Insertion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Langevin M; Synkova H; Jancuskova T ; et al. (2018)
Merle phenotypes in dogs - SILV SINE insertions from Mc to Mh.
1 Additional References
GP00002269
Pmel
Q60696
Morphology
Allele of the Merle SINE insertion : Ma+ (255-264bp)
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
PMEL17
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
PMEL17
Coloration (coat)
Cis-regulatory,
Insertion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Langevin M; Synkova H; Jancuskova T ; et al. (2018)
Merle phenotypes in dogs - SILV SINE insertions from Mc to Mh.
1 Additional References
GP00002270
Pmel
Q60696
Morphology
Allele of the Merle SINE insertion : Mh (269-277bp)
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
PMEL17
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
PMEL17
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Association Mapping
Brunberg E; Andersson L; Cothran G ; et al. (2006)
A missense mutation in PMEL17 is associated with the Silver coat color in the horse.
4 Additional References
GP00002271
Pmel
Q60696
Morphology
g.73665304C>T p.R625C
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
PMEL17
Equus caballus
horse - (species)
Published - Accepted by Curator
poils au dos (pad)
Bristle number (thorax)
Coding,
Deletion
N
Drosophila melanogaster
fruit fly - (species) D
Intraspecific
Linkage Mapping
Gibert JM; Marcellini S; David JR ; et al. (2005)
A major bristle QTL from a selected population of Drosophila uncovers the zinc-finger transcription [...]
GP00000915
pad
Q9VEW6
Morphology
29bp deletion N
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species) D
poils au dos (pad)
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
POLLED locus
Horns absence
Cis-regulatory,
Indel
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Medugorac I; Seichter D; Graf A ; et al. (2012)
Bovine polledness--an autosomal dominant trait with allelic heterogeneity.
2 Additional References
GP00000916
Morphology
complex 202-bp insertion-deletion in a non-coding region resulting in a long non-coding RNA (lncRNA) ectopic expression
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
POLLED locus
Bos taurus
cattle - (species)
Published - Accepted by Curator
POLLED locus
Horns absence
Cis-regulatory,
Insertion
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Medugorac I; Seichter D; Graf A ; et al. (2012)
Bovine polledness--an autosomal dominant trait with allelic heterogeneity.
3 Additional References
GP00002029
Morphology
a 80kb duplication is the "single causal mutation" in Holstein-Friesian cattle complex
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
POLLED locus
Bos taurus
cattle - (species)
Published - Accepted by Curator
POLLED locus
Horns absence
Cis-regulatory,
Complex Change
Bos taurus
cattle - (species) D
Bos grunniens
domestic yak - (species) D
Domesticated
Association Mapping
Medugorac I; Graf A; Grohs C ; et al. (2017)
Whole-genome analysis of introgressive hybridization and characterization of the bovine legacy of Mo[...]
GP00002030
Morphology
a complex 219-bp duplication–insertion (P219ID) beginning at 1;976;128 bp and a 7-bp deletion and 6-bp insertion (P1ID) located 621 bp upstream of this position. This rearrangement results in duplication of an 11-bp motif (5′-AAAGAAGCAAA-3′) that is entirely conserved among Bovidae and that is also duplicated in the 80-kb duplication responsible for Friesian polledness.
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Bos grunniens
domestic yak - (species) D
POLLED locus
Bos taurus
cattle - (species)
Bos grunniens
domestic yak - (species)
Published - Accepted by Curator
POLLED locus
Horns absence
Cis-regulatory,
Insertion
Bos taurus
cattle - (species) D
Domesticated
Association Mapping
Utsunomiya YT; Torrecilha RBP; Milanesi M ; et al. (2019)
Hornless Nellore cattle (Bos indicus) carrying a novel 110 kbp duplication variant of the polled loc[...]
GP00002031
Morphology
duplication of the region BTA1: 1;893;790–2;004;553 (about 110 kb)
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
POLLED locus
Bos taurus
cattle - (species)
Published - Accepted by Curator
Potassium channel subfamily K
Fin morphology (skeleton; dorsal fin; caudal fin; tail; paired fin)
Coding,
SNP
N
Carassius auratus
goldfish - (species) D
Domesticated
Association Mapping
Kon T; Omori Y; Fukuta K ; et al. (2020)
The Genetic Basis of Morphological Diversity in Domesticated Goldfish.
GP00002348
KCNK5
O95279
Morphology
Substitution of a hydrophobic amino acid (valine) with a hydrophilic amino acid (glutamic acid) appears to cause a critical alteration of channel gating. In total there are five amino acid substitutions or deletions in kcnk5bS in goldfish with the long-tail phenotype. N
Carassius auratus
goldfish - (species)
Carassius auratus
goldfish - (species) D
Potassium channel subfamily K
Carassius auratus
goldfish - (species)
Published - Accepted by Curator
PPAR-delta
Body size (height)
Unknown,
Unknown
Homo sapiens
human - (species)
Intraspecific
Association Mapping
N'Diaye A; Chen GK; Palmer CD ; et al. (2011)
Identification, replication, and fine-mapping of Loci associated with adult height in individuals of[...]
1 Additional References
GP00000918
PPARD
Q03181
Morphology
unknown
Homo sapiens
human - (species)
Homo sapiens
human - (species)
PPAR-delta
Homo sapiens
human - (species)
Published - Accepted by Curator
PPAR-delta
Ear size
Skin aspect
Coding,
SNP
Sus scrofa domesticus
domestic pig - (subspecies)
Domesticated
Linkage Mapping
Ren J; Duan Y; Qiao R ; et al. (2011)
A missense mutation in PPARD causes a major QTL effect on ear size in pigs.
GP00000919
PPARD
Q03181
Morphology
Morphology
G32E
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies)
PPAR-delta
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
PpeGID1c
Plant size (dwarfism)
Coding,
SNP
N
Prunus persica
peach - (species) D
Domesticated
Linkage Mapping
Hollender CA; Hadiarto T; Srinivasan C ; et al. (2016)
A brachytic dwarfism trait (dw) in peach trees is caused by a nonsense mutation within the gibberell[...]
GP00000920
GID1C
Q940G6
Morphology
Trp162* (TGG>TAG) N
Prunus persica
peach - (species)
Prunus persica
peach - (species) D
PpeGID1c
Prunus persica
peach - (species)
Published - Accepted by Curator
PRKG2
Body size (dwarfism)
Coding,
SNP
N
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Koltes JE; Mishra BP; Kumar D ; et al. (2009)
A nonsense mutation in cGMP-dependent type II protein kinase (PRKG2) causes dwarfism in American Ang[...]
GP00002273
PRKG2
Q13237
Morphology
c.1573C>T p.R525* N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
PRKG2
Bos taurus
cattle - (species)
Published - Accepted by Curator
PRKG2
Body size (dwarfism)
Coding,
SNP
N
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Koltes JE; Mishra BP; Kumar D ; et al. (2009)
A nonsense mutation in cGMP-dependent type II protein kinase (PRKG2) causes dwarfism in American Ang[...]
GP00002274
PRKG2
Q13237
Morphology
c.2032C>T p.R678* N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
PRKG2
Bos taurus
cattle - (species)
Published - Accepted by Curator
PROG1
Plant architecture
Unknown,
Unknown
Oryza sativa
rice - (species)
Domesticated
Candidate Gene
Tan L; Li X; Liu F ; et al. (2008)
Control of a key transition from prostrate to erect growth in rice domestication.
2 Additional References
GP00000925
PROG1
Q69NY0
Morphology
Various
Oryza rufipogon
(species)
Oryza sativa
rice - (species)
PROG1
Oryza sativa
rice - (species)
Published - Accepted by Curator
Prolactin
Hair length (long)
Coding,
SNP
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Littlejohn MD; Henty KM; Tiplady K ; et al. (2014)
Functionally reciprocal mutations of the prolactin signalling pathway define hairy and slick cattle.
GP00002032
PRL
P01239
Morphology
g.35105313A>C - c.661A>C - p.C221G
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Prolactin
Bos taurus
cattle - (species)
Published - Accepted by Curator
Prolactin
Hair length (short)
Coding,
Deletion
N
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Littlejohn MD; Henty KM; Tiplady K ; et al. (2014)
Functionally reciprocal mutations of the prolactin signalling pathway define hairy and slick cattle.
GP00002033
PRL
P01239
Morphology
1-bp deletion in exon 10 that introduces a premature stop codon (p.Leu462*) and loss of 120 C-terminal amino acids from the long isoform of the receptor (ss1067289408; chr20:39136558GC>G) N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Prolactin
Bos taurus
cattle - (species)
Published - Accepted by Curator
Prolactin receptor
Feather (slow-feathering ; delay)
Other,
Insertion
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Elferink MG; Vallée AA; Jungerius AP ; et al. (2008)
Partial duplication of the PRLR and SPEF2 genes at the late feathering locus in chicken.
1 Additional References
GP00002280
PRLR
P16471
Morphology
tandem duplication of 176324 basepairs resulting in a partially duplicated PRLR (dPRLR) gene nearly identical to the original PRLR ; except for its lack of a 149-amino acid C-terminal tail - which may titrate PRL ligands and act as a dominant-negative receptor
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
Prolactin receptor
Gallus gallus
chicken - (species)
Published - Accepted by Curator
Prolactin receptor
Feather (slow-feathering ; delay)
Coding,
Deletion
Meleagris gallopavo mexicana
(subspecies) D
Domesticated
Association Mapping
Derks MFL; Herrero-Medrano JM; Crooijmans RPMA ; et al. (2018)
Early and late feathering in turkey and chicken: same gene but different mutations.
GP00002281
PRLR
P16471
Morphology
g.9426018_9426022delTTGGT p.Glu726Aspfs*7 truncated PRLR protein that lacks 98 C-terminal AA ; this truncated PRLR protein is strikingly similar to the protein encoded by the slow feathering K allele in chicken
Meleagris gallopavo mexicana
(subspecies)
Meleagris gallopavo mexicana
(subspecies) D
Prolactin receptor
Meleagris gallopavo mexicana
(subspecies)
Published - Accepted by Curator
Prolactin receptor
Hair (slick ; short ; thermotolerance)
Thermoregulation (tolerance to warm climate)
Coding,
Deletion
N
Bos taurus
cattle - (species) D
Domesticated
Littlejohn MD; Henty KM; Tiplady K ; et al. (2014)
Functionally reciprocal mutations of the prolactin signalling pathway define hairy and slick cattle.
GP00002282
PRLR
P16471
Morphology
Physiology
g.39136559delC p.Leu462* N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Prolactin receptor
Bos taurus
cattle - (species)
Published - Accepted by Curator
Prolactin receptor
Hair (slick ; short)
Thermoregulation (tolerance to warm climate)
Coding,
SNP
N
Bos taurus
cattle - (species) D
Domesticated
Porto-Neto LR; Bickhart DM; Landaeta-Hernandez AJ ; et al. (2018)
Convergent Evolution of Slick Coat in Cattle through Truncation Mutations in the Prolactin Receptor.
GP00002283
PRLR
P16471
Morphology
Physiology
g.39136571C>A p.Ser465* N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Prolactin receptor
Bos taurus
cattle - (species)
Published - Accepted by Curator
Prolactin receptor
Hair (slick ; short)
Thermoregulation (tolerance to warm climate)
Coding,
SNP
N
Bos taurus
cattle - (species) D
Domesticated
Porto-Neto LR; Bickhart DM; Landaeta-Hernandez AJ ; et al. (2018)
Convergent Evolution of Slick Coat in Cattle through Truncation Mutations in the Prolactin Receptor.
GP00002284
PRLR
P16471
Morphology
Physiology
g.39136666C>T p.Arg497* N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Prolactin receptor
Bos taurus
cattle - (species)
Published - Accepted by Curator
prolyl endopeptidase (PREP)
Coloration (scales)
Cis-regulatory,
Unknown
Uta stansburiana
(species) D
Intraspecific
Association Mapping
Corl A; Bi K; Luke C ; et al. (2018)
The Genetic Basis of Adaptation following Plastic Changes in Coloration in a Novel Environment.
GP00002108
PREP
P48147
Morphology
no coding mutation associated with the phenotype - 2 differentiated SNPs in introns and one is a synonymous change.
Uta stansburiana
(species)
Uta stansburiana
(species) D
prolyl endopeptidase (PREP)
Uta stansburiana
(species)
Published - Accepted by Curator
protein kinase cAMP-dependent type I regulatory subunit alpha (PRKAR1A)
Coloration (scales)
Cis-regulatory,
Unknown
Uta stansburiana
(species) D
Intraspecific
Association Mapping
Corl A; Bi K; Luke C ; et al. (2018)
The Genetic Basis of Adaptation following Plastic Changes in Coloration in a Novel Environment.
GP00002109
Prkar1a
Q9DBC7
Morphology
no coding mutation associated with the phenotype - one differentiated SNP in an intron in the 5' UTR
Uta stansburiana
(species)
Uta stansburiana
(species) D
protein kinase cAMP-dependent type I regulatory subunit alpha (PRKAR1A)
Uta stansburiana
(species)
Published - Accepted by Curator
Prx1 = Mhox = Prrx1
Limb length
Cis-regulatory,
Unknown
Carollia perspicillata
Seba's short-tailed bat - (species)
Intergeneric or Higher
Candidate Gene
Cretekos CJ; Wang Y; Green ED ; et al. (2008)
Regulatory divergence modifies limb length between mammals.
GP00000934
Prrx1
P63013
Morphology
Not identified
Mus musculus
house mouse - (species)
Carollia perspicillata
Seba's short-tailed bat - (species)
Prx1 = Mhox = Prrx1
Carollia perspicillata
Seba's short-tailed bat - (species)
Published - Accepted by Curator
PsbHLH = A
Coloration (flowers)
Coding,
SNP
N
Pisum sativum
pea - (species)
Domesticated
Linkage Mapping
Hellens RP; Moreau C; Lin-Wang K ; et al. (2010)
Identification of Mendel's white flower character.
GP00000935
BHLH
E3SXU4
Morphology
Splice site mutation: a simple G to A transition in a splice donor site that leads to a mis-spliced mRNA with a premature stop codon N
Pisum sativum
pea - (species)
Pisum sativum
pea - (species)
PsbHLH = A
Pisum sativum
pea - (species)
Published - Accepted by Curator
PSMB7
Coloration (coat)
Coding,
SNP
Canis lupus familiaris
dog - (subspecies)
Domesticated
Linkage Mapping
Clark LA; Tsai KL; Starr AN ; et al. (2011)
A missense mutation in the 20S proteasome β2 subunit of Great Danes having harlequin coat patterning[...]
GP00000936
Psmb7
P70195
Morphology
c.146T>G p.V6G
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies)
PSMB7
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Ptch1
Limb morphology (skeleton)
Cis-regulatory,
Unknown
Bos taurus
cattle - (species) D
Intergeneric or Higher
Candidate Gene
Lopez-Rios J; Duchesne A; Speziale D ; et al. (2014)
Attenuated sensing of SHH by Ptch1 underlies evolution of bovine limbs.
GP00001389
Ptch1
Q61115
Morphology
LRM enhancer located between coding exons 15 and 19 at 37 kb of the transcription start site - exact causing mutation(s) unknown - Loss of activity of the LRM enhancer that normally upregulates Ptch1 expression in the limb-bud mesenchyme in response to SHH signalling
Mus musculus
house mouse - (species)
Bos taurus
cattle - (species) D
Ptch1
Bos taurus
cattle - (species)
Published - Accepted by Curator
PTS/TKD1
Leaf shape
Cis-regulatory,
Deletion
Solanum galapagense
(species) D
Interspecific
Linkage Mapping
Kimura S; Koenig D; Kang J ; et al. (2008)
Natural variation in leaf morphology results from mutation of a novel KNOX gene.
GP00000938
PTS
B2Y2G9
Morphology
1bp deletion at -1232 from start Met
Solanum cheesmaniae
(species)
Solanum galapagense
(species) D
PTS/TKD1
Solanum galapagense
(species)
Published - Accepted by Curator
Purple (Pr)
Plant color
Cis-regulatory,
Unknown
Brassica oleracea var. botrytis
(varietas)
Domesticated
Linkage Mapping
Chiu LW; Zhou X; Burke S ; et al. (2010)
The purple cauliflower arises from activation of a MYB transcription factor.
GP00000939
MYB2
E5D8F5
Morphology
unknown
Brassica oleracea
wild cabbage - (species)
Brassica oleracea var. botrytis
(varietas)
Purple (Pr)
Brassica oleracea var. botrytis
(varietas)
Published - Accepted by Curator
Q = wheat AP2-like (WAP2)
Inflorescence morphology
Spike morphology
Coding,
SNP
Triticum turgidum
(species)
Domesticated
Linkage Mapping
Simons KJ; Fellers JP; Trick HN ; et al. (2006)
Molecular characterization of the major wheat domestication gene Q.
GP00000940
WANT1
C1PH82
Morphology
Morphology
V329I
Triticum turgidum
(species)
Triticum turgidum
(species)
Q = wheat AP2-like (WAP2)
Triticum turgidum
(species)
Published - Accepted by Curator
qPE9-1
Plant architecture
Inflorescence architecture
Coding,
Indel
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Zhou Y; Zhu J; Li Z ; et al. (2009)
Deletion in a quantitative trait gene qPE9-1 associated with panicle erectness improves plant archit[...]
GP00000941
PAY1
B8Y995
Morphology
Morphology
637-bp deletion and 12-bp insertion resulting in truncated protein N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
qPE9-1
Oryza sativa
rice - (species)
Published - Accepted by Curator
qSW5
Grain size
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Shomura A; Izawa T; Ebana K ; et al. (2008)
Deletion in a gene associated with grain size increased yields during rice domestication.
1 Additional References
GP00000944
qSW5
F8SPD1
Morphology
1212bp deletion N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
qSW5
Oryza sativa
rice - (species)
Published - Accepted by Curator
R-spondin-2 (RSPO2)
Hair length (moustache / eyebrows)
Cis-regulatory,
Insertion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Cadieu E; Neff MW; Quignon P ; et al. (2009)
Coat variation in the domestic dog is governed by variants in three genes.
GP00000945
Rspo2
Q8BFU0
Morphology
a 167bp insertion within the 3'UTR at position which leads to a threefold increase in transcription of RSPO2 in muzzle skin of dogs with furnishings
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
R-spondin-2 (RSPO2)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
R/glyma09g36983
Coloration (seeds)
Coding,
SNP
N
Glycine max
soybean - (species)
Domesticated
Linkage Mapping
Gillman JD; Tetlow A; Lee JD ; et al. (2011)
Loss-of-function mutations affecting a specific Glycine max R2R3 MYB transcription factor result in [...]
1 Additional References
GP00000946
100780023
K7LFP2
Morphology
C377- creating premature Stop N
Glycine max
soybean - (species)
Glycine max
soybean - (species)
R/glyma09g36983
Glycine max
soybean - (species)
Published - Accepted by Curator
r1 colored1
Coloration (seeds)
Unknown,
Insertion
Zea mays
(species) D
Domesticated
Linkage Mapping
Hanson MA; Gaut BS; Stec AO ; et al. (1996)
Evolution of anthocyanin biosynthesis in maize kernels: the role of regulatory and enzymatic loci.
1 Additional References
GP00000947
Z138B04_Z333J11.11
Q8S483
Morphology
insertion of transposable element Ac
Zea mays
(species)
Zea mays
(species) D
r1 colored1
Zea mays
(species)
Published - Accepted by Curator
R2R3 MYB transcription factor
Trichome density (leaf)
Unknown,
Unknown
Erythranthe guttata
spotted monkey flower - (species)
Domesticated
Linkage Mapping
Hendrick MF; Finseth FR; Mathiasson ME ; et al. (2016)
The genetics of extreme microgeographic adaptation: an integrated approach identifies a major gene u[...]
GP00001598
PELAN
A0A060IEP7
Morphology
Unknown ; candidate indel in first intron and a nonsynonymous substitution (glutamine>lysine) in the 3rd exon
Erythranthe guttata
spotted monkey flower - (species)
Erythranthe guttata
spotted monkey flower - (species)
R2R3 MYB transcription factor
Erythranthe guttata
spotted monkey flower - (species)
Published - Accepted by Curator
R2R3-Myb
Coloration (flowers)
Cis-regulatory,
Unknown
Phlox drummondii
(species)
Intraspecific
Linkage Mapping
Hopkins R; Rausher MD (2011)
Identification of two genes causing reinforcement in the Texas wildflower Phlox drummondii.
GP00000948
H8ZS70
Morphology
unknown
Phlox drummondii
(species)
Phlox drummondii
(species)
R2R3-Myb
Phlox drummondii
(species)
Published - Accepted by Curator
RALY (hnRNP associated with lethal yellow)
Coloration (coat)
Cis-regulatory,
Insertion
Canis lupus
gray wolf - (species) D
Intraspecific
Association Mapping
Dreger DL; Parker HG; Ostrander EA ; et al. (2013 May-Jun)
Identification of a mutation that is associated with the saddle tan and black-and-tan phenotypes in [...]
GP00001366
RALY
Q9UKM9
Morphology
16 bpduplication g.1875_1890dupCCCCAGGTCAGAGTTT in intron
Canis lupus
gray wolf - (species)
Canis lupus
gray wolf - (species) D
RALY (hnRNP associated with lethal yellow)
Canis lupus
gray wolf - (species)
Published - Accepted by Curator
RB1
Body size (weight)
Body size (bone length)
Unknown,
Unknown
Gallus gallus
chicken - (species)
Domesticated
Linkage Mapping
Zhang H; Liu SH; Zhang Q ; et al. (2011)
Fine-mapping of quantitative trait loci for body weight and bone traits and positional cloning of th[...]
GP00000957
Morphology
Morphology
unknown
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
RB1
Gallus gallus
chicken - (species)
Published - Accepted by Curator
Rc
Coloration (seed)
Coding,
SNP
N
Oryza glaberrima
African rice - (species)
Domesticated
Candidate Gene
Gross BL; Steffen FT; Olsen KM (2010)
The molecular basis of white pericarps in African domesticated rice: novel mutations at the Rc gene.
GP00000958
Rc
A7J5U6
Morphology
Premature stop codon in exon 7; Lys>* N
Oryza glaberrima
African rice - (species)
Oryza glaberrima
African rice - (species)
Rc
Oryza glaberrima
African rice - (species)
Published - Accepted by Curator
Rc
Coloration (seed)
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Sweeney MT; Thomson MJ; Cho YG ; et al. (2007)
Global dissemination of a single mutation conferring white pericarp in rice.
GP00000959
Rc
A7J5U6
Morphology
14bp deletion N
Oryza rufipogon
(species)
Oryza sativa
rice - (species) D
Rc
Oryza sativa
rice - (species)
Published - Accepted by Curator
Rc
Coloration (seed)
Coding,
SNP
N
Oryza sativa
rice - (species)
Domesticated
Candidate Gene
Sweeney MT; Thomson MJ; Cho YG ; et al. (2007)
Global dissemination of a single mutation conferring white pericarp in rice.
2 Additional References
GP00000960
Rc
A7J5U6
Morphology
substitution; C->A in exon 6; introduces a premature stop codon (Cys>*) that truncates the protein before the bHLH domain N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Rc
Oryza sativa
rice - (species)
Published - Accepted by Curator
RCO-A
Leaf shape (simplification)
Cis-regulatory,
Unknown
Capsella grandiflora
(species)
Interspecific
Linkage Mapping
Sicard A; Thamm A; Marona C ; et al. (2014)
Repeated evolutionary changes of leaf morphology caused by mutations to a homeobox gene.
GP00000961
RCO
A0A023NDU4
Morphology
Complex haplotype
Capsella rubella
(species)
Capsella grandiflora
(species)
RCO-A
Capsella grandiflora
(species)
Published - Accepted by Curator
RCO-A/B (Reduced Complexity)
Leaf shape (simplification)
Gene Loss,
Deletion
N
Arabidopsis thaliana
thale cress - (species) D
Interspecific
Candidate Gene
Vlad D; Kierzkowski D; Rast MI ; et al. (2014)
Leaf shape evolution through duplication, regulatory diversification, and loss of a homeobox gene.
GP00000962
RCO
A0A023NDU4
Morphology
Gene deletion N
Arabidopsis
(genus)
Arabidopsis thaliana
thale cress - (species) D
RCO-A/B (Reduced Complexity)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
Reduced height-1 (Rht1)
Plant size (dwarfism)
Coding,
SNP
N
Helianthus annuus
common sunflower - (species) D
Domesticated
Linkage Mapping
Ramos ML; Altieri E; Bulos M ; et al. (2013)
Phenotypic characterization, genetic mapping and candidate gene analysis of a source conferring redu[...]
GP00001728
D8
Q9ST48
Morphology
T-to-C transition corresponding to nucleotide positions 143 - the SNP at position 143 converts a leucine residue in a proline within the conserved DELLA motif—This amino acid position corresponds to amino acid position 57 in the full-length amino acid sequence encoded by the L. sativa DELLA1 nucleotide sequence of GenBank Accession No. BAG71200.1 N
Helianthus annuus
common sunflower - (species)
Helianthus annuus
common sunflower - (species) D
Reduced height-1 (Rht1)
Helianthus annuus
common sunflower - (species)
Published - Accepted by Curator
Reduced height-B1 (RhtB1)
Plant size (dwarfism)
Coding,
SNP
N
Triticum aestivum
bread wheat - (species)
Domesticated
Linkage Mapping
Peng J; Richards DE; Hartley NM ; et al. (1999)
'Green revolution' genes encode mutant gibberellin response modulators.
GP00000965
D8
Q9ST48
Morphology
Q64*; TGA>CGA N
Triticum aestivum
bread wheat - (species)
Triticum aestivum
bread wheat - (species)
Reduced height-B1 (RhtB1)
Triticum aestivum
bread wheat - (species)
Published - Accepted by Curator
Reduced height-D1 (RhtD1)
Plant size (dwarfism)
Coding,
SNP
N
Triticum aestivum
bread wheat - (species)
Domesticated
Linkage Mapping
Peng J; Richards DE; Hartley NM ; et al. (1999)
'Green revolution' genes encode mutant gibberellin response modulators.
GP00000966
D8
Q9ST48
Morphology
E61*; GGA>TGA N
Triticum aestivum
bread wheat - (species)
Triticum aestivum
bread wheat - (species)
Reduced height-D1 (RhtD1)
Triticum aestivum
bread wheat - (species)
Published - Accepted by Curator
RNF11
Body size (dwarfism)
Cis-regulatory,
Deletion
Bos taurus
cattle - (species) D
Domesticated
Association Mapping
Sartelet A; Druet T; Michaux C ; et al. (2012)
A splice site variant in the bovine RNF11 gene compromises growth and regulation of the inflammatory[...]
GP00002275
RNF11
Q9Y3C5
Morphology
g.95601696A>G c.124-2A>G affecting splicing site
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
RNF11
Bos taurus
cattle - (species)
Published - Accepted by Curator
Root System Architecture 1
Root growth (allometry of lateral roots)
Cis-regulatory,
SNP
Arabidopsis thaliana
thale cress - (species)
Intraspecific
Association Mapping
Rosas U; Cibrian-Jaramillo A; Ristova D ; et al. (2013)
Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling [...]
GP00001285
Root System Architecture 1
F4JL94
Morphology
348bp upstream of the 5'UTR
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
Root System Architecture 1
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
ROSE INTENSITY1 (ROI1)
Coloration (flowers)
Cis-regulatory,
Unknown
Erythranthe lewisii
(species)
Interspecific
Linkage Mapping
Yuan YW; Sagawa JM; Young RC ; et al. (2013)
Genetic dissection of a major anthocyanin QTL contributing to pollinator-mediated reproductive isola[...]
GP00000996
ROI1
L7VK04
Morphology
unknown but coding variation was ruled out
Erythranthe lewisii
(species)
Erythranthe lewisii
(species)
ROSE INTENSITY1 (ROI1)
Erythranthe lewisii
(species)
Published - Accepted by Curator
ROSEA
Coloration (flowers)
Unknown,
Unknown
Antirrhinum majus
snapdragon - (species)
Intraspecific
Linkage Mapping
Whibley AC; Langlade NB; Andalo C ; et al. (2006)
Evolutionary paths underlying flower color variation in Antirrhinum.
GP00000997
ROS1
Q2VAZ7
Morphology
Not identified
Antirrhinum majus
snapdragon - (species)
Antirrhinum majus
snapdragon - (species)
ROSEA
Antirrhinum majus
snapdragon - (species)
Published - Accepted by Curator
Ruby
Coloration (fruit; cold-dependent)
Cis-regulatory,
Insertion
Citrus sinensis
sweet orange - (species) D
Domesticated
Candidate Gene
Butelli E; Licciardello C; Zhang Y ; et al. (2012)
Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood orange[...]
GP00001017
Ruby
H6U1F1
Morphology
TE (Tcs2) insertion triggering cold-dependent expression
Citrus
(genus)
Citrus sinensis
sweet orange - (species) D
Ruby
Citrus sinensis
sweet orange - (species)
Published - Accepted by Curator
Ruby
Coloration (fruit; cold-dependent)
Cis-regulatory,
Insertion
Citrus sinensis
sweet orange - (species) D
Domesticated
Candidate Gene
Butelli E; Licciardello C; Zhang Y ; et al. (2012)
Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood orange[...]
GP00001018
Ruby
H6U1F1
Morphology
TE (Tcs1) insertion triggering cold-dependent expression
Citrus
(genus)
Citrus sinensis
sweet orange - (species) D
Ruby
Citrus sinensis
sweet orange - (species)
Published - Accepted by Curator
Ruby
Coloration (fruit; cold-dependent)
Cis-regulatory,
Deletion
Citrus sinensis
sweet orange - (species) D
Domesticated
Candidate Gene
Butelli E; Licciardello C; Zhang Y ; et al. (2012)
Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood orange[...]
GP00002106
Ruby
H6U1F1
Morphology
Recombination between the LTRs of the TE (Tcs1) insertion which led to just one LTR. The single LTR still confers responsiveness to cold temperatures. This recombination event results in enhanced expression of Ruby in Maro (I).
Citrus
(genus)
Citrus sinensis
sweet orange - (species) D
Ruby
Citrus sinensis
sweet orange - (species)
Published - Accepted by Curator
RXFP2
Horns absence
Somatic sex change
Gene Amplification,
Insertion
Ovis aries
sheep - (species)
Domesticated
Linkage Mapping
Johnston SE; Gratten J; Berenos C ; et al. (2013)
Life history trade-offs at a single locus maintain sexually selected genetic variation.
1 Additional References
GP00001019
RXFP2
Q8WXD0
Morphology
Physiology
1833-bp genomic insertion located in the 3'-UTR region of RXFP2
Ovis aries
sheep - (species)
Ovis aries
sheep - (species)
RXFP2
Ovis aries
sheep - (species)
Published - Accepted by Curator
S locus supergene (GLO/CFB Cluster)
Flower morphology (heterostyly)
Other,
Complex Change
Primula vulgaris
(species)
Intraspecific
Linkage Mapping
Li J; Cocker JM; Wright J ; et al. (2016)
Genetic architecture and evolution of the S locus supergene in Primula vulgaris.
GP00001392
Morphology
Absence/presence of a supergene constituted by a cluster of 6 genes
Primula vulgaris
(species)
Primula vulgaris
(species)
S locus supergene (GLO/CFB Cluster)
Primula vulgaris
(species)
Published - Accepted by Curator
SAP (Sterile Apetala)
Petal size
Cis-regulatory,
SNP
Capsella rubella
(species) D
Interspecific
Linkage Mapping
Sicard A; Kappel C; Lee YW ; et al. (2016)
Standing genetic variation in a tissue-specific enhancer underlies selfing-syndrome evolution in Cap[...]
GP00001371
SAP
Q9FKH1
Morphology
5 SNP in intron in particular
Capsella grandiflora
(species)
Capsella rubella
(species) D
SAP (Sterile Apetala)
Capsella rubella
(species)
Published - Accepted by Curator
SBNO1
Head size
Coding,
SNP
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Taal HR; Pourcain BS; Thiering E ; et al. (2012)
Common variants at 12q15 and 12q24 are associated with infant head circumference.
GP00001023
SBNO1
A3KN83
Morphology
Ser729Asn
Homo sapiens
human - (species)
Homo sapiens
human - (species)
SBNO1
Homo sapiens
human - (species)
Published - Accepted by Curator
scabrous
Bristle number (abdomen)
Unknown,
Unknown
Drosophila melanogaster
fruit fly - (species)
Intraspecific
Linkage Mapping
Lai C; Lyman RF; Long AD ; et al. (1994)
Naturally occurring variation in bristle number and DNA polymorphisms at the scabrous locus of Droso[...]
GP00001024
sca
P21520
Morphology
unknown; but different sites than for thorax association
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species)
scabrous
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
scabrous
Bristle number (thorax)
Unknown,
Unknown
Drosophila melanogaster
fruit fly - (species)
Intraspecific
Linkage Mapping
Lai C; Lyman RF; Long AD ; et al. (1994)
Naturally occurring variation in bristle number and DNA polymorphisms at the scabrous locus of Droso[...]
GP00001025
sca
P21520
Morphology
unknown; but different sites than for abdomen association
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species)
scabrous
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
SCARB1
Carotenoid content
Coding,
SNP
N
Serinus canaria
common canary - (species) D
Intraspecific
Linkage Mapping
Toomey MB; Lopes RJ; Araújo PM ; et al. (2017)
High-density lipoprotein receptor SCARB1 is required for carotenoid coloration in birds.
GP00001681
Scarb1
Q61009
Morphology
T>G nucleotide substitution in the splice-donor site immediately downstream of exon 4 of the SCARB1 gene. This mutation results in abnormal splicing; with the most abundant transcript lacking exon 4. Isoform 4 of SCARB1; the most abundant transcript isoform in the white recessive canary; is predicted to lack 68 amino acids; a deficiency which disrupts SCARB1 protein function. N
Serinus canaria
common canary - (species)
Serinus canaria
common canary - (species) D
SCARB1
Serinus canaria
common canary - (species)
Published - Accepted by Curator
SCARB1
Coloration (silk; carotenoids)
Cis-regulatory,
Unknown
Bombyx mori
domestic silkworm - (species) D
Domesticated
Linkage Mapping
Sakudoh T; Iizuka T; Narukawa J ; et al. (2010)
A CD36-related transmembrane protein is coordinated with an intracellular lipid-binding protein in s[...]
GP00001905
Cameo2
D2KXB3
Morphology
difference in expression levels - three non synonymous mutations are also observed in the coding region - the gene is also named Cameo2
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
SCARB1
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
SCRB15
Coloration (silk; carotenoids)
Coding,
Insertion
N
Bombyx mori
domestic silkworm - (species) D
Domesticated
Linkage Mapping
Sakudoh T; Kuwazaki S; Iizuka T ; et al. (2013)
CD36 homolog divergence is responsible for the selectivity of carotenoid species migration to the si[...]
GP00001904
SCRB15
K7ZRZ1
Morphology
In the F mutant SCRB15 mRNA structure was severely disrupted due to a 1.4 kb genomic insertion in a coding exon N
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
SCRB15
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
Sd1 (=GA20ox-2)
Plant size (height)
2 Mutations:
Coding
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Asano K; Yamasaki M; Takuno S ; et al. (2011)
Artificial selection for a green revolution gene during japonica rice domestication.
GP00001027
GA20OX2
Q0JH50
Morphology
2 mutations
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Sd1 (=GA20ox-2)
Oryza sativa
rice - (species)
Published - Accepted by Curator
Sd1 (=GA20ox-2)
Plant size (dwarfism)
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Sasaki A; Ashikari M; Ueguchi-Tanaka M ; et al. (2002)
Green revolution: a mutant gibberellin-synthesis gene in rice.
3 Additional References
GP00001028
GA20OX2
Q0JH50
Morphology
383bp deletion introducing premature stop codon N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
Sd1 (=GA20ox-2)
Oryza sativa
rice - (species)
Published - Accepted by Curator
Sd1 (=GA20ox-2)
Plant size (dwarfism)
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Candidate Gene
Sasaki A; Ashikari M; Ueguchi-Tanaka M ; et al. (2002)
Green revolution: a mutant gibberellin-synthesis gene in rice.
GP00001029
GA20OX2
Q0JH50
Morphology
G94V
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Sd1 (=GA20ox-2)
Oryza sativa
rice - (species)
Published - Accepted by Curator
Sd1 (=GA20ox-2)
Plant size (dwarfism)
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Candidate Gene
Sasaki A; Ashikari M; Ueguchi-Tanaka M ; et al. (2002)
Green revolution: a mutant gibberellin-synthesis gene in rice.
GP00001030
GA20OX2
Q0JH50
Morphology
D349H
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Sd1 (=GA20ox-2)
Oryza sativa
rice - (species)
Published - Accepted by Curator
Sd1 (=GA20ox-2)
Plant size (dwarfism)
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Candidate Gene
Sasaki A; Ashikari M; Ueguchi-Tanaka M ; et al. (2002)
Green revolution: a mutant gibberellin-synthesis gene in rice.
GP00001031
GA20OX2
Q0JH50
Morphology
L266F
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Sd1 (=GA20ox-2)
Oryza sativa
rice - (species)
Published - Accepted by Curator
self-pruning (sp)
Vegetative/Reproductive state switch
Coding,
SNP
Solanum lycopersicum
tomato - (species) D
Domesticated
Linkage Mapping
Pnueli L; Carmel-Goren L; Hareven D ; et al. (1998)
The SELF-PRUNING gene of tomato regulates vegetative to reproductive switching of sympodial meristem[...]
GP00001035
SP
O82088
Morphology
P76L due to CCT->CTT
Solanum lycopersicum
tomato - (species)
Solanum lycopersicum
tomato - (species) D
self-pruning (sp)
Solanum lycopersicum
tomato - (species)
Published - Accepted by Curator
SGK3
Hair (hypotrichosis)
Coding,
Deletion
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Parker HG; Harris A; Dreger DL ; et al. (2017)
The bald and the beautiful: hairlessness in domestic dog breeds.
GP00002262
Sgk3
Q9ERE3
Morphology
Val96GlyfsTer50 deletion that removes four bases (TTAG) within exon 4 ; creating a new protein sequence for 50 amino acids and a premature stop at amino acid 157 N
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
SGK3
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
SGK3
Hair (hypotrichosis)
Coding,
Insertion
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Hytönen MK; Lohi H (2019)
A frameshift insertion in SGK3 leads to recessive hairlessness in Scottish Deerhounds: a candidate g[...]
1 Additional References
GP00002263
Sgk3
Q9ERE3
Morphology
c.137_138insT p.Glu47GlyfsTer3 N
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
SGK3
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
SHELL
Fruit shell thickness
Coding,
SNP
Elaeis guineensis
African oil palm - (species)
Domesticated
Linkage Mapping
Singh R; Low ET; Ooi LC ; et al. (2013)
The oil palm SHELL gene controls oil yield and encodes a homologue of SEEDSTICK.
GP00001047
AGL11
Q38836
Morphology
1a.a substitution in DNA binding domain
Elaeis guineensis
African oil palm - (species)
Elaeis guineensis
African oil palm - (species)
SHELL
Elaeis guineensis
African oil palm - (species)
Published - Accepted by Curator
SHELL
Fruit shell thickness
Coding,
SNP
Elaeis guineensis
African oil palm - (species)
Domesticated
Candidate Gene
Singh R; Low ET; Ooi LC ; et al. (2013)
The oil palm SHELL gene controls oil yield and encodes a homologue of SEEDSTICK.
GP00001048
AGL11
Q38836
Morphology
1a.a substitution in DNA binding domain
Elaeis guineensis
African oil palm - (species)
Elaeis guineensis
African oil palm - (species)
SHELL
Elaeis guineensis
African oil palm - (species)
Published - Accepted by Curator
SLC24A
Coloration (eyes)
Coding,
Deletion
N
Equus caballus
horse - (species) D
Domesticated
Association Mapping
Mack M; Kowalski E; Grahn R ; et al. (2017)
Two Variants in SLC24A5 Are Associated with "Tiger-Eye" Iris Pigmentation in Puerto Rican Paso Fino [...]
GP00002276
Slc24a5
Q8C261
Morphology
628 bp deletion encompassing all of exon 7 of SLC24A5 (c.875-340_1081+82del) N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
SLC24A
Equus caballus
horse - (species)
Published - Accepted by Curator
SLC24A
Coloration (eyes)
Coding,
SNP
N
Equus caballus
horse - (species) D
Domesticated
Association Mapping
Mack M; Kowalski E; Grahn R ; et al. (2017)
Two Variants in SLC24A5 Are Associated with "Tiger-Eye" Iris Pigmentation in Puerto Rican Paso Fino [...]
GP00002277
Slc24a5
Q8C261
Morphology
c.272A>T p.Phe91Tyr N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
SLC24A
Equus caballus
horse - (species)
Published - Accepted by Curator
SLC24A5 (NCKX5)
Coloration (eyes; skin)
Coding,
SNP
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Lamason RL; Mohideen MA; Mest JR ; et al. (2005)
SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans.
5 Additional References
GP00001056
Slc24a5
Q8C261
Morphology
Ala111Thr
Homo sapiens
human - (species)
Homo sapiens
human - (species)
SLC24A5 (NCKX5)
Homo sapiens
human - (species)
Published - Accepted by Curator
slc2a11b
Coloration (eyes)
Coding,
SNP
N
Columba livia
rock pigeon - (species) D
Domesticated
Linkage Mapping
Maclary ET; Phillips B; Wauer R ; et al. (2021)
Two Genomic Loci Control Three Eye Colors in the Domestic Pigeon (Columba livia).
2 Additional References
GP00002367
slc2a11b
F6P601
Morphology
"The premature stop codon in pearl-eyed pigeons falls in exon 3 of SLC2A11B, and is predicted to severely truncate the resulting protein from 504 to 57 amino acids."
"Based on genotypes at the two coding SNPs in the pearl eye haplotype, we found that gene expression in embryo head samples only shows changes associated with the pearl eye haplotype in SLC2A11B, and not in any other genes within 15 kb of the pearl eye haplotype, further supporting SLC2A11B as the primary candidate for the pearl eye phenotype (supplementary fig. S3A, Supplementary Material online). Embryo heads homozygous for the pearl allele show a significant reduction in SLC2A11B expression (P = 3.94 × 10−6, two-tailed t-test; supplementary fig. S3B, Supplementary Material online). Analysis of read distribution within the SLC2A11B gene shows a decrease in spliced reads specifically within the first three annotated exons, suggesting that alternative splicing or nonsense-mediated decay may be occurring (supplementary fig. S3D, Supplementary Material online)." N
Columba livia
rock pigeon - (species)
Columba livia
rock pigeon - (species) D
slc2a11b
Columba livia
rock pigeon - (species)
Published - Accepted by Curator
SLC36A1
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Linkage Mapping
Cook D; Brooks S; Bellone R ; et al. (2008)
Missense mutation in exon 2 of SLC36A1 responsible for champagne dilution in horses.
GP00002278
SLC36A1
Q7Z2H8
Morphology
c.188C>G p.T63R
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
SLC36A1
Equus caballus
horse - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Linkage Mapping
Mariat D; Taourit S; Guérin G (2003 Jan-Feb)
A mutation in the MATP gene causes the cream coat colour in the horse.
GP00001057
SLC45A2
Q9UMX9
Morphology
c.457G>A p.(Asp153Asn)
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
SLC45A2=MATP
Equus caballus
horse - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (feathers)
Coding,
SNP
Coturnix japonica
Japanese quail - (species)
Domesticated
Linkage Mapping
Gunnarsson U; Hellström AR; Tixier-Boichard M ; et al. (2007)
Mutations in SLC45A2 cause plumage color variation in chicken and Japanese quail.
GP00001058
SLC45A2
Q9UMX9
Morphology
G->T transversion at the splice acceptor site just preceding exon 4; causes in-frame skipping of exon 4
Coturnix japonica
Japanese quail - (species)
Coturnix japonica
Japanese quail - (species)
SLC45A2=MATP
Coturnix japonica
Japanese quail - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (feathers)
Coding,
Deletion
N
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Gunnarsson U; Hellström AR; Tixier-Boichard M ; et al. (2007)
Mutations in SLC45A2 cause plumage color variation in chicken and Japanese quail.
GP00001059
SLC45A2
Q9UMX9
Morphology
1bp deletion at codon 36; resulting in frameshift and a premature stop codon in exon 1; the corresponding mRNA appears to be degraded by Nonsense-mediated mRNA decay. N
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
SLC45A2=MATP
Gallus gallus
chicken - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (eyes; fur)
Coding,
SNP
Mus musculus
house mouse - (species)
Domesticated
Linkage Mapping
Du J; Fisher DE (2002)
Identification of Aim-1 as the underwhite mouse mutant and its transcriptional regulation by MITF.
GP00001060
SLC45A2
Q9UMX9
Morphology
N153D
Mus musculus
house mouse - (species)
Mus musculus
house mouse - (species)
SLC45A2=MATP
Mus musculus
house mouse - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (eyes; hair; skin)
Coding,
SNP
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Graf J; Hodgson R; van Daal A (2005)
Single nucleotide polymorphisms in the MATP gene are associated with normal human pigmentation varia[...]
3 Additional References
GP00001061
SLC45A2
Q9UMX9
Morphology
Phe374Leu
Homo sapiens
human - (species)
Homo sapiens
human - (species)
SLC45A2=MATP
Homo sapiens
human - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (feathers)
Coding,
SNP
Columba livia
rock pigeon - (species) D
Domesticated
Linkage Mapping
Domyan ET; Guernsey MW; Kronenberg Z ; et al. (2014)
Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon.
GP00001062
SLC45A2
Q9UMX9
Morphology
His341Arg
Columba livia
rock pigeon - (species)
Columba livia
rock pigeon - (species) D
SLC45A2=MATP
Columba livia
rock pigeon - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (coat)
Coding,
SNP
Panthera tigris
tiger - (species) D
Intraspecific
Association Mapping
Xu X; Dong GX; Hu XS ; et al. (2013)
The genetic basis of white tigers.
GP00001063
SLC45A2
Q9UMX9
Morphology
A477V
Panthera tigris
tiger - (species)
Panthera tigris
tiger - (species) D
SLC45A2=MATP
Panthera tigris
tiger - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (coat; albinism)
Coding,
SNP
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Rothammer S; Kunz E; Seichter D ; et al. (2017)
Detection of two non-synonymous SNPs in SLC45A2 on BTA20 as candidate causal mutations for oculocuta[...]
GP00002036
SLC45A2
Q9UMX9
Morphology
exact causing mutation(s) unknown - two possible amino acid changes
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
SLC45A2=MATP
Bos taurus
cattle - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (albinism)
Coding,
Insertion
Oryzias latipes
Japanese medaka - (species) D
Domesticated
Linkage Mapping
Fukamachi S; Shimada A; Shima A (2001)
Mutations in the gene encoding B, a novel transporter protein, reduce melanin content in medaka.
GP00002286
SLC45A2
Q9UMX9
Morphology
tandem insertion of 195 nt identical to the adjacent ORF sequence. This tandem repeat produces an insertion of 65 amino acids
Oryzias latipes
Japanese medaka - (species)
Oryzias latipes
Japanese medaka - (species) D
SLC45A2=MATP
Oryzias latipes
Japanese medaka - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (albinism)
Cis-regulatory,
Complex Change
Oryzias latipes
Japanese medaka - (species) D
Domesticated
Candidate Gene
Fukamachi S; Kinoshita M; Tsujimura T ; et al. (2008)
Rescue from oculocutaneous albinism type 4 using medaka slc45a2 cDNA driven by its own promoter.
GP00002287
SLC45A2
Q9UMX9
Morphology
Promoter complex change resulting in loss of expression : an inversion of 167 bp ; an insertion of 48 bp ; and a deletion of 172 bp
Oryzias latipes
Japanese medaka - (species)
Oryzias latipes
Japanese medaka - (species) D
SLC45A2=MATP
Oryzias latipes
Japanese medaka - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (feathers)
Coding,
SNP
N
Gallus gallus
chicken - (species) D
Domesticated
Association Mapping
Gunnarsson U; Hellström AR; Tixier-Boichard M ; et al. (2007)
Mutations in SLC45A2 cause plumage color variation in chicken and Japanese quail.
GP00002294
SLC45A2
Q9UMX9
Morphology
c.1039C>A p.L347M N
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
SLC45A2=MATP
Gallus gallus
chicken - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (feathers)
Coding,
SNP
N
Gallus gallus
chicken - (species) D
Domesticated
Association Mapping
Gunnarsson U; Hellström AR; Tixier-Boichard M ; et al. (2007)
Mutations in SLC45A2 cause plumage color variation in chicken and Japanese quail.
GP00002295
SLC45A2
Q9UMX9
Morphology
c.830A>G p.Y277C N
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
SLC45A2=MATP
Gallus gallus
chicken - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (coat; albinism)
Coding,
Deletion
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Winkler PA; Gornik KR; Ramsey DT ; et al. (2014)
A partial gene deletion of SLC45A2 causes oculocutaneous albinism in Doberman pinscher dogs.
GP00002296
SLC45A2
Q9UMX9
Morphology
4081 base pair deletion resulting in loss of the terminus of exon seven of SLC45A2 N
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
SLC45A2=MATP
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (coat; albinism)
Coding,
SNP
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Wijesena HR; Schmutz SM (2015 May-Jun)
A Missense Mutation in SLC45A2 Is Associated with Albinism in Several Small Long Haired Dog Breeds.
GP00002297
SLC45A2
Q9UMX9
Morphology
c.1478G>A p.G493D N
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
SLC45A2=MATP
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (coat; albinism)
Coding,
Deletion
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Caduff M; Bauer A; Jagannathan V ; et al. (2017)
A single base deletion in the SLC45A2 gene in a Bullmastiff with oculocutaneous albinism.
GP00002298
SLC45A2
Q9UMX9
Morphology
c.1287delC p.Met430CysfsTer4 N
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
SLC45A2=MATP
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Sevane N; Sanz CR; Dunner S (2019)
Explicit evidence for a missense mutation in exon 4 of SLC45A2 gene causing the pearl coat dilution [...]
GP00002304
SLC45A2
Q9UMX9
Morphology
c.985G>A p.(Ala329Thr)
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
SLC45A2=MATP
Equus caballus
horse - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Holl HM; Pflug KM; Yates KM ; et al. (2019)
A candidate gene approach identifies variants in SLC45A2 that explain dilute phenotypes, pearl and s[...]
GP00002305
SLC45A2
Q9UMX9
Morphology
c.568G>A p.(Gly190Arg)
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
SLC45A2=MATP
Equus caballus
horse - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Holl HM; Pflug KM; Yates KM ; et al. (2019)
A candidate gene approach identifies variants in SLC45A2 that explain dilute phenotypes, pearl and s[...]
GP00002306
SLC45A2
Q9UMX9
Morphology
c.305G>A p.(Arg102Gln)
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
SLC45A2=MATP
Equus caballus
horse - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (feathers)
Coding,
SNP
Coturnix japonica
Japanese quail - (species)
Domesticated
Linkage Mapping
Gunnarsson U; Hellström AR; Tixier-Boichard M ; et al. (2007)
Mutations in SLC45A2 cause plumage color variation in chicken and Japanese quail.
GP00002307
SLC45A2
Q9UMX9
Morphology
c.287C>A p.A72D
Coturnix japonica
Japanese quail - (species)
Coturnix japonica
Japanese quail - (species)
SLC45A2=MATP
Coturnix japonica
Japanese quail - (species)
Published - Accepted by Curator
SLCO1B3
Coloration (blue eggs)
Cis-regulatory,
Insertion
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Wang Z; Qu L; Yao J ; et al. (2013)
An EAV-HP insertion in 5' Flanking region of SLCO1B3 causes blue eggshell in the chicken.
GP00001064
SLCO1B3
Q9NPD5
Morphology
TE (EAV-HP) promoter insertion resulting in uterus expression
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
SLCO1B3
Gallus gallus
chicken - (species)
Published - Accepted by Curator
SLCO1B3
Coloration (blue eggs)
Cis-regulatory,
Insertion
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Wang Z; Qu L; Yao J ; et al. (2013)
An EAV-HP insertion in 5' Flanking region of SLCO1B3 causes blue eggshell in the chicken.
GP00001065
SLCO1B3
Q9NPD5
Morphology
TE (EAV-HP) promoter insertion resulting in uterus expression
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
SLCO1B3
Gallus gallus
chicken - (species)
Published - Accepted by Curator
SMAD family member 2 (SMAD2)
Body size (weight)
Cis-regulatory,
Deletion
Homo sapiens
human - (species) D
Domesticated
Association Mapping
Rimbault M; Beale HC; Schoenebeck JJ ; et al. (2013)
Derived variants at six genes explain nearly half of size reduction in dog breeds.
GP00001477
SMAD2
E2RP23
Morphology
9.9 kb deletion 24-kb dowstream from coding region
Canis lupus
gray wolf - (species)
Homo sapiens
human - (species) D
SMAD family member 2 (SMAD2)
Homo sapiens
human - (species)
Published - Accepted by Curator
smooth
Bristle number (abdomen)
Unknown,
Unknown
Drosophila melanogaster
fruit fly - (species) D
Intraspecific
Linkage Mapping
zur Lage P; Shrimpton AD; Flavell AJ ; et al. (1997)
Genetic and molecular analysis of smooth, a quantitative trait locus affecting bristle number in Dro[...]
GP00001996
Morphology
exact causing mutation(s) unknown
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species) D
smooth
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
SOX10
Coloration (feathers)
Cis-regulatory,
Deletion
Columba livia
rock pigeon - (species) D
Domesticated
Linkage Mapping
Domyan ET; Guernsey MW; Kronenberg Z ; et al. (2014)
Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon.
GP00001067
Sox10
Q04888
Morphology
melanocyte conserved enhancer deletion
Columba livia
rock pigeon - (species)
Columba livia
rock pigeon - (species) D
SOX10
Columba livia
rock pigeon - (species)
Published - Accepted by Curator
SOX10
Coloration (feathers)
Cis-regulatory,
Deletion
Columba livia
rock pigeon - (species) D
Domesticated
Linkage Mapping
Domyan ET; Guernsey MW; Kronenberg Z ; et al. (2014)
Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon.
GP00001068
Sox10
Q04888
Morphology
melanocyte conserved enhancer deletion
Columba livia
rock pigeon - (species)
Columba livia
rock pigeon - (species) D
SOX10
Columba livia
rock pigeon - (species)
Published - Accepted by Curator
SOX10
Coloration (feathers)
Cis-regulatory,
Deletion
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Gunnarsson U; Kerje S; Bed'hom B ; et al. (2011)
The Dark brown plumage color in chickens is caused by an 8.3-kb deletion upstream of SOX10.
1 Additional References
GP00001069
Sox10
Q04888
Morphology
8.3kb deletion upstream of the SOX10 transcription start site
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
SOX10
Gallus gallus
chicken - (species)
Published - Accepted by Curator
SOX5
Bird head comb (reduced comb and wattles)
Cis-regulatory,
Insertion
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Wright D; Boije H; Meadows JR ; et al. (2009)
Copy number variation in intron 1 of SOX5 causes the Pea-comb phenotype in chickens.
GP00001070
Sox5
P35710
Morphology
Copy Number Variation in Intron 1 - about 30 copies of a 3 kb sequence - corresponding to about 85 kb of extra sequence
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
SOX5
Gallus gallus
chicken - (species)
Published - Accepted by Curator
Sox5/6
Coloration (wing; mimicry)
Cis-regulatory,
Unknown
Hypolimnas misippus
(species)
Intraspecific
Association Mapping
VanKuren NW; Massardo D; Nallu S ; et al. (2019)
Butterfly Mimicry Polymorphisms Highlight Phylogenetic Limits of Gene Reuse in the Evolution of Dive[...]
GP00002429
Morphology
A 10 kb intergenic region located 48kb upstream of the Sox5/6 gene is strongly associated with the wing phenotype. This cis-regulatory change may also affect another neighboring gene, such as pink.
Hypolimnas misippus
(species)
Hypolimnas misippus
(species)
Sox5/6
Hypolimnas misippus
(species)
Published - Accepted by Curator
SPR
Coloration (ventral scales)
Cis-regulatory,
Unknown
Podarcis muralis
Common wall lizard - (species)
Intraspecific
Association Mapping
Andrade P; Pinho C; Pérez I de Lanuza G ; et al. (2019)
Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall [...]
GP00002119
Spr
Q64105
Morphology
Podarcis muralis
Common wall lizard - (species)
Podarcis muralis
Common wall lizard - (species)
SPR
Podarcis muralis
Common wall lizard - (species)
Published - Accepted by Curator
stanniocalcin 2 (STC2)
Body size (weight)
Cis-regulatory,
SNP
Homo sapiens
human - (species) D
Domesticated
Association Mapping
Rimbault M; Beale HC; Schoenebeck JJ ; et al. (2013)
Derived variants at six genes explain nearly half of size reduction in dog breeds.
GP00001478
STC2
O76061
Morphology
T>A 20-kb downstream from coding region
Canis lupus
gray wolf - (species)
Homo sapiens
human - (species) D
stanniocalcin 2 (STC2)
Homo sapiens
human - (species)
Published - Accepted by Curator
Starch branching enzyme (SBEI) = rugosus (R)
Starch structure
Seed aspect
Coding,
Insertion
N
Pisum sativum
pea - (species) D
Domesticated
Linkage Mapping
Bhattacharyya MK; Smith AM; Ellis TH ; et al. (1990)
The wrinkled-seed character of pea described by Mendel is caused by a transposon-like insertion in a[...]
GP00001078
SBEI
Q41058
Physiology
Morphology
800 bp TE insertion; probably disrupts the last 61 amino acids of the SBEI protein N
Pisum sativum
pea - (species)
Pisum sativum
pea - (species) D
Starch branching enzyme (SBEI) = rugosus (R)
Pisum sativum
pea - (species)
Published - Accepted by Curator
Style2.1
Flower morphology (style length)
Autogamy
Cis-regulatory,
Unknown
Solanum lycopersicum
tomato - (species) D
Domesticated
Linkage Mapping
Chen KY; Cong B; Wing R ; et al. (2007)
Changes in regulation of a transcription factor lead to autogamy in cultivated tomatoes.
GP00001081
100301942
B6CG44
Morphology
Physiology
Not identified
Solanum pennellii
(species)
Solanum lycopersicum
tomato - (species) D
Style2.1
Solanum lycopersicum
tomato - (species)
Published - Accepted by Curator
SUN
Fruit shape
Gene Amplification,
Complex Change
Solanum lycopersicum
tomato - (species)
Domesticated
Linkage Mapping
Xiao H; Jiang N; Schaffner E ; et al. (2008)
A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit.
GP00001084
100147716
B1N669
Morphology
Gene duplication
Solanum pimpinellifolium
(species)
Solanum lycopersicum
tomato - (species)
SUN
Solanum lycopersicum
tomato - (species)
Published - Accepted by Curator
Svb/ovo
Trichome pattern (larva)
9 Mutations:
Cis-regulatory
Drosophila sechellia
(species) D
Interspecific
Linkage Mapping
McGregor AP; Orgogozo V; Delon I ; et al. (2007)
Morphological evolution through multiple cis-regulatory mutations at a single gene.
1 Additional References
GP00001085
ovo
P51521
Morphology
9 mutations
Drosophila simulans
(species)
Drosophila mauritiana
(species)
Drosophila sechellia
(species) D
Svb/ovo
Drosophila sechellia
(species)
Published - Accepted by Curator
Svb/ovo
Trichome pattern (larva)
Cis-regulatory,
Unknown
Drosophila ezoana
(species)
Interspecific
Candidate Gene
Frankel N; Wang S; Stern DL (2012)
Conserved regulatory architecture underlies parallel genetic changes and convergent phenotypic evolu[...]
1 Additional References
GP00001086
ovo
P51521
Morphology
unknown
virilis group
(species group)
Drosophila ezoana
(species)
Svb/ovo
Drosophila ezoana
(species)
Published - Accepted by Curator
syntaxin-17
Coloration (hair ; graying with age)
Cis-regulatory,
Insertion
Equus caballus
horse - (species) D
Domesticated
Association Mapping
Rosengren Pielberg G; Golovko A; Sundström E ; et al. (2008)
A cis-acting regulatory mutation causes premature hair graying and susceptibility to melanoma in the[...]
2 Additional References
GP00002272
STX17
P56962
Morphology
4.6-kb duplication in intron 6 of STX17 ; in transgenic zebrafish a construct containing two copies of the duplicated sequence acts as a strong enhancer in neural crest cells and has subsequent melanophore-specific activity whereas a single copy of the duplicated sequence acts as a weak enhancer - consistent with the phenotypic manifestation of the mutation in horses
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
syntaxin-17
Equus caballus
horse - (species)
Published - Accepted by Curator
T-box transcription factor (TBX3)
Coloration (coat)
Cis-regulatory,
SNP
Equus caballus
horse - (species) D
Intraspecific
Linkage Mapping
Imsland F; McGowan K; Rubin CJ ; et al. (2016)
Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation that underlies Dun camouflage colo[...]
GP00001461
TBX3
O15119
Morphology
G>T predicted to affect binding of the CCAT box-binding transcription factors NF-Y and NF-I ; Differs from the wild-type allele by a SNP downstream of the wild-type TBX3 sequence (located 1067bp downstream of the start of the larger nd2 deletion described in the nd2 entry) with allele nd1 = T compared with the wild-type D allele = G); an ancient variant
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
T-box transcription factor (TBX3)
Equus caballus
horse - (species)
Published - Accepted by Curator
T-box transcription factor (TBX3)
Coloration (coat)
Cis-regulatory,
Deletion
Equus caballus
horse - (species) D
Domesticated
Linkage Mapping
Imsland F; McGowan K; Rubin CJ ; et al. (2016)
Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation that underlies Dun camouflage colo[...]
GP00001462
TBX3
O15119
Morphology
missing sequence of nearly contiguous 1609bp and 8 bp segments
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
T-box transcription factor (TBX3)
Equus caballus
horse - (species)
Published - Accepted by Curator
tan
Coloration (abdomen; female)
Cis-regulatory,
Unknown
Drosophila erecta
(species) D
Intraspecific
Linkage Mapping
Yassin A; Bastide H; Chung H ; et al. (2016)
Ancient balancing selection at tan underlies female colour dimorphism in Drosophila erecta.
GP00001097
t
Q9W369
Morphology
exact causing mutation(s) unknown - the t_MSE enhancer from the dark allele drives higher levels of GFP expression in D. melanogaster than from the light allele
Drosophila erecta
(species)
Drosophila erecta
(species) D
tan
Drosophila erecta
(species)
Published - Accepted by Curator
tan
Coloration (abdomen)
Cis-regulatory,
Unknown
Drosophila novamexicana
(species) D
Intraspecific
Linkage Mapping
Wittkopp PJ; Stewart EE; Arnold LL ; et al. (2009)
Intraspecific polymorphism to interspecific divergence: genetics of pigmentation in Drosophila.
GP00001098
t
Q9W369
Morphology
2.7kb non-coding interval; 13 SNPs + 2 indels differing between species
Drosophila americana
(species)
Drosophila novamexicana
(species) D
tan
Drosophila novamexicana
(species)
Published - Accepted by Curator
tan
Coloration (abdomen; male)
2 Mutations:
Cis-regulatory
SNP
Drosophila santomea
(species) D
Interspecific
Linkage Mapping
Jeong S; Rebeiz M; Andolfatto P ; et al. (2008)
The evolution of gene regulation underlies a morphological difference between two Drosophila sister [...]
1 Additional References
GP00001099
t
Q9W369
Morphology
2 mutations
Drosophila yakuba
(species)
Drosophila santomea
(species) D
tan
Drosophila santomea
(species)
Published - Accepted by Curator
tan
Coloration (abdomen; male)
Cis-regulatory,
Deletion
Drosophila santomea
(species) D
Interspecific
Linkage Mapping
Jeong S; Rebeiz M; Andolfatto P ; et al. (2008)
The evolution of gene regulation underlies a morphological difference between two Drosophila sister [...]
1 Additional References
GP00001100
t
Q9W369
Morphology
san MSE del30 (30bp deletion)
Drosophila yakuba
(species)
Drosophila santomea
(species) D
tan
Drosophila santomea
(species)
Published - Accepted by Curator
tan
Coloration (abdomen; male)
Cis-regulatory,
Deletion
Drosophila santomea
(species) D
Interspecific
Linkage Mapping
Jeong S; Rebeiz M; Andolfatto P ; et al. (2008)
The evolution of gene regulation underlies a morphological difference between two Drosophila sister [...]
1 Additional References
GP00001101
t
Q9W369
Morphology
san MSE del212 (212bp deletion)
Drosophila yakuba
(species)
Drosophila santomea
(species) D
tan
Drosophila santomea
(species)
Published - Accepted by Curator
tan
Coloration (thorax; abdomen; trident)
Cis-regulatory,
Unknown
Drosophila melanogaster
fruit fly - (species) D
Intraspecific
Association Mapping
Bastide H; Betancourt A; Nolte V ; et al. (2013)
A genome-wide, fine-scale map of natural pigmentation variation in Drosophila melanogaster.
3 Additional References
GP00002622
t
Q9W369
Morphology
exact causing mutation(s) unknown
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species) D
tan
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
Taqpep
Coloration (coat)
Coding,
Insertion
N
Acinonyx jubatus
cheetah - (species) D
Intraspecific
Candidate Gene
Kaelin CB; Xu X; Hong LZ ; et al. (2012)
Specifying and sustaining pigmentation patterns in domestic and wild cats.
GP00001105
Lvrn
Q2KHK3
Morphology
1bp insertion resulting in frameshift p.N977Kfs110 N
Acinonyx jubatus
cheetah - (species)
Acinonyx jubatus
cheetah - (species) D
Taqpep
Acinonyx jubatus
cheetah - (species)
Published - Accepted by Curator
Taqpep
Coloration (coat)
Coding,
SNP
Felis catus
domestic cat - (species) D
Intraspecific
Candidate Gene
Kaelin CB; Xu X; Hong LZ ; et al. (2012)
Specifying and sustaining pigmentation patterns in domestic and wild cats.
GP00001106
Lvrn
Q2KHK3
Morphology
D228N
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
Taqpep
Felis catus
domestic cat - (species)
Published - Accepted by Curator
Taqpep
Coloration (coat)
Coding,
SNP
N
Felis catus
domestic cat - (species)
Intraspecific
Candidate Gene
Kaelin CB; Xu X; Hong LZ ; et al. (2012)
Specifying and sustaining pigmentation patterns in domestic and wild cats.
GP00001107
Lvrn
Q2KHK3
Morphology
S59stop N
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species)
Taqpep
Felis catus
domestic cat - (species)
Published - Accepted by Curator
Taqpep
Coloration (coat)
Coding,
SNP
N
Felis catus
domestic cat - (species)
Intraspecific
Linkage Mapping
Kaelin CB; Xu X; Hong LZ ; et al. (2012)
Specifying and sustaining pigmentation patterns in domestic and wild cats.
GP00001108
Lvrn
Q2KHK3
Morphology
W841stop N
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species)
Taqpep
Felis catus
domestic cat - (species)
Published - Accepted by Curator
tartan
Organ size (genitalia; clasper)
Bristle number (genitalia; clasper)
Cis-regulatory,
Unknown
Drosophila mauritiana
(species) D
Interspecific
Linkage Mapping
Hagen JFD; Mendes CC; Blogg A ; et al. (2019)
tartan underlies the evolution of Drosophila male genital morphology.
GP00002047
trn
Q9VU51
Morphology
Morphology
no coding changes
Drosophila simulans
(species)
Drosophila mauritiana
(species) D
tartan
Drosophila mauritiana
(species)
Published - Accepted by Curator
TBX15
Ear shape
Cis-regulatory,
SNP
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Adhikari K; Reales G; Smith AJ ; et al. (2015)
A genome-wide association study identifies multiple loci for variation in human ear morphology.
GP00001113
TBX15
Q96SF7
Morphology
Tbx15 enhancer variation including rs17023457 T or C alleles that affect CART1 binding on a conserved site
Homo sapiens
human - (species)
Homo sapiens
human - (species)
TBX15
Homo sapiens
human - (species)
Published - Accepted by Curator
Tbx5
Limb Identity (feathered feet)
Cis-regulatory,
Unknown
Columba livia
rock pigeon - (species) D
Domesticated
Linkage Mapping
Domyan ET; Kronenberg Z; Infante CR ; et al. (2016)
Molecular shifts in limb identity underlie development of feathered feet in two domestic avian speci[...]
GP00001114
TBX5
Q9PWE8
Morphology
unknown
Columba livia
rock pigeon - (species)
Columba livia
rock pigeon - (species) D
Tbx5
Columba livia
rock pigeon - (species)
Published - Accepted by Curator
TBXT
Organ size (tail; short)
Coding,
SNP
Ovis aries
sheep - (species) D
Domesticated
Linkage Mapping
Zhi D; Da L; Liu M ; et al. (2018)
Whole Genome Sequencing of Hulunbuir Short-Tailed Sheep for Identifying Candidate Genes Related to t[...]
1 Additional References
GP00002289
Tbxt
P20293
Morphology
c.G334T p.G112W
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
TBXT
Ovis aries
sheep - (species)
Published - Accepted by Curator
TBXT
Organ size (tail; short)
Coding,
Deletion
N
Felis catus
domestic cat - (species) D
Domesticated
Candidate Gene
Buckingham KJ; McMillin MJ; Brassil MM ; et al. (2013)
Multiple mutant T alleles cause haploinsufficiency of Brachyury and short tails in Manx cats.
GP00002290
Tbxt
P20293
Morphology
c.1169delC N
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
TBXT
Felis catus
domestic cat - (species)
Published - Accepted by Curator
TBXT
Organ size (tail; short)
Coding,
Deletion
N
Felis catus
domestic cat - (species) D
Domesticated
Candidate Gene
Buckingham KJ; McMillin MJ; Brassil MM ; et al. (2013)
Multiple mutant T alleles cause haploinsufficiency of Brachyury and short tails in Manx cats.
GP00002291
Tbxt
P20293
Morphology
c.1199delC N
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
TBXT
Felis catus
domestic cat - (species)
Published - Accepted by Curator
TBXT
Organ size (tail; short)
Coding,
Deletion
N
Felis catus
domestic cat - (species) D
Domesticated
Candidate Gene
Buckingham KJ; McMillin MJ; Brassil MM ; et al. (2013)
Multiple mutant T alleles cause haploinsufficiency of Brachyury and short tails in Manx cats.
GP00002292
Tbxt
P20293
Morphology
c.998delT N
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
TBXT
Felis catus
domestic cat - (species)
Published - Accepted by Curator
TBXT
Organ size (tail; short)
Coding,
Indel
N
Felis catus
domestic cat - (species) D
Domesticated
Candidate Gene
Buckingham KJ; McMillin MJ; Brassil MM ; et al. (2013)
Multiple mutant T alleles cause haploinsufficiency of Brachyury and short tails in Manx cats.
GP00002293
Tbxt
P20293
Morphology
c.998_1014dup17delGCC N
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
TBXT
Felis catus
domestic cat - (species)
Published - Accepted by Curator
TBXT
Organ size (tail; short)
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Linkage Mapping
Haworth K; Putt W; Cattanach B ; et al. (2001)
Canine homolog of the T-box transcription factor T; failure of the protein to bind to its DNA target[...]
3 Additional References
GP00002340
Tbxt
P20293
Morphology
c.189C>G p.I63M
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
TBXT
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
teosinte branched 1 (tb1)
Plant architecture
Inflorescence architecture
Cis-regulatory,
Insertion
Zea mays
(species) D
Domesticated
Linkage Mapping
Clark RM; Wagler TN; Quijada P ; et al. (2006)
A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and[...]
2 Additional References
GP00001116
TB1
Q93WI2
Morphology
Morphology
Hopscotch TE insertion
Zea mays
(species)
Zea mays
(species) D
teosinte branched 1 (tb1)
Zea mays
(species)
Published - Accepted by Curator
teosinte branched 1 (tb1) = IntC
Plant architecture
Inflorescence architecture
Coding,
Unknown
Hordeum vulgare
(species)
Domesticated
Association Mapping
Ramsay L; Comadran J; Druka A ; et al. (2011)
INTERMEDIUM-C, a modifier of lateral spikelet fertility in barley, is an ortholog of the maize domes[...]
GP00001117
TB1
Q93WI2
Morphology
Morphology
Large haplotypes; unknown
Hordeum vulgare
(species)
Hordeum vulgare
(species)
teosinte branched 1 (tb1) = IntC
Hordeum vulgare
(species)
Published - Accepted by Curator
teosinte glume architecture (tga1)
Cupule retraction
Coding,
SNP
Zea mays
(species)
Domesticated
Linkage Mapping
Wang H; Nussbaum-Wagler T; Li B ; et al. (2005)
The origin of the naked grains of maize.
GP00001118
TGA1
Q39237
Morphology
K6N; the lysine residue being conserved in rice and wheat
Zea mays
(species)
Zea mays
(species)
teosinte glume architecture (tga1)
Zea mays
(species)
Published - Accepted by Curator
THOUSAND-GRAIN WEIGHT 6 (TGW6)
Grain yield
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Ishimaru K; Hirotsu N; Madoka Y ; et al. (2013)
Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yie[...]
GP00001126
TGW6
Q69U01
Morphology
-1bp at +313 resulting in truncated protein N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
THOUSAND-GRAIN WEIGHT 6 (TGW6)
Oryza sativa
rice - (species)
Published - Accepted by Curator
TPCN2
Coloration (coat)
Coding,
SNP
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Sulem P; Gudbjartsson DF; Stacey SN ; et al. (2008)
Two newly identified genetic determinants of pigmentation in Europeans.
GP00001131
TPCN2
Q8NHX9
Morphology
Met484Leu and/or Gly734Gln
Homo sapiens
human - (species)
Homo sapiens
human - (species)
TPCN2
Homo sapiens
human - (species)
Published - Accepted by Curator
trehalase
Coloration (wing; seasonal)
Cis-regulatory,
Unknown
Junonia coenia
buckeye - (species) D
Experimental Evolution
Association Mapping
van der Burg KRL; Lewis JJ; Brack BJ ; et al. (2020)
Genomic architecture of a genetically assimilated seasonal color pattern.
GP00002421
Treh
Q9W2M2
Morphology
Increased expression of the trehalase gene in the Red line. No variation in coding region. Strong association with cis-regulatory SNP.
Junonia coenia
buckeye - (species)
Junonia coenia
buckeye - (species) D
trehalase
Junonia coenia
buckeye - (species)
Published - Accepted by Curator
Trichohyalin
Hair type (straight)
Unknown,
Unknown
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Medland SE; Nyholt DR; Painter JN ; et al. (2009)
Common variants in the trichohyalin gene are associated with straight hair in Europeans.
GP00001134
TCHH
Q07283
Morphology
Not identified
Homo sapiens
human - (species)
Homo sapiens
human - (species)
Trichohyalin
Homo sapiens
human - (species)
Published - Accepted by Curator
TRIP11 (=GMAP-210)
Body size (height)
Unknown,
Unknown
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Lettre G (2011)
Recent progress in the study of the genetics of height.
GP00001138
TRIP11
Q15643
Morphology
unknown
Homo sapiens
human - (species)
Homo sapiens
human - (species)
TRIP11 (=GMAP-210)
Homo sapiens
human - (species)
Published - Accepted by Curator
TRPM1
Coloration (coat)
Cis-regulatory,
Insertion
Equus caballus
horse - (species) D
Intraspecific
Linkage Mapping
Bellone RR; Forsyth G; Leeb T ; et al. (2010)
Fine-mapping and mutation analysis of TRPM1: a candidate gene for leopard complex (LP) spotting and [...]
3 Additional References
GP00001140
TRPM1
Q7Z4N2
Morphology
a 1378 bp retroviral LTR insertion in intron 1 of TRPM1
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
TRPM1
Equus caballus
horse - (species)
Published - Accepted by Curator
TRPV4
Ear size (drop)
Coding,
SNP
Felis catus
domestic cat - (species) D
Domesticated
Association Mapping
Gandolfi B; Alamri S; Darby WG ; et al. (2016)
A dominant TRPV4 variant underlies osteochondrodysplasia in Scottish fold cats.
1 Additional References
GP00002279
TRPV4
Q9HBA0
Morphology
c.1024G>T p.V342F
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
TRPV4
Felis catus
domestic cat - (species)
Published - Accepted by Curator
TT8
Coloration (seed)
Coding,
Insertion
N
Brassica rapa
field mustard - (species) D
Domesticated
Linkage Mapping
Li X; Chen L; Hong M ; et al. (2012)
A large insertion in bHLH transcription factor BrTT8 resulting in yellow seed coat in Brassica rapa.
GP00002077
TT8
Q9FT81
Morphology
insertion of a Helitron transposon of 4320 bp in intron 2 starting with 5' TC and ending with 3'CTAG containing a 17 bp palindromic region forming a hairpin - prevents transcription N
Brassica rapa
field mustard - (species)
Brassica rapa
field mustard - (species) D
TT8
Brassica rapa
field mustard - (species)
Published - Accepted by Curator
Twist2
Coloration (coat; white belt)
Cis-regulatory,
Insertion
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Awasthi Mishra N; Drögemüller C; Jagannathan V ; et al. (2017)
A structural variant in the 5'-flanking region of the TWIST2 gene affects melanocyte development in [...]
2 Additional References
GP00002035
Twist2
Q9D030
Morphology
quadruplication (CNV) of a 6 kb non-coding sequence located approximately 16 kb upstream of the TWIST2 gene
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Twist2
Bos taurus
cattle - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (coat)
Coding,
SNP
Felis catus
domestic cat - (species) D
Domesticated
Linkage Mapping
Lyons LA; Imes DL; Rah HC ; et al. (2005)
Tyrosinase mutations associated with Siamese and Burmese patterns in the domestic cat (Felis catus).
1 Additional References
GP00001142
Tyr
P11344
Morphology
c.679G>T p.G227W
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
tyrosinase (TYR)
Felis catus
domestic cat - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (coat)
Coding,
SNP
Felis catus
domestic cat - (species) D
Domesticated
Linkage Mapping
Lyons LA; Imes DL; Rah HC ; et al. (2005)
Tyrosinase mutations associated with Siamese and Burmese patterns in the domestic cat (Felis catus).
1 Additional References
GP00001143
Tyr
P11344
Morphology
c. 940G>A p.G302R
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
tyrosinase (TYR)
Felis catus
domestic cat - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (eyes; hair; skin)
Coding,
SNP
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Sulem P; Gudbjartsson DF; Stacey SN ; et al. (2007)
Genetic determinants of hair, eye and skin pigmentation in Europeans.
2 Additional References
GP00001144
Tyr
P11344
Morphology
R402Q
Homo sapiens
human - (species)
Homo sapiens
human - (species)
tyrosinase (TYR)
Homo sapiens
human - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (coat)
Coding,
SNP
Panthera leo
lion - (species) D
Intraspecific
Association Mapping
Cho YS; Hu L; Hou H ; et al. (2013)
The tiger genome and comparative analysis with lion and snow leopard genomes.
GP00001346
Tyr
P11344
Morphology
c.260G>A p.Arg87Gln
Panthera leo
lion - (species)
Panthera leo
lion - (species) D
tyrosinase (TYR)
Panthera leo
lion - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (skin; coat)
Coding,
SNP
Equus asinus
ass - (species) D
Intraspecific
Candidate Gene
Utzeri VJ; Bertolini F; Ribani A ; et al. (2016)
The albinism of the feral Asinara white donkeys (Equus asinus) is determined by a missense mutation [...]
GP00001347
Tyr
P11344
Morphology
c.604C>G p.His202Asp
Equus asinus
ass - (species)
Equus asinus
ass - (species) D
tyrosinase (TYR)
Equus asinus
ass - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (skin; eye; freckles)
Coding,
SNP
Homo sapiens
human - (species) D
Intraspecific
Association Mapping
Wilde S; Timpson A; Kirsanow K ; et al. (2014)
Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the l[...]
GP00001348
Tyr
P11344
Morphology
c. C>A p.Ser192Tyr
Homo sapiens
human - (species)
Homo sapiens
human - (species) D
tyrosinase (TYR)
Homo sapiens
human - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (feathers)
Coding,
Deletion
Gallus gallus
chicken - (species) D
Domesticated
Candidate Gene
Tobita-Teramoto T; Jang GY; Kino K ; et al. (2000)
Autosomal albino chicken mutation (ca/ca) deletes hexanucleotide (-deltaGACTGG817) at a copper-bindi[...]
GP00002308
Tyr
P11344
Morphology
c.817_822del6 p.237-238delDW
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
tyrosinase (TYR)
Gallus gallus
chicken - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (feathers)
Coding,
Insertion
Gallus gallus
chicken - (species) D
Domesticated
Candidate Gene
Chang CM; Coville JL; Coquerelle G ; et al. (2006)
Complete association between a retroviral insertion in the tyrosinase gene and the recessive white m[...]
GP00002309
Tyr
P11344
Morphology
insertion of a complete avian retroviral sequence in intron 4 causes aberrant transcripts lacking exon 5
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
tyrosinase (TYR)
Gallus gallus
chicken - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (coat)
Coding,
Deletion
Mustela putorius furo
domestic ferret - (subspecies) D
Domesticated
Linkage Mapping
Blaszczyk WM; Distler C; Dekomien G ; et al. (2007)
Identification of a tyrosinase (TYR) exon 4 deletion in albino ferrets (Mustela putorius furo).
GP00002310
Tyr
P11344
Morphology
Deletion of exon 4 as detected by Southern Blot
Mustela putorius furo
domestic ferret - (subspecies)
Mustela putorius furo
domestic ferret - (subspecies) D
tyrosinase (TYR)
Mustela putorius furo
domestic ferret - (subspecies)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (coat)
Coding,
Indel
Felis catus
domestic cat - (species) D
Domesticated
Candidate Gene
Yu Y; Grahn RA; Lyons LA (2019)
Mocha tyrosinase variant: a new flavour of cat coat coloration.
GP00002311
Tyr
P11344
Morphology
c.820_936delinsAATCTC p.I274_L312delinsNL
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
tyrosinase (TYR)
Felis catus
domestic cat - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (coat)
Coding,
Deletion
N
Felis catus
domestic cat - (species) D
Domesticated
Candidate Gene
Imes DL; Geary LA; Grahn RA ; et al. (2006)
Albinism in the domestic cat (Felis catus) is associated with a tyrosinase (TYR) mutation.
GP00002312
Tyr
P11344
Morphology
a cytosine deletion in TYR at position 975 in exon 2 N
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
tyrosinase (TYR)
Felis catus
domestic cat - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (coat)
Coding,
SNP
N
Felis catus
domestic cat - (species) D
Domesticated
Candidate Gene
Abitbol M; Bossé P; Grimard B ; et al. (2017)
Allelic heterogeneity of albinism in the domestic cat.
GP00002313
Tyr
P11344
Morphology
c.1204C>T p.R402* N
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
tyrosinase (TYR)
Felis catus
domestic cat - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (skin)
Coding,
Deletion
Megaptera novaeangliae
humpback whale - (species) D
Intraspecific
Candidate Gene
Polanowski AM; Robinson-Laverick SM; Paton D ; et al. (2012 Jan-Feb)
Variation in the tyrosinase gene associated with a white humpback whale (Megaptera novaeangliae).
GP00002314
Tyr
P11344
Morphology
(264 del C) at codon 88
Megaptera novaeangliae
humpback whale - (species)
Megaptera novaeangliae
humpback whale - (species) D
tyrosinase (TYR)
Megaptera novaeangliae
humpback whale - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (coat)
Coding,
Insertion
N
Bos taurus
cattle - (species) D
Domesticated
Candidate Gene
Schmutz SM; Berryere TG; Ciobanu DC ; et al. (2004)
A form of albinism in cattle is caused by a tyrosinase frameshift mutation.
GP00002315
Tyr
P11344
Morphology
c.925_926insC N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
tyrosinase (TYR)
Bos taurus
cattle - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (coat)
Coding,
SNP
Oryctolagus cuniculus
rabbit - (species) D
Domesticated
Candidate Gene
Aigner B; Besenfelder U; Müller M ; et al. (2000)
Tyrosinase gene variants in different rabbit strains.
GP00002316
Tyr
P11344
Morphology
c.1118C>A p.T373K (also causes albinism in humans)
Oryctolagus cuniculus
rabbit - (species)
Oryctolagus cuniculus
rabbit - (species) D
tyrosinase (TYR)
Oryctolagus cuniculus
rabbit - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (coat)
Coding,
SNP
Cavia porcellus
domestic guinea pig - (species) D
Domesticated
Candidate Gene
Yu F; Jiao S; Lai W ; et al. (2018)
Conserved aspartate-to-glycine mutation in tyrosinase is associated with albino phenotype in domesti[...]
GP00002317
Tyr
P11344
Morphology
c.710A>G p.Asp237Gly
Cavia porcellus
domestic guinea pig - (species)
Cavia porcellus
domestic guinea pig - (species) D
tyrosinase (TYR)
Cavia porcellus
domestic guinea pig - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (coat)
Coding,
SNP
Bubalus bubalis
water buffalo - (species) D
Domesticated
Candidate Gene
Damé MC; Xavier GM; Oliveira-Filho JP ; et al. (2012)
A nonsense mutation in the tyrosinase gene causes albinism in water buffalo.
GP00002318
Tyr
P11344
Morphology
c.1431G>A p.W477*
Bubalus bubalis
water buffalo - (species)
Bubalus bubalis
water buffalo - (species) D
tyrosinase (TYR)
Bubalus bubalis
water buffalo - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (coat)
Coding,
SNP
Neovison vison
American mink - (species) D
Domesticated
Candidate Gene
Anistoroaei R; Fredholm M; Christensen K ; et al. (2008)
Albinism in the American mink (Neovison vison) is associated with a tyrosinase nonsense mutation.
GP00002319
Tyr
P11344
Morphology
c.138T>A p.C46*
Neovison vison
American mink - (species)
Neovison vison
American mink - (species) D
tyrosinase (TYR)
Neovison vison
American mink - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (coat)
Coding,
SNP
Neovison vison
American mink - (species) D
Domesticated
Candidate Gene
Benkel BF; Rouvinen-Watt K; Farid H ; et al. (2009)
Molecular characterization of the Himalayan mink.
GP00002320
Tyr
P11344
Morphology
c.1835C>G p.H420Q
Neovison vison
American mink - (species)
Neovison vison
American mink - (species) D
tyrosinase (TYR)
Neovison vison
American mink - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (skin)
Coding,
SNP
Fejervarya kawamurai
(species) D
Intraspecific
Candidate Gene
Miura I; Tagami M; Fujitani T ; et al. (2018)
Spontaneous tyrosinase mutations identified in albinos of three wild frog species.
GP00002321
Tyr
P11344
Morphology
c.169G>A p.Gly57Arg
Fejervarya kawamurai
(species)
Fejervarya kawamurai
(species) D
tyrosinase (TYR)
Fejervarya kawamurai
(species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (amelanism)
Coding,
Insertion
N
Oryzias latipes
Japanese medaka - (species) D
Domesticated
Candidate Gene
Koga A; Hori H (1997)
Albinism due to transposable element insertion in fish.
GP00002372
Tyr
P11344
Morphology
"i4 allele was found to contain a 4.7- kb transposable element in the 5th exon"
"Tyr-i4 contains a 4.7-kb insertion in exon 5 (Fig. 3). If the inserted fragment was transcribed, the amino acid sequence would be altered after the 469th residue, with a termination codon (UAG) at amino acid position 471. The i4/i4 genotype exhibits a quasi-albino phenotype. This may be explained by generation of a tyrosinase protein that only lacks its C-terminus region. The wild-type tyrosinase has a highly hydrophobic amino acid block at its C terminus (aa 480 - aa 500) which is thought to be part of a membrane spanning domain (Inagaki et al., 1994). A possible explanation is that the mutant tyrosinase encoded by Tyr- i4 lacks this region, so that it cannot be positioned properly on the membrane" N
Oryzias latipes
Japanese medaka - (species)
Oryzias latipes
Japanese medaka - (species) D
tyrosinase (TYR)
Oryzias latipes
Japanese medaka - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (coat; albinism)
Coding,
Deletion
N
Nyctereutes procyonoides viverrinus
(subspecies) D
Intraspecific
Candidate Gene
Mae Y; Nagara K; Miyazaki M ; et al. (2020)
Complex intragene deletion leads to oculocutaneous albinism in tanuki (Japanese raccoon dog).
GP00002374
Tyr
P11344
Morphology
"We examined the structure and nucleotide sequence of TYR in an albino tanuki and found that the third exon was removed due to a deletion of approximately 11 kb. In addition, two nonsynonymous nucleotide substitutions were found in the fifth exon. These mutations are possible causes of the albino phenotype; however, the order of occurrence is unclear. Even if the 11-kb deletion was not the first of these mutations, it is considered to cause a total loss of the tyrosinase function because the third exon carries codons for one of the two copper-binding sites of tyrosinase and these sites are essential for the enzyme function. Intriguingly, the deletion was not a simple removal of an 11-kb segment: an internal portion was retained as a segment in the reverse orientation. We propose possible formation processes for this mutation that involve multiple DNA scission events, or an inversion followed by a deletion." N
Nyctereutes procyonoides viverrinus
(subspecies)
Nyctereutes procyonoides viverrinus
(subspecies) D
tyrosinase (TYR)
Nyctereutes procyonoides viverrinus
(subspecies)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (coat)
Coding,
SNP
Cervus elaphus
red deer - (species) D
Intraspecific
Candidate Gene
Reiner G; Tramberend K; Nietfeld F ; et al. (2020)
A genome-wide scan study identifies a single nucleotide substitution in the tyrosinase gene associat[...]
GP00002375
Tyr
P11344
Morphology
"a non-synonymous mutation with exchange of a glycine residue at position 291 of the tyrosinase protein by arginine was identified as the cause of dilution of the coat colour"
The mutation is on nucleotide 871 (G > A) but the exact codons are not specified in the paper.
Cervus elaphus
red deer - (species)
Cervus elaphus
red deer - (species) D
tyrosinase (TYR)
Cervus elaphus
red deer - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
SNP
Bos taurus
cattle - (species)
Domesticated
Linkage Mapping
Berryere TG; Schmutz SM; Schimpf RJ ; et al. (2003)
TYRP1 is associated with dun coat colour in Dexter cattle or how now brown cow?
GP00001145
Tyrp1
P07147
Morphology
c.1300C>T p.H434Y
Bos taurus
cattle - (species)
Bos taurus
cattle - (species)
tyrosinase-related protein 1 (TYRP1)
Bos taurus
cattle - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
Deletion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Schmutz SM; Berryere TG; Goldfinch AD (2002)
TYRP1 and MC1R genotypes and their effects on coat color in dogs.
GP00001146
Tyrp1
P07147
Morphology
deletion of a proline residue in exon 5 (345delP)
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
tyrosinase-related protein 1 (TYRP1)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
SNP
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Schmutz SM; Berryere TG; Goldfinch AD (2002)
TYRP1 and MC1R genotypes and their effects on coat color in dogs.
GP00001147
Tyrp1
P07147
Morphology
premature stop codon in exon 5 (Q331ter) N
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
tyrosinase-related protein 1 (TYRP1)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (feathers)
Coding,
SNP
Columba livia
rock pigeon - (species) D
Domesticated
Linkage Mapping
Domyan ET; Guernsey MW; Kronenberg Z ; et al. (2014)
Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon.
GP00001149
Tyrp1
P07147
Morphology
Ala23Pro
Columba livia
rock pigeon - (species)
Columba livia
rock pigeon - (species) D
tyrosinase-related protein 1 (TYRP1)
Columba livia
rock pigeon - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (feathers)
Coding,
SNP
N
Columba livia
rock pigeon - (species) D
Domesticated
Linkage Mapping
Domyan ET; Guernsey MW; Kronenberg Z ; et al. (2014)
Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon.
GP00001150
Tyrp1
P07147
Morphology
Arg72* N
Columba livia
rock pigeon - (species)
Columba livia
rock pigeon - (species) D
tyrosinase-related protein 1 (TYRP1)
Columba livia
rock pigeon - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (feathers)
Coding,
Deletion
N
Columba livia
rock pigeon - (species) D
Domesticated
Linkage Mapping
Domyan ET; Guernsey MW; Kronenberg Z ; et al. (2014)
Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon.
GP00001151
Tyrp1
P07147
Morphology
7-bp deletion 411-418del resulting in null allele N
Columba livia
rock pigeon - (species)
Columba livia
rock pigeon - (species) D
tyrosinase-related protein 1 (TYRP1)
Columba livia
rock pigeon - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (feathers)
Coding,
SNP
Coturnix japonica
Japanese quail - (species)
Domesticated
Linkage Mapping
Nadeau NJ; Mundy NI; Gourichon D ; et al. (2007)
Association of a single-nucleotide substitution in TYRP1 with roux in Japanese quail (Coturnix japon[...]
GP00001152
Tyrp1
P07147
Morphology
Phe282Ser
Coturnix japonica
Japanese quail - (species)
Coturnix japonica
Japanese quail - (species)
tyrosinase-related protein 1 (TYRP1)
Coturnix japonica
Japanese quail - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
SNP
N
Felis catus
domestic cat - (species) D
Domesticated
Linkage Mapping
Schmidt-Küntzel A; Eizirik E; O'Brien SJ ; et al. (2005 Jul-Aug)
Tyrosinase and tyrosinase related protein 1 alleles specify domestic cat coat color phenotypes of th[...]
1 Additional References
GP00001153
Tyrp1
P07147
Morphology
premature UAG stop codon at position 100 of TYRP1; AAG>TAG c.298C>T p.R100* N
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
tyrosinase-related protein 1 (TYRP1)
Felis catus
domestic cat - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
Unknown
Felis catus
domestic cat - (species) D
Domesticated
Linkage Mapping
Schmidt-Küntzel A; Eizirik E; O'Brien SJ ; et al. (2005 Jul-Aug)
Tyrosinase and tyrosinase related protein 1 alleles specify domestic cat coat color phenotypes of th[...]
GP00001154
Tyrp1
P07147
Morphology
Two mutations associated with the chocolate (b) allele - one leading to a TYRP1-A3G substitution in the signal peptide and another to an in-frame insertion TYRP1-421ins17/18 caused by a donor splice site mutation in intron 6 -exact causing change unknown
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
tyrosinase-related protein 1 (TYRP1)
Felis catus
domestic cat - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
SNP
Homo sapiens
human - (species) D
Intraspecific
Association Mapping
Kenny EE; Timpson NJ; Sikora M ; et al. (2012)
Melanesian blond hair is caused by an amino acid change in TYRP1.
GP00001155
Tyrp1
P07147
Morphology
R93C
Homo sapiens
human - (species)
Homo sapiens
human - (species) D
tyrosinase-related protein 1 (TYRP1)
Homo sapiens
human - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
SNP
Ovis aries
sheep - (species) D
Domesticated
Linkage Mapping
Gratten J; Beraldi D; Lowder BV ; et al. (2007)
Compelling evidence that a single nucleotide substitution in TYRP1 is responsible for coat-colour po[...]
GP00001156
Tyrp1
P07147
Morphology
c. 869G>T p.C290F ; Cys residue involved shows a high degree of evolutionary conservation; it is conserved not only across vertebrates but also in the two paralogues of TYRP1, DCT and TYR
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
tyrosinase-related protein 1 (TYRP1)
Ovis aries
sheep - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (eyes; hair; skin)
Unknown,
Unknown
Homo sapiens
human - (species)
Intraspecific
Association Mapping
Frudakis T; Thomas M; Gaskin Z ; et al. (2003)
Sequences associated with human iris pigmentation.
1 Additional References
GP00001157
Tyrp1
P07147
Morphology
unknown
Homo sapiens
human - (species)
Homo sapiens
human - (species)
tyrosinase-related protein 1 (TYRP1)
Homo sapiens
human - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
Deletion
Sus scrofa domesticus
domestic pig - (subspecies) D
Domesticated
Candidate Gene
Wu X; Zhang Y; Shen L ; et al. (2016)
A 6-bp deletion in exon 8 and two mutations in introns of TYRP1 are associated with blond coat color[...]
GP00001327
Tyrp1
P07147
Morphology
g.17599_17604del 6bp deletion in exon 8 resulting in deletion of Met and Gly residues at positions 495 and 496 in TYRP1 protein ; c.1484_1489del6 p.Met495_Gly496del
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies) D
tyrosinase-related protein 1 (TYRP1)
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (feathers)
Coding,
SNP
Gallus gallus
chicken - (species)
Domesticated
Linkage Mapping
Li J; Bed'hom B; Marthey S ; et al. (2019)
A missense mutation in TYRP1 causes the chocolate plumage color in chicken and alters melanosome str[...]
GP00002126
Tyrp1
P07147
Morphology
g.30830367C>A c.640C>A p.His214Asn
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
tyrosinase-related protein 1 (TYRP1)
Gallus gallus
chicken - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Schmutz SM; Berryere TG; Goldfinch AD (2002)
TYRP1 and MC1R genotypes and their effects on coat color in dogs.
GP00002233
Tyrp1
P07147
Morphology
c.121T>A p.Cys41Ser
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
tyrosinase-related protein 1 (TYRP1)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
SNP
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Hrckova Turnova E; Majchrakova Z; Bielikova M ; et al. (2017)
A novel mutation in the TYRP1 gene associated with brown coat colour in the Australian Shepherd Dog [...]
GP00002234
Tyrp1
P07147
Morphology
c.555T>G p.Tyr185* N
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
tyrosinase-related protein 1 (TYRP1)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Wright HE; Schofield E; Mellersh CS ; et al. (2019)
A novel TYRP1 variant is associated with liver and tan coat colour in Lancashire Heelers.
GP00002235
Tyrp1
P07147
Morphology
c.1025T>G p.Phe342Cys
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
tyrosinase-related protein 1 (TYRP1)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
SNP
Capra hircus
goat - (species) D
Domesticated
Candidate Gene
Becker D; Otto M; Ammann P ; et al. (2015)
The brown coat colour of Coppernecked goats is associated with a non-synonymous variant at the TYRP1[...]
GP00002236
Tyrp1
P07147
Morphology
c.1487G>A p.Gly496Asp
Capra hircus
goat - (species)
Capra hircus
goat - (species) D
tyrosinase-related protein 1 (TYRP1)
Capra hircus
goat - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
SNP
Ovis aries
sheep - (species) D
Domesticated
Linkage Mapping
Raadsma HW; Jonas E; Fleet MR ; et al. (2013)
QTL and association analysis for skin and fibre pigmentation in sheep provides evidence of a major c[...]
GP00002237
Tyrp1
P07147
Morphology
c.2240C>G p.A746V
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
tyrosinase-related protein 1 (TYRP1)
Ovis aries
sheep - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
Deletion
N
Ovis aries
sheep - (species) D
Domesticated
Linkage Mapping
Paris JM; Letko A; Häfliger IM ; et al. (2019)
Identification of two TYRP1 loss-of-function alleles in Valais Red sheep.
GP00002238
Tyrp1
P07147
Morphology
c.86_87delGA p.(Glu29ValfsTer5) N
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
tyrosinase-related protein 1 (TYRP1)
Ovis aries
sheep - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
SNP
N
Ovis aries
sheep - (species) D
Domesticated
Linkage Mapping
Paris JM; Letko A; Häfliger IM ; et al. (2019)
Identification of two TYRP1 loss-of-function alleles in Valais Red sheep.
GP00002239
Tyrp1
P07147
Morphology
c.1066C>T p.(Arg356*) N
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
tyrosinase-related protein 1 (TYRP1)
Ovis aries
sheep - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
SNP
N
Oryctolagus cuniculus
rabbit - (species) D
Domesticated
Linkage Mapping
Utzeri VJ; Ribani A; Fontanesi L (2014)
A premature stop codon in the TYRP1 gene is associated with brown coat colour in the European rabbit[...]
GP00002240
Tyrp1
P07147
Morphology
c.570G>A p.Trp190ter N
Oryctolagus cuniculus
rabbit - (species)
Oryctolagus cuniculus
rabbit - (species) D
tyrosinase-related protein 1 (TYRP1)
Oryctolagus cuniculus
rabbit - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Cis-regulatory,
Insertion
N
Neovison vison
American mink - (species) D
Domesticated
Candidate Gene
Cirera S; Markakis MN; Kristiansen T ; et al. (2016)
A large insertion in intron 2 of the TYRP1 gene associated with American Palomino phenotype in Ameri[...]
GP00002241
Tyrp1
P07147
Morphology
Large insertion in intron 2 resulting in aberrant transcript N
Neovison vison
American mink - (species)
Neovison vison
American mink - (species) D
tyrosinase-related protein 1 (TYRP1)
Neovison vison
American mink - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (feathers)
Coding,
Insertion
N
Falco cherrug
Saker falcon - (species) D
Intraspecific
Candidate Gene
Cortimiglia C; Castiglioni B; Pizzi F ; et al. (2017)
Involvement of tyrosinase-related protein 1 gene in the light brown plumage phenotype of Falco cherr[...]
GP00002285
Tyrp1
P07147
Morphology
c.79_80insT in exon 1 resulting in a frameshift change and a premature stop codon at position 81 of the deduced protein sequence ; which in the wild-type form contains 536 amino acids N
Falco cherrug
Saker falcon - (species)
Falco cherrug
Saker falcon - (species) D
tyrosinase-related protein 1 (TYRP1)
Falco cherrug
Saker falcon - (species)
Published - Accepted by Curator
Tyrosine hydroxylase
Coloration (body)
Cis-regulatory,
Unknown
Bombyx mori
domestic silkworm - (species) D
Domesticated
Candidate Gene
Yu HS; Shen YH; Yuan GX ; et al. (2011)
Evidence of selection at melanin synthesis pathway loci during silkworm domestication.
GP00001158
ple
P18459
Morphology
Variation in intron; possibly loss of AbdA binding site
Bombyx mandarina
wild silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
Tyrosine hydroxylase
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
TZP
Plant growth (hypocotyl growth - light and temperature dependant)
Coding,
Insertion
N
Arabidopsis thaliana
thale cress - (species)
Intraspecific
Linkage Mapping
Loudet O; Michael TP; Burger BT ; et al. (2008)
A zinc knuckle protein that negatively controls morning-specific growth in Arabidopsis thaliana.
GP00001269
TZP
Q9FIX7
Morphology
8bp insertion causing premature stop N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
TZP
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
Ultrabithorax (Ubx)
Trichome pattern (leg)
Cis-regulatory,
Unknown
Drosophila simulans
(species)
Interspecific
Candidate Gene
Stern DL (1998)
A role of Ultrabithorax in morphological differences between Drosophila species.
GP00001161
Ubx
P83949
Morphology
Not identified
Drosophila melanogaster
fruit fly - (species)
Drosophila simulans
(species)
Ultrabithorax (Ubx)
Drosophila simulans
(species)
Published - Accepted by Curator
Unpaired-like
Wing shape (sex-specific)
Wing size
Cis-regulatory,
Unknown
Nasonia giraulti
(species)
Interspecific
Linkage Mapping
Loehlin DW; Werren JH (2012)
Evolution of shape by multiple regulatory changes to a growth gene.
GP00001163
upd1
O96525
Morphology
Morphology
three regions
Nasonia vitripennis
jewel wasp - (species)
Nasonia giraulti
(species)
Unpaired-like
Nasonia giraulti
(species)
Published - Accepted by Curator
Vertnin (VRTN)
Vertebrae number
Cis-regulatory,
Unknown
Sus scrofa domesticus
domestic pig - (subspecies)
Domesticated
Linkage Mapping
Mikawa S; Sato S; Nii M ; et al. (2011)
Identification of a second gene associated with variation in vertebral number in domestic pigs.
GP00001165
Vrtn
Q3SYK4
Morphology
unknown ; observed transposon insertion in intron and promoter variation
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies)
Vertnin (VRTN)
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
Vertnin (VRTN) [possibly a pseudo-replicate of other Pig entry]
Vertebrae number
Unknown,
Unknown
Sus scrofa domesticus
domestic pig - (subspecies)
Domesticated
Linkage Mapping
Ren DR; Ren J; Ruan GF ; et al. (2012)
Mapping and fine mapping of quantitative trait loci for the number of vertebrae in a White Duroc × C[...]
GP00001166
Vrtn
Q3SYK4
Morphology
unknown
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies)
Vertnin (VRTN) [possibly a pseudo-replicate of other Pig entry]
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
VRS1 = SIX-ROWED SPIKE 1
Plant architecture
Inflorescence architecture
Coding,
Deletion
N
Hordeum vulgare
(species) D
Domesticated
Linkage Mapping
Komatsuda T; Pourkheirandish M; He C ; et al. (2007)
Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene.
1 Additional References
GP00001189
Vrs1
A1IHK8
Morphology
Morphology
1bp deletion resulting in frameshift N
Hordeum vulgare
(species)
Hordeum vulgare
(species) D
VRS1 = SIX-ROWED SPIKE 1
Hordeum vulgare
(species)
Published - Accepted by Curator
VRS1 = SIX-ROWED SPIKE 1
Plant architecture
Inflorescence architecture
Coding,
Insertion
N
Hordeum vulgare
(species) D
Domesticated
Linkage Mapping
Komatsuda T; Pourkheirandish M; He C ; et al. (2007)
Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene.
1 Additional References
GP00001190
Vrs1
A1IHK8
Morphology
Morphology
1bp insertion resulting in frameshift N
Hordeum vulgare
(species)
Hordeum vulgare
(species) D
VRS1 = SIX-ROWED SPIKE 1
Hordeum vulgare
(species)
Published - Accepted by Curator
VRS1 = SIX-ROWED SPIKE 1
Plant architecture
Inflorescence architecture
Coding,
SNP
Hordeum vulgare
(species)
Domesticated
Linkage Mapping
Komatsuda T; Pourkheirandish M; He C ; et al. (2007)
Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene.
1 Additional References
GP00001191
Vrs1
A1IHK8
Morphology
Morphology
Phe75Leu
Hordeum vulgare
(species)
Hordeum vulgare
(species)
VRS1 = SIX-ROWED SPIKE 1
Hordeum vulgare
(species)
Published - Accepted by Curator
VvMYBA1
Coloration (fruit)
Cis-regulatory,
Insertion
Vitis vinifera
wine grape - (species) D
Domesticated
Candidate Gene
Kobayashi S; Goto-Yamamoto N; Hirochika H (2004)
Retrotransposon-induced mutations in grape skin color.
GP00001192
VvmybA1
Q6L973
Morphology
Gret1 retrotransposon insertion
Vitis vinifera
wine grape - (species)
Vitis vinifera
wine grape - (species) D
VvMYBA1
Vitis vinifera
wine grape - (species)
Published - Accepted by Curator
VvMYBA1
Coloration (fruit)
Unknown,
Unknown
Vitis vinifera
wine grape - (species)
Domesticated
Linkage Mapping
Fournier-Level A; Le Cunff L; Gomez C ; et al. (2009)
Quantitative genetic bases of anthocyanin variation in grape (Vitis vinifera L. ssp. sativa) berry: [...]
GP00001193
VvmybA1
Q6L973
Morphology
Gret1 insertion polymorphism + R188S + Q213P
Vitis vinifera
wine grape - (species)
Vitis vinifera
wine grape - (species)
VvMYBA1
Vitis vinifera
wine grape - (species)
Published - Accepted by Curator
VvMYBA1
Coloration (fruit)
Cis-regulatory,
Deletion
Vitis vinifera
wine grape - (species) D
Domesticated
Candidate Gene
Kobayashi S; Goto-Yamamoto N; Hirochika H (2004)
Retrotransposon-induced mutations in grape skin color.
1 Additional References
GP00001194
VvmybA1
Q6L973
Morphology
Gret1 retrotransposon deletion; leaving behind its 3'-LTR flanked by 5 bp of a duplicated target site
Vitis vinifera
wine grape - (species)
Vitis vinifera
wine grape - (species) D
VvMYBA1
Vitis vinifera
wine grape - (species)
Published - Accepted by Curator
VvMYBA1
Coloration (fruit)
Cis-regulatory,
Deletion
Vitis vinifera
wine grape - (species) D
Domesticated
Candidate Gene
Ferreira V; Matus JT; Pinto-Carnide O ; et al. (2019)
Genetic analysis of a white-to-red berry skin color reversion and its transcriptomic and metabolic c[...]
GP00002096
VvmybA1
Q6L973
Morphology
partial excision of the Gret1 retrotransposon from the promoter region of the MYBA1 anthocyanin regulator - associated with white-to-red berry skin color reversion
Vitis vinifera
wine grape - (species)
Vitis vinifera
wine grape - (species) D
VvMYBA1
Vitis vinifera
wine grape - (species)
Published - Accepted by Curator
VvMYBA1
Coloration (fruit)
Cis-regulatory,
Insertion
Vitis vinifera
wine grape - (species) D
Domesticated
Candidate Gene
Shimazaki M; Fujita K; Kobayashi H ; et al. (2011)
Pink-colored grape berry is the result of short insertion in intron of color regulatory gene.
GP00002097
VvmybA1
Q6L973
Morphology
33 bp insertion in the second intron of the MYBA1 red allele which affects messenger RNA (mRNA) stability - 16 bp of the 3' end in the insertion is a key structure for a defect in splicing of MybA1 transcripts
Vitis vinifera
wine grape - (species)
Vitis vinifera
wine grape - (species) D
VvMYBA1
Vitis vinifera
wine grape - (species)
Published - Accepted by Curator
VvMYBA1
Coloration (fruit)
Other,
Deletion
Vitis vinifera
wine grape - (species) D
Domesticated
Candidate Gene
Azuma A; Kobayashi S; Goto-Yamamoto N ; et al. (2009)
Color recovery in berries of grape (Vitis vinifera L.) 'Benitaka', a bud sport of 'Italia', is cause[...]
GP00002099
VvmybA1
Q6L973
Morphology
homologous recombination between the non-functional allele of MybA1 and the truncated MybA3 gene at their promoter region, resulting in the recovery of MybA1 genomic integrity (and therefore its transcription) on cv. ‘Benitaka’. The VvmybA1 locus of 'Benitaka' is heterozygous for the VvmybA1a allele (non-functional) and a novel VvmybA1(BEN) allele. VvmybA1(BEN) restores VvmybA1 transcripts.
Vitis vinifera
wine grape - (species)
Vitis vinifera
wine grape - (species) D
VvMYBA1
Vitis vinifera
wine grape - (species)
Published - Accepted by Curator
VvMybA1 VvMybA2 VvMybA3 and VvMybA4
Coloration (fruit)
Gene Loss,
Complex Change
N
Vitis vinifera
wine grape - (species) D
Domesticated
Candidate Gene
Carbonell-Bejerano P; Royo C; Torres-Pérez R ; et al. (2017)
Catastrophic Unbalanced Genome Rearrangements Cause Somatic Loss of Berry Color in Grapevine.
GP00002098
VvmybA3
Q6L9M7
Morphology
catastrophic genome rearrangement: intrachromosomal and interchromosomal translocations and the deletion of 313 genes including the loss of the functional copy for the MYB transcription factors required for anthocyanin pigmentation in the berry skin N
Vitis vinifera
wine grape - (species)
Vitis vinifera
wine grape - (species) D
VvMybA1 VvMybA2 VvMybA3 and VvMybA4
Vitis vinifera
wine grape - (species)
Published - Accepted by Curator
VvMYBA2
Coloration (fruit)
2 Mutations:
Coding
N
Vitis vinifera
wine grape - (species) D
Domesticated
Linkage Mapping
Fournier-Level A; Le Cunff L; Gomez C ; et al. (2009)
Quantitative genetic bases of anthocyanin variation in grape (Vitis vinifera L. ssp. sativa) berry: [...]
GP00001195
VvmybA2
Q6L9M8
Morphology
2 mutations
Vitis vinifera
wine grape - (species)
Vitis vinifera
wine grape - (species) D
VvMYBA2
Vitis vinifera
wine grape - (species)
Published - Accepted by Curator
VvMYBA3
Coloration (fruit)
Cis-regulatory,
SNP
Vitis vinifera
wine grape - (species)
Domesticated
Linkage Mapping
Fournier-Level A; Le Cunff L; Gomez C ; et al. (2009)
Quantitative genetic bases of anthocyanin variation in grape (Vitis vinifera L. ssp. sativa) berry: [...]
GP00001196
VvmybA3
Q6L9M7
Morphology
Substitution in promoter
Vitis vinifera
wine grape - (species)
Vitis vinifera
wine grape - (species)
VvMYBA3
Vitis vinifera
wine grape - (species)
Published - Accepted by Curator
WDR1
Coloration (flowers; seeds; stems)
Coding,
Deletion
N
Ipomoea nil
Japanese morning glory - (species) D
Domesticated
Candidate Gene
Morita Y; Saitoh M; Hoshino A ; et al. (2006)
Isolation of cDNAs for R2R3-MYB, bHLH and WDR transcriptional regulators and identification of c and[...]
GP00002090
InWDR1
Q1JUZ7
Morphology
frameshift mutation caused by a 7 bp insertion in the gene encoding a WDR transcriptional regulator N
Ipomoea nil
Japanese morning glory - (species)
Ipomoea nil
Japanese morning glory - (species) D
WDR1
Ipomoea nil
Japanese morning glory - (species)
Published - Accepted by Curator
WDR1
Coloration (flowers)
Coding,
Insertion
N
Petunia axillaris
(species) D
Domesticated
Candidate Gene
de Vetten N; Quattrocchio F; Mol J ; et al. (1997)
The an11 locus controlling flower pigmentation in petunia encodes a novel WD-repeat protein conserve[...]
GP00002093
InWDR1
Q1JUZ7
Morphology
insertion of a 300-bp dTph1 transposon in the WDR gene in the first WD-repeat (321-bp downstream of the transcription start site) N
Petunia axillaris
(species)
Petunia axillaris
(species) D
WDR1
Petunia axillaris
(species)
Published - Accepted by Curator
WIF1
Ear size
Coding,
SNP
Sus scrofa
pig - (species) D
Domesticated
Candidate Gene
Liang J; Zhang Y; Wang L ; et al. (2019)
Molecular cloning of WIF1 and HMGA2 reveals ear-preferential expression while uncovering a missense [...]
GP00002255
WIF1
Q9Y5W5
Morphology
p.Phe236Leu
Sus scrofa
pig - (species)
Sus scrofa
pig - (species) D
WIF1
Sus scrofa
pig - (species)
Published - Accepted by Curator
wingless (wg)
Coloration (wing)
3 Mutations:
Cis-regulatory
Unknown
Drosophila guttifera
(species) D
Interspecific
Candidate Gene
Koshikawa S; Giorgianni MW; Vaccaro K ; et al. (2015)
Gain of cis-regulatory activities underlies novel domains of wingless gene expression in Drosophila.
1 Additional References
GP00001384
wg
P09615
Morphology
3 mutations
Drosophila melanogaster
fruit fly - (species)
Drosophila guttifera
(species) D
wingless (wg)
Drosophila guttifera
(species)
Published - Accepted by Curator
Wnt receptor
Fin morphology (skeleton; dorsal fin)
Cis-regulatory,
Unknown
Carassius auratus
goldfish - (species) D
Domesticated
Association Mapping
Kon T; Omori Y; Fukuta K ; et al. (2020)
The Genetic Basis of Morphological Diversity in Domesticated Goldfish.
GP00002347
Lrp6
O88572
Morphology
Lrp6 gene expression is reduced in goldfish with the dorsal fin loss phenotype. Only four amino acid substitutions in the coding region and all of them are conserved or semi-conserved in zebrafish or medaka lrp6 orthologs. There is a 313-bp deletion in intron 21 of lrp6S in goldfish with the dorsal fin loss phenotype. This intronic deletion may affect induction and proper production of lrp6S mRNA at embryonic stages.
Carassius auratus
goldfish - (species)
Carassius auratus
goldfish - (species) D
Wnt receptor
Carassius auratus
goldfish - (species)
Published - Accepted by Curator
Wnt1
Coloration (larval color pattern)
Cis-regulatory,
Complex Change
Bombyx mori
domestic silkworm - (species) D
Domesticated
Linkage Mapping
Yamaguchi J; Banno Y; Mita K ; et al. (2013)
Periodic Wnt1 expression in response to ecdysteroid generates twin-spot markings on caterpillars.
2 Additional References
GP00001385
wg
P09615
Morphology
Fine-resolution mapping of a 34kb regulatory region driving Ecdysteroid-dependent Wnt gain-of-function. The L-specific structural variations upstream of Wnt1-1 may cause its ectopic expression in the spot marking region of the epidermis, resulting in the L phenotype.
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
Wnt1
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
Wnt1
Coloration (larval color pattern)
Cis-regulatory,
Deletion
Bombyx mori
domestic silkworm - (species) D
Domesticated
Association Mapping
Tong X; Han MJ; Lu K ; et al. (2022)
High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecologic[...]
GP00002403
wg
P09615
Morphology
A specific large deletion (271 kb) is present in the 3′-flanking region of Wnt1. Wnt1 expression is significantly higher in the epidermis of heterozygous LC (LC/+) mutants than in normal strains (+/+).
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
Wnt1
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
WntA
Coloration (wing, Mullerian mimicry)
Cis-regulatory,
Unknown
Heliconius erato
crimson-patched longwing - (species)
Intraspecific
Association Mapping
Martin A; Papa R; Nadeau NJ ; et al. (2012)
Diversification of complex butterfly wing patterns by repeated regulatory evolution of a Wnt ligand.
GP00001205
WntA
A0A077DF90
Morphology
unknown
Heliconius erato
crimson-patched longwing - (species)
Heliconius erato
crimson-patched longwing - (species)
WntA
Heliconius erato
crimson-patched longwing - (species)
Published - Accepted by Curator
WntA
Coloration (wing, Mullerian mimicry)
Cis-regulatory,
Unknown
Heliconius hecale
(species)
Intraspecific
Linkage Mapping
Martin A; Papa R; Nadeau NJ ; et al. (2012)
Diversification of complex butterfly wing patterns by repeated regulatory evolution of a Wnt ligand.
GP00001206
WntA
A0A077DF90
Morphology
unknown
Heliconius hecale
(species)
Heliconius hecale
(species)
WntA
Heliconius hecale
(species)
Published - Accepted by Curator
WntA
Coloration (wing, Mullerian mimicry)
Cis-regulatory,
Unknown
Heliconius ismenius
(species)
Intraspecific
Linkage Mapping
Martin A; Papa R; Nadeau NJ ; et al. (2012)
Diversification of complex butterfly wing patterns by repeated regulatory evolution of a Wnt ligand.
GP00001207
WntA
A0A077DF90
Morphology
unknown
Heliconius ismenius
(species)
Heliconius ismenius
(species)
WntA
Heliconius ismenius
(species)
Published - Accepted by Curator
WntA
Coloration (wing; Batesian mimicry)
Cis-regulatory,
Unknown
Limenitis arthemis
white admiral - (species)
Intraspecific
Linkage Mapping
Gallant JR; Imhoff VE; Martin A ; et al. (2014)
Ancient homology underlies adaptive mimetic diversity across butterflies.
GP00001208
WntA
A0A077DF90
Morphology
Complex Haplotype in first intron perfectly associated with phenotype: 173 fixed single-nucleotide polymorphisms (SNPs) in complete linkage disequilibrium (LD) located 23
Limenitis arthemis
white admiral - (species)
Limenitis arthemis
white admiral - (species)
WntA
Limenitis arthemis
white admiral - (species)
Published - Accepted by Curator
WntA
Coloration (wing, Mullerian mimicry)
Cis-regulatory,
Indel
Heliconius cydno
(species)
Intraspecific
Linkage Mapping
Gallant JR; Imhoff VE; Martin A ; et al. (2014)
Ancient homology underlies adaptive mimetic diversity across butterflies.
1 Additional References
GP00001209
WntA
A0A077DF90
Morphology
1.8-kb indel that was perfectly associated with variation in forewing melanin patterning
Heliconius cydno
(species)
Heliconius cydno
(species)
WntA
Heliconius cydno
(species)
Published - Accepted by Curator
WntA
Coloration (wing, Mullerian mimicry)
Cis-regulatory,
Unknown
Heliconius pachinus
(species)
Intraspecific
Linkage Mapping
Martin A; Papa R; Nadeau NJ ; et al. (2012)
Diversification of complex butterfly wing patterns by repeated regulatory evolution of a Wnt ligand.
1 Additional References
GP00001210
WntA
A0A077DF90
Morphology
Complex cis-regulatory haplotype : 170 fixed differences were detected among comparisons of allopatric H. c. galanthus and H. pachinus
Heliconius cydno
(species)
Heliconius pachinus
(species)
WntA
Heliconius pachinus
(species)
Published - Accepted by Curator
WntA
Coloration (wing, Mullerian mimicry)
Cis-regulatory,
Unknown
Heliconius erato
crimson-patched longwing - (species)
Intraspecific
Linkage Mapping
Martin A; Papa R; Nadeau NJ ; et al. (2012)
Diversification of complex butterfly wing patterns by repeated regulatory evolution of a Wnt ligand.
GP00001211
WntA
A0A077DF90
Morphology
Not identified
Heliconius himera
(species)
Heliconius erato
crimson-patched longwing - (species)
WntA
Heliconius erato
crimson-patched longwing - (species)
Published - Accepted by Curator
WntA
Coloration (wing, Mullerian mimicry)
Cis-regulatory,
Unknown
Heliconius erato
crimson-patched longwing - (species)
Intraspecific
Linkage Mapping
Martin A; Papa R; Nadeau NJ ; et al. (2012)
Diversification of complex butterfly wing patterns by repeated regulatory evolution of a Wnt ligand.
GP00001212
WntA
A0A077DF90
Morphology
Not identified
Heliconius himera
(species)
Heliconius erato
crimson-patched longwing - (species)
WntA
Heliconius erato
crimson-patched longwing - (species)
Published - Accepted by Curator
WntA
Coloration (wing, Mullerian mimicry)
Cis-regulatory,
Unknown
Heliconius erato
crimson-patched longwing - (species)
Intraspecific
Linkage Mapping
Martin A; Papa R; Nadeau NJ ; et al. (2012)
Diversification of complex butterfly wing patterns by repeated regulatory evolution of a Wnt ligand.
GP00001213
WntA
A0A077DF90
Morphology
Not identified
Heliconius himera
(species)
Heliconius erato
crimson-patched longwing - (species)
WntA
Heliconius erato
crimson-patched longwing - (species)
Published - Accepted by Curator
WntA
Coloration (wing, Mullerian mimicry)
Cis-regulatory,
Unknown
Heliconius melpomene
postman butterfly - (species)
Intraspecific
Linkage Mapping
Martin A; Papa R; Nadeau NJ ; et al. (2012)
Diversification of complex butterfly wing patterns by repeated regulatory evolution of a Wnt ligand.
GP00001214
WntA
A0A077DF90
Morphology
unknown ; non-coding with effect on spatial gene expression
Heliconius melpomene
postman butterfly - (species)
Heliconius melpomene
postman butterfly - (species)
WntA
Heliconius melpomene
postman butterfly - (species)
Published - Accepted by Curator
Y
Coloration (fruit)
Coding,
Insertion
Sorghum bicolor
sorghum - (species) D
Domesticated
Candidate Gene
Chopra S; Brendel V; Zhang J ; et al. (1999)
Molecular characterization of a mutable pigmentation phenotype and isolation of the first active tra[...]
GP00002068
P1
O24579
Morphology
insertion of a transposable element named Candystripe1 (Cs1) in the second intron of the Y gene - Cs1 is 23,018 bp in size and is bordered by 20-bp terminal inverted repeat sequences. It generated a 3-bp target site duplication upon insertion within the Y gene. Cs1 shares features of the CACTA superfamily of transposons.
Sorghum bicolor
sorghum - (species)
Sorghum bicolor
sorghum - (species) D
Y
Sorghum bicolor
sorghum - (species)
Published - Accepted by Curator
yellow
Coloration (abdomen)
Cis-regulatory,
Unknown
Drosophila kikkawai
(species)
Interspecific
Candidate Gene
Jeong S; Rokas A; Carroll SB (2006)
Regulation of body pigmentation by the Abdominal-B Hox protein and its gain and loss in Drosophila e[...]
GP00001220
y
P09957
Morphology
indel and/or SNP located within a cis-regulatory element
Drosophila melanogaster
fruit fly - (species)
Drosophila kikkawai
(species)
yellow
Drosophila kikkawai
(species)
Published - Accepted by Curator
yellow
Coloration (wing spot)
Cis-regulatory,
SNP
Drosophila gunungcola
(species)
Interspecific
Candidate Gene
Prud'homme B; Gompel N; Rokas A ; et al. (2006)
Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene.
1 Additional References
GP00001221
y
P09957
Morphology
within a 740bp-element; at least two and no more than seven point mutations involved
Drosophila elegans
(species)
Drosophila gunungcola
(species)
yellow
Drosophila gunungcola
(species)
Published - Accepted by Curator
yellow
Coloration (wing spot)
Cis-regulatory,
Unknown
Drosophila biarmipes
(species) D
Interspecific
Candidate Gene
Gompel N; Prud'homme B; Wittkopp PJ ; et al. (2005)
Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila[...]
GP00001222
y
P09957
Morphology
wing spot activator element; within a 196bp fragment; sequences required for activation in the spot are located within or overlap with bp 425-453
Drosophila
(subgenus)
Drosophila biarmipes
(species) D
yellow
Drosophila biarmipes
(species)
Published - Accepted by Curator
yellow
Coloration (wing spot)
Cis-regulatory,
Unknown
Drosophila biarmipes
(species) D
Interspecific
Candidate Gene
Gompel N; Prud'homme B; Wittkopp PJ ; et al. (2005)
Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila[...]
GP00001223
y
P09957
Morphology
wing spot repressor element; within a 675-bp fragment;
Drosophila
(subgenus)
Drosophila biarmipes
(species) D
yellow
Drosophila biarmipes
(species)
Published - Accepted by Curator
yellow
Coloration (wing spot)
Cis-regulatory,
Unknown
Drosophila mimetica
(species)
Interspecific
Candidate Gene
Prud'homme B; Gompel N; Rokas A ; et al. (2006)
Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene.
GP00001224
y
P09957
Morphology
within a 740bp-element
Drosophila
(subgenus)
Drosophila mimetica
(species)
yellow
Drosophila mimetica
(species)
Published - Accepted by Curator
yellow
Coloration (wing spot)
Cis-regulatory,
Unknown
Drosophila tristis
(species)
Interspecific
Candidate Gene
Prud'homme B; Gompel N; Rokas A ; et al. (2006)
Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene.
GP00001225
y
P09957
Morphology
within a 927 bp-element
Drosophila
(subgenus)
Drosophila tristis
(species)
yellow
Drosophila tristis
(species)
Published - Accepted by Curator
yellow
Coloration (male-specific)
Unknown,
Unknown
Drosophila merina
(species)
Interspecific
Linkage Mapping
Signor SA; Liu Y; Rebeiz M ; et al. (2016)
Genetic Convergence in the Evolution of Male-Specific Color Patterns in Drosophila.
GP00001550
y
P09957
Morphology
unknown
Drosophila ercepeae
(species)
Drosophila merina
(species)
yellow
Drosophila merina
(species)
Published - Accepted by Curator
yellow
Coloration (male-specific)
Unknown,
Unknown
Drosophila bipectinata
(species)
Interspecific
Linkage Mapping
Signor SA; Liu Y; Rebeiz M ; et al. (2016)
Genetic Convergence in the Evolution of Male-Specific Color Patterns in Drosophila.
GP00001551
y
P09957
Morphology
unknown
Drosophila malerkotliana
(species)
Drosophila bipectinata
(species)
yellow
Drosophila bipectinata
(species)
Published - Accepted by Curator
yellow
Coloration (body; wing)
Cis-regulatory,
Inversion
Drosophila melanogaster
fruit fly - (species) D
Intraspecific
Candidate Gene
Zakharenko LP; p6acheva EM; Romanova OA ; et al. (2000)
hobo-induced rearrangements are responsible for mutation bursts at the yellow locus in a natural pop[...]
GP00001961
y
P09957
Morphology
y[2-717] - Inversion that occurred between two hobo elements: one located 129 bp from the start site of yellow transcription and the other in the distal telomere region. The yellow phenotype is caused by the separation of the body and wing enhancers from the transcription unit.
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species) D
yellow
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
yellow
Coloration (abdomen; male)
Cis-regulatory,
Unknown
Drosophila santomea
(species) D
Interspecific
Linkage Mapping
Liu Y; Ramos-Womack M; Han C ; et al. (2019)
Changes throughout a Genetic Network Mask the Contribution of Hox Gene Evolution.
GP00002023
y
P09957
Morphology
change in a cis-regulatory region - exact causing mutation(s) unknown - decreased yellow abdominal expression associated with lighter color
Drosophila yakuba
(species)
Drosophila santomea
(species) D
yellow
Drosophila santomea
(species)
Published - Accepted by Curator
yellow
Coloration (wing)
Cis-regulatory,
Unknown
Danaus chrysippus
African queen - (species)
Intraspecific
Association Mapping
Martin SH; Singh KS; Gordon IJ ; et al. (2020)
Whole-chromosome hitchhiking driven by a male-killing endosymbiont.
GP00002430
y
P09957
Morphology
A cluster of SNPs most strongly associated with background colour (B locus) is found just upstream of the gene yellow and a phylogenetic network for a 30-kb region around yellow groups individuals nearly perfectly by phenotype; although some individuals classed as heterozygous were intermingled with homozygotes.
Danaus chrysippus
African queen - (species)
Danaus chrysippus
African queen - (species)
yellow
Danaus chrysippus
African queen - (species)
Published - Accepted by Curator
yellow
Coloration (body; wing)
Coding,
Insertion
N
Musca domestica
house fly - (species) D
Intraspecific
Candidate Gene
Heinze SD; Kohlbrenner T; Ippolito D ; et al. (2017)
CRISPR-Cas9 targeted disruption of the yellow ortholog in the housefly identifies the brown body loc[...]
GP00002623
y
P09957
Morphology
a 4 bp insertion at amino acid position 67 that causes a frameshift and a premature stop codon N
Musca domestica
house fly - (species)
Musca domestica
house fly - (species) D
yellow
Musca domestica
house fly - (species)
Published - Accepted by Curator
zeb1a
Coloration (fish fins)
Cis-regulatory,
SNP
Tropheops sp. 'red cheek'
(species)
Interspecific
Linkage Mapping
Albertson RC; Powder KE; Hu Y ; et al. (2014)
Genetic basis of continuous variation in the levels and modular inheritance of pigmentation in cichl[...]
GP00001418
zeb1a
F1QMZ5
Morphology
intronic SNP
Labeotropheus fuelleborni
blue mbuna - (species)
Tropheops sp. 'red cheek'
(species)
zeb1a
Tropheops sp. 'red cheek'
(species)
Published - Accepted by Curator
zic1/zic4
Fin morphology (skeleton; dorsal fin; caudal fin)
Pigmentation (ventralized trunk)
Cis-regulatory,
Insertion
Oryzias latipes
Japanese medaka - (species) D
Intraspecific
Linkage Mapping
Moriyama Y; Kawanishi T; Nakamura R ; et al. (2012)
The medaka zic1/zic4 mutant provides molecular insights into teleost caudal fin evolution.
1 Additional References
GP00002038
Zic1
P46684
Morphology
Morphology
The mutant phenotype is caused by a dramatic decrease of zic1/zic4 expression in the dorsal somites. The insertion of a transposon (“Albatross”) into an enhancer region (downstream of zic4) of the transcription factors zic1 and zic4 causes this phenotype. Both genes are expressed by a bi-directional promoter. The transposon insertion is proposed to interfere with the transcriptional regulation of zic1/zic4; resulting in the disturbance of the expression of the transcription factors in the dorsal somites (the expression of zic1/zic4 in other parts of the body is not affected in this mutant) and ultimately causing a ventralized trunk phenotype. In Inoue et al. (2017) it was shown that the transposon “Albatross” is actually larger than originally predicted; and is now called “Teratorn”. Teratorn is around 180kb long and appears to originate from the fusion of a DNA transposon and a herpesvirus.
Oryzias latipes
Japanese medaka - (species)
Oryzias latipes
Japanese medaka - (species) D
zic1/zic4
Oryzias latipes
Japanese medaka - (species)
Published - Accepted by Curator
zic1/zic4
Fin morphology (skeleton; caudal fin)
Cis-regulatory,
Deletion
Betta splendens
Siamese fighting fish - (species) D
Domesticated
Linkage Mapping
Wang L; Sun F; Wan ZY ; et al. (2021)
Genomic Basis of Striking Fin Shapes and Colors in the Fighting Fish.
GP00002385
Zic1
P46684
Morphology
"We further sequenced the genomes of both homozygous single- and double-tail fish and found in double tail no large sequence variation except for a ∼180-bp deletion ∼15-kb downstream of zic4 (fig. 4C and supplementary fig. S19a, Supplementary Material online). This deletion was located in a cluster of CNEs and coincided with predicted CNE.006008 (supplementary fig. S19b, Supplementary Material online)."
"We observed that the wild-type ST allele significantly enhanced green fluorescent protein (GFP) expression in embryos at 24 hpf, when both zic1 and zic4 show differential expression between double-tail and wild-type fish (Moriyama et al. 2012), whereas no visible GFP expression was detected for the st allele (fig. 4E and supplementary table S11, Supplementary Material online). The efficiency of the two alleles as candidate enhancers was further examined using a Dual-Luciferase Reporter Assay, which showed that the ST allele enhanced luciferase expression by ∼10× relative to st allele in Singapore grouper embryonic cell line (fig. 4F)."
"Finally, we deleted this enhancer using the CRISPR-Cas9 system in fighting fish. Considering the efficiency of tested gRNAs and the cluster of CNEs that could have unpredicted functions, we limited the modification to the CNE.006008 region and did not involve the other CNEs (supplementary fig. S20, Supplementary Material online). Genetic analysis revealed that none of these fish had completely deleted CNE.006008, suggesting nonsimultaneous cutting at multiple targeted gRNA positions. These mosaic fish (n = 7) had significantly more fin rays than the noninjected controls (P < 0.01; fig. 4G). "
Betta splendens
Siamese fighting fish - (species)
Betta splendens
Siamese fighting fish - (species) D
zic1/zic4
Betta splendens
Siamese fighting fish - (species)
Published - Accepted by Curator