Gephebase

Gephebase Search Results

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Your research retrieved 471 results.

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Gene	Trait	Mutation	Taxon B	Taxonomic Status	Evidence	Main Reference	Gephe ID	UniProtKB	Trait Category	Mutation Details	Taxon A	Taxon B	Edit Gene-GePhe	Taxon B	Status
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
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
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 Wooldridge TB; Kautt AF; Lassance JM (2022) An enhancer of Agouti contributes to parallel evolution of cryptically colored beach mice.	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 (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 Robic A; Morisson M; Leroux S (2019) Two new structural mutations in the 5' region of the ASIP gene cause diluted feather color phenotype[...]	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)	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 Barrett RDH; Laurent S; Mallarino R (2019) Linking a mutation to survival in wild mice.	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)	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 (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 Sulem P; Gudbjartsson DF; Stacey SN (2008) Two newly identified genetic determinants of pigmentation in Europeans. Voisey J; Gomez-Cabrera Mdel C; Smit DJ (2006) A polymorphism in the agouti signalling protein (ASIP) is associated with decreased levels of mRNA.	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)	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)	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)	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)	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-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 Kratochwil CF; Liang Y; Urban S (2019) Evolutionary Dynamics of Structural Variation at a Key Locus for Color Pattern Diversification in Ci[...]	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 Kratochwil CF; Liang Y; Urban S (2019) Evolutionary Dynamics of Structural Variation at a Key Locus for Color Pattern Diversification in Ci[...]	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
alcohol dehydrogenase (Adh)	Xenobiotic resistance (alcohol)	6 Mutations:	Drosophila melanogaster fruit fly - (species) D	Intraspecific	Linkage Mapping	Choudhary M; Laurie CC (1991) Use of in vitro mutagenesis to analyze the molecular basis of the difference in Adh expression assoc[...] 4 Additional References Laurie CC; Bridgham JT; Choudhary M (1991) Associations between DNA sequence variation and variation in expression of the Adh gene in natural p[...] King EG; Merkes CM; McNeil CL (2012) Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource. Siddiq MA; Loehlin DW; Montooth KL (2017) Experimental test and refutation of a classic case of molecular adaptation in Drosophila melanogaste[...] Loehlin DW; Ames JR; Vaccaro K (2019) A major role for noncoding regulatory mutations in the evolution of enzyme activity.	GP00001962	Adh P00334	Physiology	6 mutations	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species) D	alcohol dehydrogenase (Adh)	Drosophila melanogaster fruit fly - (species)	Published - Accepted by Curator
alcohol dehydrogenase (Adh)	Xenobiotic resistance (alcohol)	4 Mutations:	Drosophila yakuba (species)	Interspecific	Candidate Gene	Loehlin DW; Ames JR; Vaccaro K ; et al. (2019) A major role for noncoding regulatory mutations in the evolution of enzyme activity.	GP00001963	Adh P00334	Physiology	4 mutations	Drosophila santomea (species)	Drosophila yakuba (species)	alcohol dehydrogenase (Adh)	Drosophila yakuba (species)	Published - Accepted by Curator
alcohol dehydrogenase (Adh)	Xenobiotic resistance (alcohol)	4 Mutations:	Drosophila erecta (species)	Interspecific	Candidate Gene	Loehlin DW; Ames JR; Vaccaro K ; et al. (2019) A major role for noncoding regulatory mutations in the evolution of enzyme activity.	GP00001964	Adh P00334	Physiology	4 mutations	Drosophila orena (species)	Drosophila erecta (species)	alcohol dehydrogenase (Adh)	Drosophila erecta (species)	Published - Accepted by Curator
alcohol dehydrogenase (Adh)	Xenobiotic resistance (alcohol)	5 Mutations:	Drosophila virilis (species) D	Interspecific	Candidate Gene	Loehlin DW; Ames JR; Vaccaro K ; et al. (2019) A major role for noncoding regulatory mutations in the evolution of enzyme activity.	GP00001965	Adh P00334	Physiology	5 mutations	Drosophila americana (species)	Drosophila virilis (species) D	alcohol dehydrogenase (Adh)	Drosophila virilis (species)	Published - Accepted by Curator
alcohol dehydrogenase (Adh)	Xenobiotic resistance (alcohol)	Cis-regulatory, Insertion	Drosophila melanogaster fruit fly - (species) D	Intraspecific	Candidate Gene	Strand DJ; McDonald JF (1989) Insertion of a copia element 5' to the Drosophila melanogaster alcohol dehydrogenase gene (adh) is a[...]	GP00001989	Adh P00334	Physiology	insertion of a complete 5.2kb copia retroviral-like transposable element 240 bp upstream from the distal (adult) adh transcriptional start site	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species) D	alcohol dehydrogenase (Adh)	Drosophila melanogaster fruit fly - (species)	Published - Accepted by Curator
ALMT1	Metal tolerance	Cis-regulatory, Unknown	Triticum aestivum bread wheat - (species)	Domesticated	Linkage Mapping	Raman H; Zhang K; Cakir M ; et al. (2005) Molecular characterization and mapping of ALMT1, the aluminium-tolerance gene of bread wheat (Tritic[...] 2 Additional References Cai S; Bai GH; Zhang D (2008) Quantitative trait loci for aluminum resistance in Chinese wheat landrace FSW. Ryan PR; Raman H; Gupta S (2010) The multiple origins of aluminium resistance in hexaploid wheat include Aegilops tauschii and more r[...]	GP00000080	ALMT1 Q76LB1	Physiology	multiple regulatory changes	Triticum aestivum bread wheat - (species)	Triticum aestivum bread wheat - (species)	ALMT1	Triticum aestivum bread wheat - (species)	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 (anthocyanin accumulation in entire plant)	Cis-regulatory, Insertion	Capsicum annuum (species) D	Domesticated	Candidate Gene	Jung S; Venkatesh J; Kang MY ; et al. (2019) A non-LTR retrotransposon activates anthocyanin biosynthesis by regulating a MYB transcription facto[...]	GP00002051	AN2 A4GRU8	Morphology; Physiology	insertion of a 4.2 kb non-LTR retrotransposon in the promoter (672 bp upstream of the start codon of CaAn2) which may activate expression of CaAn2 by recruiting transcription factors at the 3' UTR	Capsicum annuum (species)	Capsicum annuum (species) D	anthocyanin2 (an2)	Capsicum annuum (species)	Published - Accepted by Curator
APJ1	Xenobiotic resistance (alcohol, ethanol)	Cis-regulatory, Unknown	Saccharomyces cerevisiae baker's yeast - (species)	Domesticated	Linkage Mapping	Swinnen S; Schaerlaekens K; Pais T ; et al. (2012) Identification of novel causative genes determining the complex trait of high ethanol tolerance in y[...]	GP00000097	APJ1 P53940	Physiology	unknown	Saccharomyces cerevisiae baker's yeast - (species)	Saccharomyces cerevisiae baker's yeast - (species)	APJ1	Saccharomyces cerevisiae baker's yeast - (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 Xiang H; Liu X; Li M (2018) The evolutionary road from wild moth to domestic silkworm. Tomihara K; Andolfatto P; Kiuchi T (2022) Allele-specific knockouts reveal a role for apontic-like in the evolutionary loss of larval melanin [...]	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
ARHGEF3	Hematopoiesis (mean blood platelet volume & blood platelet count)	Cis-regulatory, SNP	Homo sapiens human - (species)	Intraspecific	Association Mapping	Guo MH; Nandakumar SK; Ulirsch JC ; et al. (2017) Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mech[...]	GP00001605	ARHGEF3 Q9NR81	Physiology	T>C at the associated SNP that disrupts a conserved GATA motif. This variant overlaps with a common-myeloid progenitor (CMP-) and megakaryocyte-erythroid progenitor (MEP-) specific regulatory element that affects the transcription of ARHGEF3	Homo sapiens human - (species)	Homo sapiens human - (species)	ARHGEF3	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
AtHKT1	Salt tolerance	Cis-regulatory, Deletion	Arabidopsis thaliana thale cress - (species) D	Intraspecific	Linkage Mapping	Rus A; Baxter I; Muthukumar B ; et al. (2006) Natural variants of AtHKT1 enhance Na+ accumulation in two wild populations of Arabidopsis. 1 Additional References Baxter I; Brazelton JN; Yu D (2010) A coastal cline in sodium accumulation in Arabidopsis thaliana is driven by natural variation of the[...]	GP00000124	HKT1 Q84TI7	Physiology	725bp deletion of part of upstream repeat region	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species) D	AtHKT1	Arabidopsis thaliana thale cress - (species)	Published - Accepted by Curator
AtHKT1	Salt tolerance	Cis-regulatory, Deletion	Arabidopsis thaliana thale cress - (species) D	Intraspecific	Linkage Mapping	Rus A; Baxter I; Muthukumar B ; et al. (2006) Natural variants of AtHKT1 enhance Na+ accumulation in two wild populations of Arabidopsis. 1 Additional References Baxter I; Brazelton JN; Yu D (2010) A coastal cline in sodium accumulation in Arabidopsis thaliana is driven by natural variation of the[...]	GP00000125	HKT1 Q84TI7	Physiology	687bp deletion of part of upstream repeat region	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species) D	AtHKT1	Arabidopsis thaliana thale cress - (species)	Published - Accepted by Curator
avpr1a	Male sexual fidelity (monogamous regime)	Cis-regulatory, Unknown	Microtus ochrogaster prairie vole - (species)	Intraspecific	Candidate Gene	Okhovat M; Berrio A; Wallace G ; et al. (2015) Sexual fidelity trade-offs promote regulatory variation in the prairie vole brain. 1 Additional References Berrio A; Guerrero RF; Aglyamova GV (2018) Complex selection on a regulator of social cognition: Evidence of balancing selection, regulatory in[...]	GP00000129	Avpr1a Q62463	Behavior	unknown	Microtus ochrogaster prairie vole - (species)	Microtus ochrogaster prairie vole - (species)	avpr1a	Microtus ochrogaster prairie vole - (species)	Published - Accepted by Curator
AZI1	Root growth (root growth responses to low zinc conditions)	Cis-regulatory, Unknown	Arabidopsis thaliana thale cress - (species)	Intraspecific	Association Mapping	Bouain N; Satbhai SB; Korte A ; et al. (2018) Natural allelic variation of the AZI1 gene controls root growth under zinc-limiting condition.	GP00001769	AZI1 Q9SU35	Physiology	exact causing mutation(s) unknown	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species)	AZI1	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
B4GALNT2	Fertility (increased ovulation rate)	Cis-regulatory, Unknown	Ovis aries sheep - (species) D	Domesticated	Linkage Mapping	Drouilhet L; Mansanet C; Sarry J ; et al. (2013) The highly prolific phenotype of Lacaune sheep is associated with an ectopic expression of the B4GAL[...]	GP00001979	B4galnt2 Q09199	Physiology	candidate region to 197kb ; putative mutation (g.36938224T>A) in intron 7or (g.37034573A>G) 96 kb away in an intergenic region	Ovis aries sheep - (species)	Ovis aries sheep - (species) D	B4GALNT2	Ovis aries sheep - (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	Insect pheromone attraction	Cis-regulatory, Unknown	Ostrinia nubilalis European corn borer - (species)	Intraspecific	Association Mapping	Unbehend M; Kozak GM; Koutroumpa F ; et al. (2021) bric à brac controls sex pheromone choice by male European corn borer moths.	GP00002424	bab1 Q9W0K7	Behavior; Physiology	A genome-wide association study of pheromone preference under field conditions indicates that preference is controlled by sequence variation within the 293 kb bab intron 1.	Ostrinia nubilalis European corn borer - (species)	Ostrinia nubilalis European corn borer - (species)	bab	Ostrinia nubilalis European corn borer - (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 Bickel RD; Kopp A; Nuzhdin SV (2011) Composite effects of polymorphisms near multiple regulatory elements create a major-effect QTL.	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
BCMO1	Carotenoid content	2 Mutations: Cis-regulatory SNP	Gallus gallus chicken - (species)	Domesticated	Linkage Mapping	Le Bihan-Duval E; Nadaf J; Berri C ; et al. (2011) Detection of a Cis [corrected] eQTL controlling BCMO1 gene expression leads to the identification of[...]	GP00000137	BCO1 Q9HAY6	Morphology; Physiology	2 mutations	Gallus gallus chicken - (species)	Gallus gallus chicken - (species)	BCMO1	Gallus gallus chicken - (species)	Published - Accepted by Curator
BCO2 = beta-carotene oxygenase 2	Carotenoid content (skin ; shanks)	Cis-regulatory, Unknown	Gallus sonneratii gray junglefowl - (species) D Gallus gallus chicken - (species) D	Interspecific	Linkage Mapping	Eriksson J; Larson G; Gunnarsson U ; et al. (2008) Identification of the yellow skin gene reveals a hybrid origin of the domestic chicken. 1 Additional References Fallahshahroudi A; Sorato E; Altimiras J (2019) The Domestic BCO2 Allele Buffers Low-Carotenoid Diets in Chickens: Possible Fitness Increase Through[...]	GP00000139	BCO2 Q9BYV7	Morphology; Physiology	Not identified	Gallus gallus chicken - (species)	Gallus sonneratii gray junglefowl - (species) D Gallus gallus chicken - (species) D	BCO2 = beta-carotene oxygenase 2	Gallus sonneratii gray junglefowl - (species) Gallus gallus chicken - (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	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	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
benzoic acid/salicylic acid carboxyl methyltransferase (BSMT)	Fragrance	Cis-regulatory, Unknown	Petunia axillaris (species) D	Interspecific	Linkage Mapping	Amrad A; Moser M; Mandel T ; et al. (2016) Gain and Loss of Floral Scent Production through Changes in Structural Genes during Pollinator-Media[...]	GP00001766	BSMT1 Q6XMI3	Physiology	Allele-specific expression in hybrids - de novo expression in P. axillaris	Petunia integrifolia subsp. inflata (subspecies)	Petunia axillaris (species) D	benzoic acid/salicylic acid carboxyl methyltransferase (BSMT)	Petunia axillaris (species)	Published - Accepted by Curator
benzoyl-CoA:benzylalcohol/2-phenylethanol benzoyltransferase (BPBT)	Fragrance	Cis-regulatory, Unknown	Petunia axillaris (species) D	Interspecific	Linkage Mapping	Amrad A; Moser M; Mandel T ; et al. (2016) Gain and Loss of Floral Scent Production through Changes in Structural Genes during Pollinator-Media[...]	GP00001765	BPBT A0A172W606	Physiology	Allele-specific expression in hybrids - de novo expression in P. axillaris	Petunia integrifolia subsp. inflata (subspecies)	Petunia axillaris (species) D	benzoyl-CoA:benzylalcohol/2-phenylethanol benzoyltransferase (BPBT)	Petunia axillaris (species)	Published - Accepted by Curator
BMP15	Fertility (increased ovulation rate)	Cis-regulatory, SNP	Ovis aries sheep - (species) D	Domesticated	Association Mapping	Demars J; Fabre S; Sarry J ; et al. (2013) Genome-wide association studies identify two novel BMP15 mutations responsible for an atypical hyper[...]	GP00002329	Bmp15 Q9Z0L4	Physiology	T>A SPN upstream of the BMP15 gene associated with the prolificacy variability (P = 1.93E-11). Effect of +0.20 lamb per lambing at the heterozygous state.	Ovis aries sheep - (species)	Ovis aries sheep - (species) D	BMP15	Ovis aries sheep - (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 Johnsson M; Rubin CJ; Höglund A (2014) The role of pleiotropy and linkage in genes affecting a sexual ornament and bone allocation in the c[...]	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
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 Ellis NA; Glazer AM; Donde NN (2015) Distinct developmental genetic mechanisms underlie convergently evolved tooth gain in sticklebacks. Erickson PA; Cleves PA; Ellis NA (2015) A 190 base pair, TGF-β responsive tooth and fin enhancer is required for stickleback Bmp6 expression[...]	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
BOLTING TIME CONTROL 1 (BvBTC1)	Flowering time	Cis-regulatory, Unknown	Beta vulgaris (species)	Domesticated	Linkage Mapping	Pin PA; Zhang W; Vogt SH ; et al. (2012) The role of a pseudo-response regulator gene in life cycle adaptation and domestication of beet.	GP00000155	BTC1 I3NN18	Physiology	unknown	Beta vulgaris (species)	Beta vulgaris (species)	BOLTING TIME CONTROL 1 (BvBTC1)	Beta vulgaris (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 Hanson MA; Gaut BS; Stec AO (1996) Evolution of anthocyanin biosynthesis in maize kernels: the role of regulatory and enzymatic loci.	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
Callipyge (CLPG1)	Muscular mass (double-muscling ; paternal effect)	Cis-regulatory, SNP	Ovis aries sheep - (species)	Domesticated	Linkage Mapping	Takeda H; Caiment F; Smit M ; et al. (2006) The callipyge mutation enhances bidirectional long-range DLK1-GTL2 intergenic transcription in cis. 5 Additional References Freking BA; Murphy SK; Wylie AA (2002) Identification of the single base change causing the callipyge muscle hypertrophy phenotype, the onl[...] Murphy SK; Nolan CM; Huang Z (2006) Callipyge mutation affects gene expression in cis: a potential role for chromatin structure. Smit M; Segers K; Carrascosa LG (2003) Mosaicism of Solid Gold supports the causality of a noncoding A-to-G transition in the determinism o[...] Georges M; Charlier C; Cockett N (2003) The callipyge locus: evidence for the trans interaction of reciprocally imprinted genes. Gao YQ; Chen X; Wang P (2015) Regulation of DLK1 by the maternally expressed miR-379/miR-544 cluster may underlie callipyge polar [...]	GP00000168	DIO3 Q6DN07	Morphology; Physiology	1bp change in the regulatory region of the DLK1-GTL2 imprinted gene cluster	Ovis aries sheep - (species)	Ovis aries sheep - (species)	Callipyge (CLPG1)	Ovis aries sheep - (species)	Published - Accepted by Curator
CAST	Meat tenderness	Cis-regulatory, Unknown	Sus scrofa domesticus domestic pig - (subspecies)	Domesticated	Linkage Mapping	Nonneman D; Lindholm-Perry AK; Shackelford SD ; et al. (2011) Predictive markers in calpastatin for tenderness in commercial pig populations.	GP00000170	CAST P20810	Physiology	4 candidate SNPs in putative enhancers with nuclear factor-binding properties	Sus scrofa pig - (species)	Sus scrofa domesticus domestic pig - (subspecies)	CAST	Sus scrofa domesticus domestic pig - (subspecies)	Published - Accepted by Curator
catechol-O-methyltransferase (COMT)	Pain sensitivity	Cis-regulatory, SNP	Homo sapiens human - (species)	Intraspecific	Candidate Gene	Nackley AG; Shabalina SA; Tchivileva IE ; et al. (2006) Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary[...]	GP00000171	COMT P21964	Behavior	G/C - The synonymous mutation(s) affect mRNA stability and loop structures	Homo sapiens human - (species)	Homo sapiens human - (species)	catechol-O-methyltransferase (COMT)	Homo sapiens human - (species)	Published - Accepted by Curator
CCAAT-enhancer-binding protein alpha (CEBPA)	Hematopoiesis (blood basophil count)	Cis-regulatory, SNP	Homo sapiens human - (species)	Intraspecific	Association Mapping	Guo MH; Nandakumar SK; Ulirsch JC ; et al. (2017) Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mech[...]	GP00001603	CEBPA P49715	Physiology	C>T at the associated SNP which resides 39kb dowstream from CEBPA near a separate enhancer that influences CEBPA expression along various myeloid lineages. T allele was associated with a 28.6% reduction in enhancer activity.	Homo sapiens human - (species)	Homo sapiens human - (species)	CCAAT-enhancer-binding protein alpha (CEBPA)	Homo sapiens human - (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 Hellström AR; Sundström E; Gunnarsson U (2010) Sex-linked barring in chickens is controlled by the CDKN2A /B tumour suppressor locus.	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 Hellström AR; Sundström E; Gunnarsson U (2010) Sex-linked barring in chickens is controlled by the CDKN2A /B tumour suppressor locus.	GP00002162	CDKN2A P42771	Morphology	2 mutations	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	CDKN2A	Gallus gallus chicken - (species)	Published - Accepted by Curator
CG11699	Xenobiotic resistance	Cis-regulatory, Insertion	Drosophila melanogaster fruit fly - (species) D	Intraspecific	Association Mapping	Mateo L; Ullastres A; González J (2014) A transposable element insertion confers xenobiotic resistance in Drosophila.	GP00001399	Dmel\CG11699 Q9VYX5	Physiology	insertion of a 186bp POGON1 element in the 3'UTR	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species) D	CG11699	Drosophila melanogaster fruit fly - (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
Chit beta-GlcNAcase	Silk fineness	Cis-regulatory, Unknown	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[...]	GP00002401	P49010	Physiology	BmChit β-GlcNAcase gene is expressed at a significantly higher level in fine silk strains (Suxiu, Chunfeng) compared to coarse silk strains. CRISPR-cas9 mediated knockout of the BmChit β-GlcNAcase gene produced coarser silk.	Bombyx mori domestic silkworm - (species)	Bombyx mori domestic silkworm - (species) D	Chit beta-GlcNAcase	Bombyx mori domestic silkworm - (species)	Published - Accepted by Curator
Cinnamate-CoA ligase 1 (CNL1)	Fragrance	3 Mutations: N	Petunia exserta (species) D	Interspecific	Linkage Mapping	Amrad A; Moser M; Mandel T ; et al. (2016) Gain and Loss of Floral Scent Production through Changes in Structural Genes during Pollinator-Media[...]	GP00001391	CNL A0A172W603	Physiology	3 mutations	Petunia axillaris (species)	Petunia exserta (species) D	Cinnamate-CoA ligase 1 (CNL1)	Petunia exserta (species)	Published - Accepted by Curator
CIS1	Xenobiotic resistance (citrinin)	Cis-regulatory, Unknown	Saccharomyces paradoxus (species) D	Domesticated	Association Mapping	Naranjo S; Smith JD; Artieri CG ; et al. (2015) Dissecting the Genetic Basis of a Complex cis-Regulatory Adaptation.	GP00001313	ATG31 Q12421	Physiology	mutations within 1kb in promotor region	Saccharomyces cerevisiae baker's yeast - (species)	Saccharomyces paradoxus (species) D	CIS1	Saccharomyces paradoxus (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 Turuspekov Y; Mano Y; Honda I (2004) Identification and mapping of cleistogamy genes in barley.	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 Turuspekov Y; Mano Y; Honda I (2004) Identification and mapping of cleistogamy genes in barley.	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
CmWIP1	Flower sex determination (female vs. hermaphrodite)	Cis-regulatory, Insertion	Cucumis melo muskmelon - (species) D	Domesticated	Linkage Mapping	Martin A; Troadec C; Boualem A ; et al. (2009) A transposon-induced epigenetic change leads to sex determination in melon.	GP00000188	WIP1 Q8GXA4	Physiology	Promoter insertion of a Transcription Factor Binding Site allowing propagation of heritable methylation	Cucumis melo muskmelon - (species)	Cucumis melo muskmelon - (species) D	CmWIP1	Cucumis melo muskmelon - (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
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; 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
CS	Plant secondary metabolite (pungency)	Cis-regulatory, Deletion N	Capsicum annuum (species) D	Domesticated	Candidate Gene	Kim S; Park M; Yeom SI ; et al. (2014) Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum speci[...] 1 Additional References Stewart C; Kang BC; Liu K (2005) The Pun1 gene for pungency in pepper encodes a putative acyltransferase.	GP00001447	csy1 Q09UW1	Physiology	Large 2.5 kb deletion spanning 1.8 kb of the putative promoter and 0.7 kb of the first exon was observed in the C. annuum Bellpeppers N	Capsicum frutescens (species)	Capsicum annuum (species) D	CS	Capsicum annuum (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
CYCD5;1	Endoreduplication	Cis-regulatory, Unknown	Arabidopsis thaliana thale cress - (species)	Intraspecific	Linkage Mapping	Sterken R; Kiekens R; Boruc J ; et al. (2012) Combined linkage and association mapping reveals CYCD5;1 as a quantitative trait gene for endoredupl[...]	GP00000196	CYCD5-1 Q2V3B2	Physiology	unknown	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species)	CYCD5;1	Arabidopsis thaliana thale cress - (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
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
CYP321A8	Xenobiotic resistance (organophosphate; chlorpyrifos; pyrethroid; cypermethrin; deltamethrin)	Cis-regulatory, SNP	Spodoptera exigua beet armyworm - (species) D	Intraspecific	Candidate Gene	Hu B; Huang H; Hu S ; et al. (2021) Changes in both trans- and cis-regulatory elements mediate insecticide resistance in a lepidopteron [...]	GP00002394	CYP321A8 A0A286QUG5	Physiology	A > G at position -197bp in a cis-regulatory region, leading to increased expression of the gene	Spodoptera exigua beet armyworm - (species)	Spodoptera exigua beet armyworm - (species) D	CYP321A8	Spodoptera exigua beet armyworm - (species)	Published - Accepted by Curator
CYP392E8	Xenobiotic resistance	Cis-regulatory, Unknown	Tetranychus urticae two-spotted spider mite - (species) D	Intraspecific	Linkage Mapping	Fotoukkiaii SM; Wybouw N; Kurlovs AH ; et al. (2021) High-resolution genetic mapping reveals cis-regulatory and copy number variation in loci associated [...]	GP00002397		Physiology	increase in transcription of CYP392E8.	Tetranychus urticae two-spotted spider mite - (species)	Tetranychus urticae two-spotted spider mite - (species) D	CYP392E8	Tetranychus urticae two-spotted spider mite - (species)	Published - Accepted by Curator
CYP6AY1	Xenobiotic resistance (imidacloprid; buprofezin)	Cis-regulatory, Unknown	Nilaparvata lugens brown planthopper - (species) D	Intraspecific	Candidate Gene	Pang R; Li Y; Dong Y ; et al. (2014) Identification of promoter polymorphisms in the cytochrome P450 CYP6AY1 linked with insecticide resi[...]	GP00002399	CYP6AY1 A0A1L1VFS3	Physiology	CYP6AY1 is expressed at a higher level in a field-collected BPH strain that is highly resistant to both imidacloprid and buprofezin. Polymorphism in the promoter region associated with various levels of resistance.	Nilaparvata lugens brown planthopper - (species)	Nilaparvata lugens brown planthopper - (species) D	CYP6AY1	Nilaparvata lugens brown planthopper - (species)	Published - Accepted by Curator
CYP6BG1	Xenobiotic resistance (insecticide)	Cis-regulatory, Unknown	Plutella xylostella diamondback moth - (species) D	Intraspecific	Candidate Gene	Li X; Shan C; Li F ; et al. (2019) Transcription factor FTZ-F1 and cis-acting elements mediate expression of CYP6BG1 conferring resista[...] 1 Additional References Mallott M; Hamm S; Troczka BJ (2019) A flavin-dependent monooxgenase confers resistance to chlorantraniliprole in the diamondback moth, P[...]	GP00002064	CYP6BG1 A0A222NX20	Physiology	promoters tested in luciferase assays	Plutella xylostella diamondback moth - (species)	Plutella xylostella diamondback moth - (species) D	CYP6BG1	Plutella xylostella diamondback moth - (species)	Published - Accepted by Curator
CYP6CM1	Xenobiotic resistance (insecticide; imidacloprid)	Cis-regulatory, SNP	Bemisia tabaci (species) D	Intraspecific	Candidate Gene	Karunker I; Benting J; Lueke B ; et al. (2008) Over-expression of cytochrome P450 CYP6CM1 is associated with high resistance to imidacloprid in the[...]	GP00002608	A0A6C0PTH9	Physiology	three single-nucleotide polymorphic (SNP) markers in the intron region of CYP6CM1 that discriminate between the resistant and susceptible CYP6CM1 alleles	Bemisia tabaci (species)	Bemisia tabaci (species) D	CYP6CM1	Bemisia tabaci (species)	Published - Accepted by Curator
CYP6CY3	Xenobiotic resistance (insecticide; neonicotinoid; host plant)	Cis-regulatory, Insertion	Myzus persicae green peach aphid - (species) D	Intraspecific	Candidate Gene	Bass C; Zimmer CT; Riveron JM ; et al. (2013) Gene amplification and microsatellite polymorphism underlie a recent insect host shift. 1 Additional References Bass C; Zimmer CT; Riveron JM (2013) Gene amplification and microsatellite polymorphism underlie a recent insect host shift.	GP00001474	CYP6CY3 V5SQ25	Physiology	Expansion of a AC dinucleotide microsatellite (from 15 to 48 repeat units) in the promoter 198 bp upstream of the start codon that enhances gene expression	Myzus persicae green peach aphid - (species)	Myzus persicae green peach aphid - (species) D	CYP6CY3	Myzus persicae green peach aphid - (species)	Published - Accepted by Curator
CYP6D1	Xenobiotic resistance (insecticide)	Cis-regulatory, Insertion	Musca domestica house fly - (species) D	Intraspecific	Candidate Gene	Gao J; Scott JG (2006) Role of the transcriptional repressor mdGfi-1 in CYP6D1v1-mediated insecticide resistance in the hou[...]	GP00002118	CYP6D1 Q27698	Physiology	15 bp insertion which disrupts a putative mdGfi-1 binding site in the CYP6D1v1 promoter. mdGfi-1 is a negative regulator of transcription so this leads to increased expression of CYP6D1	Musca domestica house fly - (species)	Musca domestica house fly - (species) D	CYP6D1	Musca domestica house fly - (species)	Published - Accepted by Curator
CYP6ER1	Xenobiotic resistance (insecticide; imidacloprid)	Cis-regulatory, Unknown	Nilaparvata lugens brown planthopper - (species) D	Intraspecific	Candidate Gene	Zimmer CT; Garrood WT; Singh KS ; et al. (2018) Neofunctionalization of Duplicated P450 Genes Drives the Evolution of Insecticide Resistance in the [...]	GP00002475	cyp6er1 A0A2I8B6P1	Physiology	A significant (up to 9.5-fold) increase in expression driven by the promoter of CYP6ER1vA was observed in comparison to all other promoter variants. This suggests that cis-acting elements in the region upstream of CYP6ER1vA are responsible for the high expression of this variant in BPH populations across Southeast Asia.	Nilaparvata lugens brown planthopper - (species)	Nilaparvata lugens brown planthopper - (species) D	CYP6ER1	Nilaparvata lugens brown planthopper - (species)	Published - Accepted by Curator
CYP6FU1	Xenobiotic resistance (insecticide; deltamethrin)	Cis-regulatory, Unknown	Laodelphax striatellus small brown planthopper - (species) D	Intraspecific	Candidate Gene	Pu J; Sun H; Wang J ; et al. (2016) Multiple cis-acting elements involved in up-regulation of a cytochrome P450 gene conferring resistan[...]	GP00002117	CYP6FU1 A0A1S5R631	Physiology	Four cis-acting elements were identified whose influence on up-regulation was much more pronounced in combination than when present singly.	Laodelphax striatellus small brown planthopper - (species)	Laodelphax striatellus small brown planthopper - (species) D	CYP6FU1	Laodelphax striatellus small brown planthopper - (species)	Published - Accepted by Curator
cyp6g1	Xenobiotic resistance (insecticide)	4 Mutations: Insertion	Drosophila melanogaster fruit fly - (species) D	Intraspecific	Linkage Mapping	Chung H; Bogwitz MR; McCart C ; et al. (2007) Cis-regulatory elements in the Accord retrotransposon result in tissue-specific expression of the Dr[...]	GP00000207	Cyp6g1 Q9V674	Physiology	4 mutations	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species) D	cyp6g1	Drosophila melanogaster fruit fly - (species)	Published - Accepted by Curator
cyp6g1	Xenobiotic resistance (insecticide)	Cis-regulatory, Insertion	Drosophila simulans (species) D	Intraspecific	Candidate Gene	Schlenke TA; Begun DJ (2004) Strong selective sweep associated with a transposon insertion in Drosophila simulans.	GP00002019	Cyp6g1 Q9V674	Physiology	insertion of a Doc transposable element around 200 bp upstream of the putative transcription start site - mutation associated with increased expression of the gene	Drosophila simulans (species)	Drosophila simulans (species) D	cyp6g1	Drosophila simulans (species)	Published - Accepted by Curator
cyp6g1	Xenobiotic resistance (insecticide)	Cis-regulatory, Insertion	Drosophila simulans (species) D	Intraspecific	Candidate Gene	Wurmser F; Mary-Huard T; Daudin JJ ; et al. (2013) Variation of gene expression associated with colonisation of an anthropized environment: comparison [...]	GP00002020	Cyp6g1 Q9V674	Physiology	insertion of a Juan transposable element in the regulatory sequence. The insertion is almost fixed in the Rhône Valley but barely present in Mayotte - mutation associated with increased expression of the gene	Drosophila simulans (species)	Drosophila simulans (species) D	cyp6g1	Drosophila simulans (species)	Published - Accepted by Curator
CYP6P9 cluster (CYP6P9a and CYP6P9b)	Xenobiotic resistance (insecticide)	Cis-regulatory, Unknown	Anopheles funestus African malaria mosquito - (species) D	Intraspecific	Candidate Gene	Riveron JM; Irving H; Ndula M ; et al. (2013) Directionally selected cytochrome P450 alleles are driving the spread of pyrethroid resistance in th[...] 1 Additional References Mugenzi LMJ; Menze BD; Tchouakui M (2019) Cis-regulatory CYP6P9b P450 variants associated with loss of insecticide-treated bed net efficacy ag[...]	GP00000208	CYP2C9 P11712	Physiology	Cis-regulatory variation in CYP6P9b gene	Anopheles funestus African malaria mosquito - (species)	Anopheles funestus African malaria mosquito - (species) D	CYP6P9 cluster (CYP6P9a and CYP6P9b)	Anopheles funestus African malaria mosquito - (species)	Published - Accepted by Curator
CYP6P9; CYP6P4 cluster	Xenobiotic resistance (insecticide)	5 Mutations:	Anopheles funestus African malaria mosquito - (species) D	Intraspecific	Linkage Mapping	Wondji CS; Irving H; Morgan J ; et al. (2009) Two duplicated P450 genes are associated with pyrethroid resistance in Anopheles funestus, a major m[...] 2 Additional References Weedall GD; Mugenzi LMJ; Menze BD (2019) A cytochrome P450 allele confers pyrethroid resistance on a major African malaria vector, reducing i[...] Wondji CS; Hearn J; Irving H (2022) RNAseq-based gene expression profiling of the Anopheles funestus pyrethroid-resistant strain FUMOZ h[...]	GP00000209	Q2YH43	Physiology	5 mutations	Anopheles funestus African malaria mosquito - (species)	Anopheles funestus African malaria mosquito - (species) D	CYP6P9; CYP6P4 cluster	Anopheles funestus African malaria mosquito - (species)	Published - Accepted by Curator
CYP81F2	Glucosinolate content Herbivore resistance (aphids)	Cis-regulatory, Unknown	Arabidopsis thaliana thale cress - (species)	Intraspecific	Linkage Mapping	Pfalz M; Vogel H; Kroymann J (2009) The gene controlling the indole glucosinolate modifier1 quantitative trait locus alters indole gluco[...]	GP00000212	CYP81F2 Q9LVD6	Physiology Physiology	unknown	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species)	CYP81F2	Arabidopsis thaliana thale cress - (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 McKechnie SW; Blacket MJ; Song SV (2010) A clinally varying promoter polymorphism associated with adaptive variation in wing size in Drosophi[...]	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
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
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 Genissel A; Pastinen T; Dowell A (2004) No evidence for an association between common nonsynonymous polymorphisms in delta and bristle numbe[...]	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 Genissel A; Pastinen T; Dowell A (2004) No evidence for an association between common nonsynonymous polymorphisms in delta and bristle numbe[...]	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
desatF	Pheromone production	Cis-regulatory, Unknown	Drosophila melanogaster fruit fly - (species)	Interspecific	Candidate Gene	Legendre A; Miao XX; Da Lage JL ; et al. (2008) Evolution of a desaturase involved in female pheromonal cuticular hydrocarbon biosynthesis and court[...] 1 Additional References Shirangi TR; Dufour HD; Williams TM (2009) Rapid evolution of sex pheromone-producing enzyme expression in Drosophila.	GP00000219	desatF A7DZ97	Physiology	Enrichment/gain of DSX binding sites	Drosophila (subgenus)	Drosophila melanogaster fruit fly - (species)	desatF	Drosophila melanogaster fruit fly - (species)	Published - Accepted by Curator
desatF	Pheromone production	Cis-regulatory, Deletion	Drosophila (subgenus) D	Interspecific	Candidate Gene	Shirangi TR; Dufour HD; Williams TM ; et al. (2009) Rapid evolution of sex pheromone-producing enzyme expression in Drosophila.	GP00000220	desatF A7DZ97	Physiology	Inactivation of DSX-binding site	Drosophila takahashii (species)	Drosophila (subgenus) D	desatF	Drosophila (subgenus)	Published - Accepted by Curator
desaturase 2 (desat2)	Pheromone production	Cis-regulatory, Deletion	Drosophila melanogaster fruit fly - (species) D	Intraspecific	Linkage Mapping	Takahashi A; Tsaur SC; Coyne JA ; et al. (2001) The nucleotide changes governing cuticular hydrocarbon variation and their evolution in Drosophila m[...] 1 Additional References Dallerac R; Labeur C; Jallon JM (2000) A delta 9 desaturase gene with a different substrate specificity is responsible for the cuticular di[...]	GP00000221	Desat2 Q9VG68	Physiology	16bp deletion about 150bp upstream of transcription start site	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species) D	desaturase 2 (desat2)	Drosophila melanogaster fruit fly - (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
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
DOG1 (DELAY OF GERMINATION 1)	Seed dormancy	Cis-regulatory, Unknown	Arabidopsis thaliana thale cress - (species)	Intraspecific	Linkage Mapping	Bentsink L; Jowett J; Hanhart CJ ; et al. (2006) Cloning of DOG1, a quantitative trait locus controlling seed dormancy in Arabidopsis. 3 Additional References Atwell S; Huang YS; Vilhjálmsson BJ (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Horton MW; Hancock AM; Huang YS (2012) Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegM[...] Nakabayashi K; Bartsch M; Ding J (2015) Seed Dormancy in Arabidopsis Requires Self-Binding Ability of DOG1 Protein and the Presence of Multi[...]	GP00000231	DOG1 A0SVK0	Physiology	Not identified (possibly polyallelic as each cross to the Ler accession showed different DOG1 effects)	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species)	DOG1 (DELAY OF GERMINATION 1)	Arabidopsis thaliana thale cress - (species)	Published - Accepted by Curator
DOG1 (DELAY OF GERMINATION 1)	Seed dormancy	Cis-regulatory, SNP	Arabidopsis thaliana thale cress - (species)	Intraspecific	Association Mapping	Kerdaffrec E; Filiault DL; Korte A ; et al. (2016) Multiple alleles at a single locus control seed dormancy in Swedish Arabidopsis.	GP00001397	DOG1 A0SVK0	Physiology	At least 3 haplotypes defined by 4 SNPs in a putative regulatory region of DOG-1.	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species)	DOG1 (DELAY OF GERMINATION 1)	Arabidopsis thaliana thale cress - (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
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 (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
Drip	Fertility	Cis-regulatory, Unknown	Drosophila melanogaster fruit fly - (species)	Intraspecific	Linkage Mapping	Bergland AO; Chae HS; Kim YJ ; et al. (2012) Fine-scale mapping of natural variation in fly fecundity identifies neuronal domain of expression an[...]	GP00000237	Drip Q9V5Z7	Physiology	unknown	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species)	Drip	Drosophila melanogaster fruit fly - (species)	Published - Accepted by Curator
Duffy	Pathogen resistance (Plasmodium; malaria parasite) (malaria)	Cis-regulatory, SNP	Homo sapiens human - (species)	Intraspecific	Candidate Gene	Tournamille C; Colin Y; Cartron JP ; et al. (1995) Disruption of a GATA motif in the Duffy gene promoter abolishes erythroid gene expression in Duffy-n[...]	GP00000240	ACKR1 Q16570	Physiology	T to C substitution in 5' region at pos -46	Homo sapiens human - (species)	Homo sapiens human - (species)	Duffy	Homo sapiens human - (species)	Published - Accepted by Curator
E2F1	Silk yield	Cis-regulatory, Unknown	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[...]	GP00002400	E2f1 Q27368	Physiology	There are one deletion and three insertions in the cis-regulatory region and introns of the E2F1 gene of the improved strain. Higher expression in the improves strain. CRISPR-cas9 mediated knockout of BmE2F1 reduces the number of silk gland cells by 7.68% and silk yield by 22%.	Bombyx mori domestic silkworm - (species)	Bombyx mori domestic silkworm - (species) D	E2F1	Bombyx mori domestic silkworm - (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 Lamb Abigail M; Wang Zinan; Simmer Patricia (2020 ) ebony affects pigmentation divergence and cuticular hydrocarbons in Drosophila americana and D. nova[...]	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 Endler L; Gibert JM; Nolte V (2018) Pleiotropic effects of regulatory variation in tan result in correlation of two pigmentation traits [...]	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 (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
Ecdysone oxidase	Developmental time	Cis-regulatory, Insertion	Bombyx mori domestic silkworm - (species) D	Domesticated	Candidate Gene	Sun W; Shen YH; Han MJ ; et al. (2014) An adaptive transposable element insertion in the regulatory region of the EO gene in the domesticat[...] 1 Additional References Xu X; Wang M; Wang Y (2013) Green cocoons in silkworm Bombyx mori resulting from the quercetin 5-O-glucosyltransferase of UGT86,[...]	GP00001102	Eo Q9VY01	Physiology	insertion of a 512bp fragment of a Taguchi transposable element 462 bp upstream of the transcription start site of the EO gene. The TE insertion enhances the transcription of flanking genes after 20-hydroxyecdysone treatment.	Bombyx mori domestic silkworm - (species)	Bombyx mori domestic silkworm - (species) D	Ecdysone oxidase	Bombyx mori domestic silkworm - (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 Jones FC; Grabherr MG; Chan YF (2012) The genomic basis of adaptive evolution in threespine sticklebacks. O'Brown NM; Summers BR; Jones FC (2015) A recurrent regulatory change underlying altered expression and Wnt response of the stickleback armo[...]	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
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
EGNL1	High-altitude adaptation Hypoxia response	Cis-regulatory, Unknown	Anas cyanoptera cinnamon teal - (species) D	Intraspecific	Candidate Gene	Graham AM; McCracken KG (2019) Convergent evolution on the hypoxia-inducible factor (HIF) pathway genes EGLN1 and EPAS1 in high-alt[...]	GP00002134	EGLN1 Q9GZT9	Physiology Physiology	probably cis-regulatory because no nonsynonymous mutations in the coding exon with high Fst	Anas cyanoptera cinnamon teal - (species)	Anas cyanoptera cinnamon teal - (species) D	EGNL1	Anas cyanoptera cinnamon teal - (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
Epithiospecifier Modifier1 (ESM1)	Nitrile content	Cis-regulatory, Unknown	Arabidopsis thaliana thale cress - (species)	Intraspecific	Linkage Mapping	Zhang Z; Ober JA; Kliebenstein DJ (2006) The gene controlling the quantitative trait locus EPITHIOSPECIFIER MODIFIER1 alters glucosinolate hy[...]	GP00000277	ESM1 Q9LJG3	Physiology	Not identified	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species)	Epithiospecifier Modifier1 (ESM1)	Arabidopsis thaliana thale cress - (species)	Published - Accepted by Curator
Epithiospecifier protein (ESP)	Plant secondary metabolite (glucosinolate) Herbivore resistance	Cis-regulatory, Unknown	Arabidopsis thaliana thale cress - (species)	Intraspecific	Linkage Mapping	Lambrix V; Reichelt M; Mitchell-Olds T ; et al. (2001) The Arabidopsis epithiospecifier protein promotes the hydrolysis of glucosinolates to nitriles and i[...]	GP00000278	ESP Q8RY71	Physiology Physiology	Not identified	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species)	Epithiospecifier protein (ESP)	Arabidopsis thaliana thale cress - (species)	Published - Accepted by Curator
ESR1	Aggression behavior	Cis-regulatory, Unknown	Zonotrichia albicollis white-throated sparrow - (species) D	Intraspecific	Linkage Mapping	Merritt JR; Grogan KE; Zinzow-Kramer WM ; et al. (2020) A supergene-linked estrogen receptor drives alternative phenotypes in a polymorphic songbird.	GP00002440	Esr1 P19785	Behavior	Increase in expression of the gene in the white-striped morph. Differential allelic expression in heterozygotes.	Zonotrichia albicollis white-throated sparrow - (species)	Zonotrichia albicollis white-throated sparrow - (species) D	ESR1	Zonotrichia albicollis white-throated sparrow - (species)	Published - Accepted by Curator
eve	Developmental time	Cis-regulatory, Deletion	Drosophila melanogaster fruit fly - (species) D	Intraspecific	Candidate Gene	Palsson A; Wesolowska N; Reynisdóttir S ; et al. (2014) Naturally occurring deletions of hunchback binding sites in the even-skipped stripe 3+7 enhancer.	GP00001986	eve P06602	Physiology	72bp deletion that removes one of the hb protein-binding sites in the stripe 3+7 enhancer of eve. The deletion also removes half of a putative slp1 protein-binding site.	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species) D	eve	Drosophila melanogaster fruit fly - (species)	Published - Accepted by Curator
exp-1	Aggregation behavior	Cis-regulatory, Unknown	Caenorhabditis elegans (species)	Intraspecific	Linkage Mapping	Bendesky A; Pitts J; Rockman MV ; et al. (2012) Long-range regulatory polymorphisms affecting a GABA receptor constitute a quantitative trait locus [...]	GP00000300	exp-1 G5ECJ0	Behavior	unidentified; 6.2kb wide genetic interval 3' of the exp-1 gene	Caenorhabditis elegans (species)	Caenorhabditis elegans (species)	exp-1	Caenorhabditis elegans (species)	Published - Accepted by Curator
FaO-methyl-transferase (FaOMT)	Fragrance (flavor)	Cis-regulatory, Unknown	Fragaria x ananassa strawberry - (species)	Domesticated	Linkage Mapping	Zorrilla-Fontanesi Y; Rambla JL; Cabeza A ; et al. (2012) Genetic analysis of strawberry fruit aroma and identification of O-methyltransferase FaOMT as the lo[...]	GP00000303	omt1 Q9M602	Physiology	Promoter variation _ there are several single nucleotide polymorphisms (SNPs); insertion/deletions (indels); and rearrangements in the promoter	Fragaria x ananassa strawberry - (species)	Fragaria x ananassa strawberry - (species)	FaO-methyl-transferase (FaOMT)	Fragaria x ananassa strawberry - (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
fatty acid synthase	Dessication tolerance Pheromone production (mbCHC)	Cis-regulatory, Unknown	Drosophila birchii (species)	Interspecific	Candidate Gene	Chung H; Loehlin DW; Dufour HD ; et al. (2014) A single gene affects both ecological divergence and mate choice in Drosophila.	GP00002063	FASN3 Q7PLB8	Physiology Physiology	No expression of the gene in D. birchii. The coding region of the D. birchii gene is intact. Cis-regulatory region tested in reporter assays in D. melanogaster - exact causing mutation(s) unknown. RNAi against mFAS/CG17354 in D. serrata recapitylates the D. birchii phenotype.	Drosophila serrata (species)	Drosophila birchii (species)	fatty acid synthase	Drosophila birchii (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
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
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
Fkh	Silk yield	Cis-regulatory, Unknown	Bombyx mori domestic silkworm - (species) D	Domesticated	Association Mapping	Xia Q; Guo Y; Zhang Z ; et al. (2009) Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx).	GP00002411	fkh P14734	Physiology	Increased expression in high yield strains. The Fkh gene encodes a transcription factor that activates glue genes together with Sage in salivary glands of Drosophila melanogaster.	Bombyx mori domestic silkworm - (species)	Bombyx mori domestic silkworm - (species) D	Fkh	Bombyx mori domestic silkworm - (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';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 (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
FLC (Flowering Locus C)	Flowering time	2 Mutations: Cis-regulatory SNP	Arabidopsis thaliana thale cress - (species)	Intraspecific	Linkage Mapping	Coustham V; Li P; Strange A ; et al. (2012) Quantitative modulation of polycomb silencing underlies natural variation in vernalization. 1 Additional References Ågren J; Oakley CG; Lundemo S (2017) Adaptive divergence in flowering time among natural populations of Arabidopsis thaliana: Estimates o[...]	GP00000331	FLC Q9S7Q7	Physiology	2 mutations	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species)	FLC (Flowering Locus C)	Arabidopsis thaliana thale cress - (species)	Published - Accepted by Curator
FLC (Flowering Locus C)	Flowering time	Cis-regulatory, Insertion	Arabidopsis thaliana thale cress - (species) D	Intraspecific	Candidate Gene	Michaels SD; He Y; Scortecci KC ; et al. (2003) Attenuation of FLOWERING LOCUS C activity as a mechanism for the evolution of summer-annual flowerin[...] 3 Additional References Gazzani S; Gendall AR; Lister C (2003) Analysis of the molecular basis of flowering time variation in Arabidopsis accessions. Ågren J; Oakley CG; Lundemo S (2017) Adaptive divergence in flowering time among natural populations of Arabidopsis thaliana: Estimates o[...] Liu J; He Y; Amasino R (2004) siRNAs targeting an intronic transposon in the regulation of natural flowering behavior in Arabidops[...]	GP00000332	FLC Q9S7Q7	Physiology	TE insertion in intron 1; a region required for normal FLC regulation. The transposable element renders FLC-Ler subject to repressive chromatin modifications mediated by short interfering RNAs generated from homologous transposable elements in the genome.	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species) D	FLC (Flowering Locus C)	Arabidopsis thaliana thale cress - (species)	Published - Accepted by Curator
FLC (Flowering Locus C)	Flowering time	Cis-regulatory, Unknown	Arabidopsis thaliana thale cress - (species)	Intraspecific	Candidate Gene	Michaels SD; He Y; Scortecci KC ; et al. (2003) Attenuation of FLOWERING LOCUS C activity as a mechanism for the evolution of summer-annual flowerin[...] 1 Additional References Ågren J; Oakley CG; Lundemo S (2017) Adaptive divergence in flowering time among natural populations of Arabidopsis thaliana: Estimates o[...]	GP00000333	FLC Q9S7Q7	Physiology	Not identified	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species)	FLC (Flowering Locus C)	Arabidopsis thaliana thale cress - (species)	Published - Accepted by Curator
FLC (Flowering Locus C)	Flowering time	Cis-regulatory, Unknown	Arabidopsis thaliana thale cress - (species)	Intraspecific	Linkage Mapping	Werner JD; Borevitz JO; Uhlenhaut NH ; et al. (2005) FRIGIDA-independent variation in flowering time of natural Arabidopsis thaliana accessions. 1 Additional References Ågren J; Oakley CG; Lundemo S (2017) Adaptive divergence in flowering time among natural populations of Arabidopsis thaliana: Estimates o[...]	GP00000334	FLC Q9S7Q7	Physiology	unknown	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species)	FLC (Flowering Locus C)	Arabidopsis thaliana thale cress - (species)	Published - Accepted by Curator
FLC (Flowering Locus C)	Flowering time	Cis-regulatory, Deletion	Arabidopsis thaliana thale cress - (species) D	Intraspecific	Linkage Mapping	Sánchez-Bermejo E; Méndez-Vigo B; Picó FX ; et al. (2012) Novel natural alleles at FLC and LVR loci account for enhanced vernalization responses in Arabidopsi[...] 1 Additional References Ågren J; Oakley CG; Lundemo S (2017) Adaptive divergence in flowering time among natural populations of Arabidopsis thaliana: Estimates o[...]	GP00000336	FLC Q9S7Q7	Physiology	50bp deletion in 5'UTR	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species) D	FLC (Flowering Locus C)	Arabidopsis thaliana thale cress - (species)	Published - Accepted by Curator
FLC-2	Flowering time	Cis-regulatory, Unknown	Brassica rapa field mustard - (species)	Domesticated	Linkage Mapping	Zhao J; Kulkarni V; Liu N ; et al. (2010) BrFLC2 (FLOWERING LOCUS C) as a candidate gene for a vernalization response QTL in Brassica rapa.	GP00000340	FLC Q9S7Q7	Physiology	unknown	Brassica rapa field mustard - (species)	Brassica rapa field mustard - (species)	FLC-2	Brassica rapa field mustard - (species)	Published - Accepted by Curator
Flowering locus T (=HvFT=VRN3)	Flowering time	Cis-regulatory, Unknown	Hordeum vulgare (species)	Domesticated	Linkage Mapping	Yan L; Fu D; Li C ; et al. (2006) The wheat and barley vernalization gene VRN3 is an orthologue of FT.	GP00000343	FT Q9SXZ2	Physiology	Regulatory variation in first intron	Hordeum vulgare (species)	Hordeum vulgare (species)	Flowering locus T (=HvFT=VRN3)	Hordeum vulgare (species)	Published - Accepted by Curator
Flowering locus T (=TaFT=VRN3)	Flowering time	Cis-regulatory, Insertion	Triticum aestivum bread wheat - (species) D	Domesticated	Linkage Mapping	Yan L; Fu D; Li C ; et al. (2006) The wheat and barley vernalization gene VRN3 is an orthologue of FT.	GP00000344	FT Q9SXZ2	Physiology	Retrotranspostion in promoter region	Triticum aestivum bread wheat - (species)	Triticum aestivum bread wheat - (species) D	Flowering locus T (=TaFT=VRN3)	Triticum aestivum bread wheat - (species)	Published - Accepted by Curator
Flowering locus T (FT)	Flowering time	Cis-regulatory, Unknown	Arabidopsis thaliana thale cress - (species)	Domesticated	Linkage Mapping	Kojima S; Takahashi Y; Kobayashi Y ; et al. (2002) Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1[...] 1 Additional References Schwartz C; Balasubramanian S; Warthmann N (2009) Cis-regulatory changes at FLOWERING LOCUS T mediate natural variation in flowering responses of Arab[...]	GP00000345	FT Q9SXZ2	Physiology	Promoter region	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species)	Flowering locus T (FT)	Arabidopsis thaliana thale cress - (species)	Published - Accepted by Curator
Flowering locus T (LpFT3)	Flowering time	Cis-regulatory, Unknown	Lolium perenne (species)	Domesticated	Candidate Gene	Skøt L; Sanderson R; Thomas A ; et al. (2011) Allelic variation in the perennial ryegrass FLOWERING LOCUS T gene is associated with changes in flo[...]	GP00000347	FT Q9SXZ2	Physiology	unknown	Lolium perenne (species)	Lolium perenne (species)	Flowering locus T (LpFT3)	Lolium perenne (species)	Published - Accepted by Curator
FMO2	Xenobiotic resistance (insecticide)	Cis-regulatory, Insertion	Plutella xylostella diamondback moth - (species) D	Intraspecific	Candidate Gene	Mallott M; Hamm S; Troczka BJ ; et al. (2019) A flavin-dependent monooxgenase confers resistance to chlorantraniliprole in the diamondback moth, P[...]	GP00002065	FMO2 Q99518	Physiology	a putatative transposon (233bp) insertion in the HAW promoter sequence just 140 bp upstream of the start codon of PxFMO2 which was absent in the ROTH promoter, the boundaries of all copies of this element were found to be defined by 34 bp imperfect terminal inverted repeats, increase the expression of the gene PxFMO2 downstream	Plutella xylostella diamondback moth - (species)	Plutella xylostella diamondback moth - (species) D	FMO2	Plutella xylostella diamondback moth - (species)	Published - Accepted by Curator
foraging	Food-search behavior	Cis-regulatory, SNP	Drosophila melanogaster fruit fly - (species)	Intraspecific	Linkage Mapping	Osborne KA; Robichon A; Burgess E ; et al. (1997) Natural behavior polymorphism due to a cGMP-dependent protein kinase of Drosophila. 2 Additional References Mery F; Belay AT; So AK (2007) Natural polymorphism affecting learning and memory in Drosophila. Anreiter I; Kramer JM; Sokolowski MB (2017) Epigenetic mechanisms modulate differences in Drosophila foraging behavior.	GP00000350	for Q03043	Behavior	The fors (sitter) and forR (rover) alleles differ in a SNP that lies within a predicted Mad protein-binding site in a region upstream of the pr4 transcription start site. The SNP is a C in fors and an A in forR (the latter is predicted to reduce Mad protein binding).	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species)	foraging	Drosophila melanogaster fruit fly - (species)	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 Kocer A; Pinheiro I; Pannetier M (2008) R-spondin1 and FOXL2 act into two distinct cellular types during goat ovarian differentiation. Boulanger L; Pannetier M; Gall L (2014) FOXL2 is a female sex-determining gene in the goat.	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
Frigida (FRI)	Flowering time Water use efficiency	Cis-regulatory, Deletion	Arabidopsis thaliana thale cress - (species) D	Intraspecific	Linkage Mapping	Lovell JT; Juenger TE; Michaels SD ; et al. (2013) Pleiotropy of FRIGIDA enhances the potential for multivariate adaptation.	GP00000375	FRI P0DH90	Physiology Physiology	376 bp deletion within the promoter of the TSU-1 FRI allele	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species) D	Frigida (FRI)	Arabidopsis thaliana thale cress - (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
FRM2	Xenobiotic resistance (citrinin)	Cis-regulatory, Unknown	Saccharomyces paradoxus (species) D	Domesticated	Association Mapping	Naranjo S; Smith JD; Artieri CG ; et al. (2015) Dissecting the Genetic Basis of a Complex cis-Regulatory Adaptation.	GP00001311	FRM2 P37261	Physiology	mutations within 1kb in promotor region	Saccharomyces cerevisiae baker's yeast - (species)	Saccharomyces paradoxus (species) D	FRM2	Saccharomyces paradoxus (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 Kim KW; Jackson BC; Zhang H (2019) Genetics and evidence for balancing selection of a sex-linked colour polymorphism in a songbird.	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
FTO	Body size (weight; variance)	Cis-regulatory, SNP	Homo sapiens human - (species)	Intraspecific	Association Mapping	Frayling TM; Timpson NJ; Weedon MN ; et al. (2007) A common variant in the FTO gene is associated with body mass index and predisposes to childhood and[...] 4 Additional References Dina C; Meyre D; Gallina S (2007) Variation in FTO contributes to childhood obesity and severe adult obesity. Scuteri A; Sanna S; Chen WM (2007) Genome-wide association scan shows genetic variants in the FTO gene are associated with obesity-rela[...] Yang J; Loos RJ; Powell JE (2012) FTO genotype is associated with phenotypic variability of body mass index. Claussnitzer M; Dankel SN; Kim KH (2015) FTO Obesity Variant Circuitry and Adipocyte Browning in Humans.	GP00000378	FTO Q9C0B1	Morphology; Physiology	rs1421085 T-to-C single-nucleotide variant disrupts a conserved motif for the ARID5B repressor	Homo sapiens human - (species)	Homo sapiens human - (species)	FTO	Homo sapiens human - (species)	Published - Accepted by Curator
FUMARASE 2	Plant metabolism (fumarate/malate ratio) Plant growth (bio-mass production)	Cis-regulatory, Indel	Arabidopsis thaliana thale cress - (species)	Intraspecific	Linkage Mapping	Riewe D; Jeon HJ; Lisec J ; et al. (2016) A naturally occurring promoter polymorphism of the Arabidopsis FUM2 gene causes expression variation[...] 1 Additional References Lisec J; Meyer RC; Steinfath M (2008) Identification of metabolic and biomass QTL in Arabidopsis thaliana in a parallel analysis of RIL an[...]	GP00001286	FUM2 Q9FI53	Physiology Physiology	2068 bp in promotor region @position -395. AND 3833bp in promotor region @position -1107	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species)	FUMARASE 2	Arabidopsis thaliana thale cress - (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 Nesbitt TC; Tanksley SD (2002) Comparative sequencing in the genus Lycopersicon. Implications for the evolution of fruit size in th[...]	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
GAL1	Carbohydrate metabolism (galactose)	Cis-regulatory, Complex Change	Saccharomyces cerevisiae baker's yeast - (species)	Intergeneric or Higher	Candidate Gene	Hittinger CT; Carroll SB (2007) Gene duplication and the adaptive evolution of a classic genetic switch.	GP00000385	GAL1 P09608	Physiology	Helical phasing of GAL4 elements in promoter region following duplication	Kluyveromyces lactis (species)	Saccharomyces cerevisiae baker's yeast - (species)	GAL1	Saccharomyces cerevisiae baker's yeast - (species)	Published - Accepted by Curator
GAL1	Carbohydrate metabolism	Cis-regulatory, Unknown	Saccharomyces cerevisiae baker's yeast - (species) D	Interspecific	Candidate Gene	Roop JI; Chang KC; Brem RB (2016) Polygenic evolution of a sugar specialization trade-off in yeast.	GP00001425	GAL1 P04385	Physiology	unknown	Saccharomyces bayanus (species)	Saccharomyces cerevisiae baker's yeast - (species) D	GAL1	Saccharomyces cerevisiae baker's yeast - (species)	Published - Accepted by Curator
GAL10	Carbohydrate metabolism	Cis-regulatory, Unknown	Saccharomyces cerevisiae baker's yeast - (species) D	Interspecific	Candidate Gene	Roop JI; Chang KC; Brem RB (2016) Polygenic evolution of a sugar specialization trade-off in yeast.	GP00001428	GAL10 P04397	Physiology	unknown	Saccharomyces bayanus (species)	Saccharomyces cerevisiae baker's yeast - (species) D	GAL10	Saccharomyces cerevisiae baker's yeast - (species)	Published - Accepted by Curator
GAL3	Carbohydrate metabolism	Cis-regulatory, Unknown	Saccharomyces cerevisiae baker's yeast - (species) D	Interspecific	Candidate Gene	Roop JI; Chang KC; Brem RB (2016) Polygenic evolution of a sugar specialization trade-off in yeast.	GP00001426	GAL3 P13045	Physiology	unknown	Saccharomyces bayanus (species)	Saccharomyces cerevisiae baker's yeast - (species) D	GAL3	Saccharomyces cerevisiae baker's yeast - (species)	Published - Accepted by Curator
GAL4	Carbohydrate metabolism	Cis-regulatory, Unknown	Saccharomyces cerevisiae baker's yeast - (species) D	Interspecific	Candidate Gene	Roop JI; Chang KC; Brem RB (2016) Polygenic evolution of a sugar specialization trade-off in yeast.	GP00001427	GAL4 P04386	Physiology	unknown	Saccharomyces bayanus (species)	Saccharomyces cerevisiae baker's yeast - (species) D	GAL4	Saccharomyces cerevisiae baker's yeast - (species)	Published - Accepted by Curator
GATA-binding protein 2 (GATA2)	Hematopoiesis (blood basophil count)	Cis-regulatory, SNP	Homo sapiens human - (species)	Intraspecific	Association Mapping	Guo MH; Nandakumar SK; Ulirsch JC ; et al. (2017) Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mech[...]	GP00001610	GATA2 P23769	Physiology	G>A at the associated SNP. Another variant (rs6782812) in a pleiotropic myeloid enhancer near GATA2 reduced enhancer activity by 69%	Homo sapiens human - (species)	Homo sapiens human - (species)	GATA-binding protein 2 (GATA2)	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
glycerol-3-phosphate dehydrogenase (Gpdh)	Enzymatic activity	Cis-regulatory, Unknown	Drosophila melanogaster fruit fly - (species) D	Intraspecific	Linkage Mapping	Bewley Glenn C (1981 ) Genetic control of the developmental program of L‐glycerol‐3‐phosphate dehydrogenase isozymes in Dro[...]	GP00001992	Gpdh P13706	Physiology	Exact causal mutation(s) unknown.	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species) D	glycerol-3-phosphate dehydrogenase (Gpdh)	Drosophila melanogaster fruit fly - (species)	Published - Accepted by Curator
glycerol-3-phosphate dehydrogenase (Gpdh)	Enzymatic activity	Cis-regulatory, Insertion	Drosophila melanogaster fruit fly - (species) D	Intraspecific	Candidate Gene	Wilanowski TM; Gibson JB; Symonds JE (1995) Retrotransposon insertion induces an isozyme of sn-glycerol-3-phosphate dehydrogenase in Drosophila [...]	GP00001998	Gpdh P13706	Physiology	insertion of a 8kb blood retrotransposon in the 3' region of the Gpdh gene 66bp downstream of the stop codon. This mutation induces a GPDH isozyme-GPDH-4-and alters the pattern of expression of the three normal isozymes-GPDH-1 to GPDH-3.	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species) D	glycerol-3-phosphate dehydrogenase (Gpdh)	Drosophila melanogaster fruit fly - (species)	Published - Accepted by Curator
Glypican-3 (Gpc3)	Body size (weight)	Cis-regulatory, Unknown	Mus musculus house mouse - (species)	Domesticated	Linkage Mapping	Oliver F; Christians JK; Liu X ; et al. (2005) Regulatory variation at glypican-3 underlies a major growth QTL in mice.	GP00000407	Gpc3 Q8CFZ4	Physiology	unknown; possible 3'UTR variation	Mus musculus house mouse - (species)	Mus musculus house mouse - (species)	Glypican-3 (Gpc3)	Mus musculus house mouse - (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 (weight)	Cis-regulatory, Unknown	Mus musculus house mouse - (species)	Domesticated	Association Mapping	Chan YF; Jones FC; McConnell E ; et al. (2012) Parallel selection mapping using artificially selected mice reveals body weight control loci.	GP00000411	ADGRD1 Q6QNK2	Physiology	unknown	Mus musculus house mouse - (species)	Mus musculus house mouse - (species)	GPR133	Mus musculus house mouse - (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
GPX2	Xenobiotic resistance (citrinin)	Cis-regulatory, Unknown	Saccharomyces paradoxus (species) D	Interspecific	Association Mapping	Naranjo S; Smith JD; Artieri CG ; et al. (2015) Dissecting the Genetic Basis of a Complex cis-Regulatory Adaptation.	GP00001310	GPX2 P38143	Physiology	mutations within 1kb in promotor region	Saccharomyces cerevisiae baker's yeast - (species)	Saccharomyces paradoxus (species) D	GPX2	Saccharomyces paradoxus (species)	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
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
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
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 Johnsson M; Rubin CJ; Höglund A (2014) The role of pleiotropy and linkage in genes affecting a sexual ornament and bone allocation in the c[...]	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
HBS1L-MYB	Hematopoiesis (mean blood corpuscular hemoglobin)	Cis-regulatory, SNP	Homo sapiens human - (species)	Intraspecific	Association Mapping	Guo MH; Nandakumar SK; Ulirsch JC ; et al. (2017) Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mech[...]	GP00001607	HBS1L Q9Y450	Physiology	T>C at the associated SNP. Variants in MEP/erythroid-specific elements are putative functional variants	Homo sapiens human - (species)	Homo sapiens human - (species)	HBS1L-MYB	Homo sapiens human - (species)	Published - Accepted by Curator
HBS1L-MYB	Hematopoiesis (mean blood corpuscular hemoglobin)	Cis-regulatory, SNP	Homo sapiens human - (species)	Intraspecific	Association Mapping	Guo MH; Nandakumar SK; Ulirsch JC ; et al. (2017) Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mech[...]	GP00001608	HBS1L Q9Y450	Physiology	A>G at the associated SNP. Variants in MEP/erythroid-specific elements are putative functional variants	Homo sapiens human - (species)	Homo sapiens human - (species)	HBS1L-MYB	Homo sapiens human - (species)	Published - Accepted by Curator
HBS1L-MYB	Hematopoiesis (red blood cell count)	Cis-regulatory, SNP	Homo sapiens human - (species)	Intraspecific	Association Mapping	Guo MH; Nandakumar SK; Ulirsch JC ; et al. (2017) Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mech[...]	GP00001609	HBS1L Q9Y450	Physiology	C>T at the associated SNP. Variants in MEP/erythroid-specific elements are putative functional variants	Homo sapiens human - (species)	Homo sapiens human - (species)	HBS1L-MYB	Homo sapiens human - (species)	Published - Accepted by Curator
HEADING DATE 1	Flowering time (latitudinal adaptation)	Cis-regulatory, Insertion N	Oryza sativa Japonica Group Japanese rice - (no rank) D	Domesticated	Candidate Gene	Goretti D; Martignago D; Landini M ; et al. (2017) Transcriptional and Post-transcriptional Mechanisms Limit Heading Date 1 (Hd1) Function to Adapt Ric[...]	GP00001674	HD1 Q9FDX8	Physiology	Hd1(EH) allele with a 4.4 kb mobile element inserted at position -166pb that suppressed gene transcription N	Oryza sativa rice - (species)	Oryza sativa Japonica Group Japanese rice - (no rank) D	HEADING DATE 1	Oryza sativa Japonica Group Japanese rice - (no rank)	Published - Accepted by Curator
heavy metal atpase4 (HMA4)	Metal tolerance	Cis-regulatory, Unknown	Arabidopsis halleri (species)	Interspecific	Linkage Mapping	Hanikenne M; Talke IN; Haydon MJ ; et al. (2008) Evolution of metal hyperaccumulation required cis-regulatory changes and triplication of HMA4. 1 Additional References Hanikenne M; Kroymann J; Trampczynska A (2013) Hard selective sweep and ectopic gene conversion in a gene cluster affording environmental adaptatio[...]	GP00000449	HMA4 O64474	Physiology	unknown	Arabidopsis thaliana thale cress - (species)	Arabidopsis halleri (species)	heavy metal atpase4 (HMA4)	Arabidopsis halleri (species)	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
HLA-DQA1	Histocompatibility	Cis-regulatory, Unknown	Papio baboons - (genus)	Intraspecific	Candidate Gene	Loisel DA; Rockman MV; Wray GA ; et al. (2006) Ancient polymorphism and functional variation in the primate MHC-DQA1 5' cis-regulatory region.	GP00000478	HLA-DQA1 P01909	Physiology	Promoter variation	Papio baboons - (genus)	Papio baboons - (genus)	HLA-DQA1	Papio baboons - (genus)	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
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
hsp70Ba	Temperature tolerance	Cis-regulatory, Insertion	Drosophila melanogaster fruit fly - (species) D	Intraspecific	Candidate Gene	Lerman DN; Michalak P; Helin AB ; et al. (2003) Modification of heat-shock gene expression in Drosophila melanogaster populations via transposable e[...]	GP00002004	Hsp70Ba Q8INI8	Physiology	A 1447 bp fragment corresponding to the 39 end of a jockey element is inserted 107 bps upstream of the hsp70Ba transcription start site in the T strain. The insertion intervenes between HSEs 2 and 3; displacing HSEs 3 and 4 as well as three GAGA elements.	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species) D	hsp70Ba	Drosophila melanogaster fruit fly - (species)	Published - Accepted by Curator
hsp70Ba	Temperature tolerance	Cis-regulatory, Insertion	Drosophila melanogaster fruit fly - (species) D	Intraspecific	Candidate Gene	Lerman DN; Michalak P; Helin AB ; et al. (2003) Modification of heat-shock gene expression in Drosophila melanogaster populations via transposable e[...]	GP00002005	Hsp70Ba Q8INI8	Physiology	Insertion of a 1222bp non-autonomous P-element at position -184 relative to the Hsp70Ba transcription start site. The P-element intervenes between the second and third heat shock response elements (HSEs).	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species) D	hsp70Ba	Drosophila melanogaster fruit fly - (species)	Published - Accepted by Curator
hsp70Ba	Temperature tolerance	Cis-regulatory, Insertion	Drosophila melanogaster fruit fly - (species) D	Intraspecific	Candidate Gene	Lerman DN; Michalak P; Helin AB ; et al. (2003) Modification of heat-shock gene expression in Drosophila melanogaster populations via transposable e[...]	GP00002006	Hsp70Ba Q8INI8	Physiology	A non-autonomous 1383bp P-element is inserted 97bp upstream of the Hsp70Ba transcription start site. The P-element intervenes between the second and third heat shock response elements (HSEs).	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species) D	hsp70Ba	Drosophila melanogaster fruit fly - (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 Tabib A; Vishwanathan S; Seleznev A (2016) A Polynucleotide Repeat Expansion Causing Temperature-Sensitivity Persists in Wild Irish Accessions [...]	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
IL4	Immune response	Cis-regulatory, SNP	Homo sapiens human - (species)	Intraspecific	Linkage Mapping	Rockman MV; Hahn MW; Soranzo N ; et al. (2003) Positive selection on a human-specific transcription factor binding site regulating IL4 expression.	GP00000497	IL4 P05112	Physiology	_524T promoter single base-pair substitution affecting binding of the NFAT transcription factor	Homo sapiens human - (species)	Homo sapiens human - (species)	IL4	Homo sapiens human - (species)	Published - Accepted by Curator
Immune deficiency	Pathogen resistance	Cis-regulatory, Unknown	Drosophila melanogaster fruit fly - (species)	Intraspecific	Candidate Gene	Lazzaro BP; Sceurman BK; Clark AG (2004) Genetic basis of natural variation in D. melanogaster antibacterial immunity.	GP00000499	imd Q9NHG0	Physiology	unknown	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species)	Immune deficiency	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 Rimbault M; Beale HC; Schoenebeck JJ (2013) Derived variants at six genes explain nearly half of size reduction in dog breeds.	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
interleukin-4	Immune response	Cis-regulatory, SNP	Homo sapiens human - (species)	Interspecific	Candidate Gene	Rockman MV; Hahn MW; Soranzo N ; et al. (2003) Positive selection on a human-specific transcription factor binding site regulating IL4 expression.	GP00000504	IL4R P24394	Physiology	1bp substitution in promoter	Primates (order)	Homo sapiens human - (species)	interleukin-4	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 Visser M; Palstra RJ; Kayser M (2015) Allele-specific transcriptional regulation of IRF4 in melanocytes is mediated by chromatin looping o[...]	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
Jheh1-Jheh2-Jheh3 complex	Oxidative stress resistance	Cis-regulatory, Insertion	Drosophila melanogaster fruit fly - (species) D	Intraspecific	Association Mapping	González J; Macpherson JM; Petrov DA (2009) A recent adaptive transposable element insertion near highly conserved developmental loci in Drosoph[...] 1 Additional References Guio L; González J (2015) The dominance effect of the adaptive transposable element insertion Bari-Jheh depends on the genetic[...]	GP00001782	JHEH Q6U6J0	Physiology	insertion of a transposable element Bari-Jheh associated with downregulation of Juvenile hormone epoxy hydroxylase 2 (Jheh2) and Jheh3 in nonstress conditions and with upregulation of Jheh1 and Jheh2 and downregulation of Jheh3 under oxidative stress conditions	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species) D	Jheh1-Jheh2-Jheh3 complex	Drosophila melanogaster fruit fly - (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)	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)	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 Pielberg G; Day AE; Plastow GS (2003) A sensitive method for detecting variation in copy numbers of duplicated genes.	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)	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 Pielberg G; Day AE; Plastow GS (2003) A sensitive method for detecting variation in copy numbers of duplicated genes.	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)	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)	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 Pielberg G; Day AE; Plastow GS (2003) A sensitive method for detecting variation in copy numbers of duplicated genes.	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 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 Sulem P; Gudbjartsson DF; Stacey SN (2007) Genetic determinants of hair, eye and skin pigmentation in Europeans.	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
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
lactase (LCT)	Lactose tolerance (adult)	Cis-regulatory, SNP	Homo sapiens human - (species)	Intraspecific	Linkage Mapping	Enattah NS; Sahi T; Savilahti E ; et al. (2002) Identification of a variant associated with adult-type hypolactasia. 1 Additional References Tishkoff SA; Reed FA; Ranciaro A (2007) Convergent adaptation of human lactase persistence in Africa and Europe.	GP00000529	LCT P09848	Physiology	C-13910T	Homo sapiens human - (species)	Homo sapiens human - (species)	lactase (LCT)	Homo sapiens human - (species)	Published - Accepted by Curator
lactase (LCT)	Lactose tolerance (adult)	Cis-regulatory, SNP	Homo sapiens human - (species)	Intraspecific	Association Mapping	Tishkoff SA; Reed FA; Ranciaro A ; et al. (2007) Convergent adaptation of human lactase persistence in Africa and Europe.	GP00000530	LCT P09848	Physiology	C-13907G	Homo sapiens human - (species)	Homo sapiens human - (species)	lactase (LCT)	Homo sapiens human - (species)	Published - Accepted by Curator
lactase (LCT)	Lactose tolerance (adult)	Cis-regulatory, SNP	Homo sapiens human - (species) D	Intraspecific	Association Mapping	Tishkoff SA; Reed FA; Ranciaro A ; et al. (2007) Convergent adaptation of human lactase persistence in Africa and Europe.	GP00000531	LCT P09848	Physiology	T-13915G	Homo sapiens human - (species)	Homo sapiens human - (species) D	lactase (LCT)	Homo sapiens human - (species)	Published - Accepted by Curator
lactase (LCT)	Lactose tolerance (adult)	Cis-regulatory, SNP	Homo sapiens human - (species)	Intraspecific	Association Mapping	Tishkoff SA; Reed FA; Ranciaro A ; et al. (2007) Convergent adaptation of human lactase persistence in Africa and Europe. 1 Additional References Breton G; Schlebusch CM; Lombard M (2014) Lactase persistence alleles reveal partial East African ancestry of southern African Khoe pastoralis[...]	GP00000532	LCT P09848	Physiology	G14010C ; In Khoe Pastoralist group lactase persistence (LP)-regulatory region 2 SNPs with greatest frequencies 13910C>T and 14010G>C	Homo sapiens human - (species)	Homo sapiens human - (species)	lactase (LCT)	Homo sapiens human - (species)	Published - Accepted by Curator
lactase (LCT)	Lactose tolerance (adult)	Cis-regulatory, SNP	Homo sapiens human - (species) D	Intraspecific	Association Mapping	Jones BL; Raga TO; Liebert A ; et al. (2013) Diversity of lactase persistence alleles in Ethiopia: signature of a soft selective sweep. 1 Additional References Liebert A; Jones BL; Danielsen ET (2016) In Vitro Functional Analyses of Infrequent Nucleotide Variants in the Lactase Enhancer Reveal Differ[...]	GP00001714	LCT P09848	Physiology	T14009G (rs869051967) (ss 820486563)	Homo sapiens human - (species)	Homo sapiens human - (species) D	lactase (LCT)	Homo sapiens human - (species)	Published - Accepted by Curator
lactate dehydrogenase-B (Ldh-B)	Stress response	Cis-regulatory, Unknown	Fundulus heteroclitus mummichog - (species)	Intraspecific	Linkage Mapping	Schulte PM; Glemet HC; Fiebig AA ; et al. (2000) Adaptive variation in lactate dehydrogenase-B gene expression: role of a stress-responsive regulator[...]	GP00000533	ldhb P20373	Physiology	unknown - candidate 1 bp change in southern populatin generates mammary tumor virus glucocorticoid responsive element	Fundulus heteroclitus mummichog - (species)	Fundulus heteroclitus mummichog - (species)	lactate dehydrogenase-B (Ldh-B)	Fundulus heteroclitus mummichog - (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
Lectin-24A	Pathogen resistance (parasitic wasp)	Cis-regulatory, Deletion	Drosophila melanogaster fruit fly - (species) D	Intraspecific	Linkage Mapping	Arunkumar Ramesh; Zhou Shuyu Olivia; Day Jonathan P ; et al. (2022 ) Recurrent loss of an immunity gene that protects Drosophila against a major natural parasite	GP00002655	lectin-24A Q9VQU4	Physiology	A cis-regulatory polymorphism in the gene Lectin-24A abolishes expression after infection and strongly reduces survival. 21bp indel (c.-171_-151del)	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species) D	Lectin-24A	Drosophila melanogaster fruit fly - (species)	Published - Accepted by Curator
LeSPL-CNR	Fruit ripening	Cis-regulatory, Epigenetic Change	Solanum lycopersicum tomato - (species) D	Domesticated	Linkage Mapping	Manning K; Tör M; Poole M ; et al. (2006) A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibit[...]	GP00000539	101256245 Q0PY35	Physiology	Stable methylation in a 286bp region of the promoter	Solanum cheesmaniae (species)	Solanum lycopersicum tomato - (species) D	LeSPL-CNR	Solanum lycopersicum tomato - (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 Wang X; Chamberlin HM (2004) Evolutionary innovation of the excretory system in Caenorhabditis elegans.	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
LPAR1	Hematopoiesis (blood monocyte count)	Cis-regulatory, SNP	Homo sapiens human - (species)	Intraspecific	Association Mapping	Guo MH; Nandakumar SK; Ulirsch JC ; et al. (2017) Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mech[...]	GP00001612	LPAR1 Q92633	Physiology	A>G at the associated SNP. 2 variants located in an uncharacterized long noncoding RNA	Homo sapiens human - (species)	Homo sapiens human - (species)	LPAR1	Homo sapiens human - (species)	Published - Accepted by Curator
MADS AFFECTING FLOWERING 2 (MAF2)	Flowering time	Cis-regulatory, Insertion	Arabidopsis thaliana thale cress - (species)	Intraspecific	Linkage Mapping	Rosloski SM; Jali SS; Balasubramanian S ; et al. (2010) Natural diversity in flowering responses of Arabidopsis thaliana caused by variation in a tandem gen[...]	GP00000561	MAF2 Q84J38	Physiology	Insertion alleles - several	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species)	MADS AFFECTING FLOWERING 2 (MAF2)	Arabidopsis thaliana thale cress - (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
MATE1/AltSB/SbMATE	Metal tolerance	Cis-regulatory, Unknown	Sorghum bicolor sorghum - (species)	Domesticated	Linkage Mapping	Magalhaes JV; Liu J; Guimarães CT ; et al. (2007) A gene in the multidrug and toxic compound extrusion (MATE) family confers aluminum tolerance in sor[...]	GP00000565		Physiology	unknown	Sorghum bicolor sorghum - (species)	Sorghum bicolor sorghum - (species)	MATE1/AltSB/SbMATE	Sorghum bicolor sorghum - (species)	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
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 Chagné D; Lin-Wang K; Espley RV (2013) An ancient duplication of apple MYB transcription factors is responsible for novel red fruit-flesh p[...]	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
metallothionein (MtnA)	Oxidative stress resistance	Cis-regulatory, Deletion	Drosophila melanogaster fruit fly - (species) D	Intraspecific	Association Mapping	Catalán A; Glaser-Schmitt A; Argyridou E ; et al. (2016) An Indel Polymorphism in the MtnA 3' Untranslated Region Is Associated with Gene Expression Variatio[...]	GP00002018	MtnA P04357	Physiology	49bp deletion in the MtnA 3'UTR	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species) D	metallothionein (MtnA)	Drosophila melanogaster fruit fly - (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
MGAM	Starch processing	Cis-regulatory, Unknown	Canis lupus familiaris dog - (subspecies)	Domesticated	Association Mapping	Axelsson E; Ratnakumar A; Arendt ML ; et al. (2013) The genomic signature of dog domestication reveals adaptation to a starch-rich diet.	GP00000654	MGAM O43451	Physiology	unknown	Canis lupus gray wolf - (species)	Canis lupus familiaris dog - (subspecies)	MGAM	Canis lupus familiaris dog - (subspecies)	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 Baranowska Körberg I; Sundström E; Meadows JR (2014) A simple repeat polymorphism in the MITF-M promoter is a key regulator of white spotting in dogs.	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 (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 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
Molybdenum transporter1 (MOT1)	Metal tolerance	Cis-regulatory, Deletion	Arabidopsis thaliana thale cress - (species) D	Intraspecific	Linkage Mapping	Baxter I; Muthukumar B; Park HC ; et al. (2008) Variation in molybdenum content across broadly distributed populations of Arabidopsis thaliana is co[...] 1 Additional References Forsberg SK; Andreatta ME; Huang XY (2015) The Multi-allelic Genetic Architecture of a Variance-Heterogeneity Locus for Molybdenum Concentratio[...]	GP00000676	MOT1 Q9SL95	Physiology	53bp deletion in promoter	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species) D	Molybdenum transporter1 (MOT1)	Arabidopsis thaliana thale cress - (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
MYB1	Coloration (inner flesh)	Cis-regulatory, Unknown	Beta vulgaris (species)	Domesticated	Candidate Gene	Hatlestad GJ; Akhavan NA; Sunnadeniya RM ; et al. (2015) The beet Y locus encodes an anthocyanin MYB-like protein that activates the betalain red pigment pat[...]	GP00001396	MYB1 M1ETA5	Physiology	unknown mutations within 460bp of putative 5 prime UTR	Beta vulgaris (species)	Beta vulgaris (species)	MYB1	Beta vulgaris (species)	Published - Accepted by Curator
MYB1	Coloration (inner flesh)	Cis-regulatory, Epigenetic Change	Raphanus sativus radish - (species) D	Domesticated	Candidate Gene	Wang Q; Wang Y; Sun H ; et al. (2020) Transposon-induced methylation of the RsMYB1 promoter disturbs the anthocyanin accumulation in red-f[...]	GP00002094	MYB1 M1ETA5	Physiology	The taproot white-fleshed mutant is the result of altered DNA methylation in the RsMYB1 promoter. This heritable epigenetic change is due to a hypermethylated CACTA transposon (a 7372-bp TE) which induces the spreading of DNA methylation to the promoter region of RsMYB1. RsMYB1 expression is considerably downregulated and this inhibits anthocyanin biosynthesis in white-fleshed mutants.	Raphanus sativus radish - (species)	Raphanus sativus radish - (species) D	MYB1	Raphanus sativus radish - (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 9	Heat tolerance Racing performance	Cis-regulatory, SNP	Canis lupus familiaris dog - (subspecies) D	Domesticated	Association Mapping	Huson HJ; vonHoldt BM; Rimbault M ; et al. (2012) Breed-specific ancestry studies and genome-wide association analysis highlight an association betwee[...]	GP00000684	MYH9 P35579	Physiology Physiology	Several candidate SNPs - exact causing mutation(s) unknown	Canis lupus gray wolf - (species)	Canis lupus familiaris dog - (subspecies) D	Myosin heavy chain 9	Canis lupus familiaris dog - (subspecies)	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)	Racing performance	Cis-regulatory, Insertion	Equus caballus horse - (species) D	Domesticated	Candidate Gene	Binns MM; Boehler DA; Lambert DH (2010) Identification of the myostatin locus (MSTN) as having a major effect on optimum racing distance in [...] 3 Additional References Petersen JL; Mickelson JR; Rendahl AK (2013) Genome-wide analysis reveals selection for important traits in domestic horse breeds. Tozaki T; Hill EW; Hirota K (2012) A cohort study of racing performance in Japanese Thoroughbred racehorses using genome information on[...] Rooney MF; Hill EW; Kelly VP (2018) The "speed gene" effect of myostatin arises in Thoroughbred horses due to a promoter proximal SINE i[...]	GP00000698	MSTN O14793	Morphology; Physiology	227-bp SINE insertion in promoter	Equus caballus horse - (species)	Equus caballus horse - (species) D	Myostatin (MSTN = GDF8)	Equus caballus horse - (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 Poelstra JW; Vijay N; Hoeppner MP (2015) Transcriptomics of colour patterning and coloration shifts in crows. Weissensteiner MH; Bunikis I; Catalán A (2020) Discovery and population genomics of structural variation in a songbird genus.	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)	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
NUDT7	Meat color	Cis-regulatory, Unknown	Sus scrofa domesticus domestic pig - (subspecies)	Domesticated	Linkage Mapping	Taniguchi M; Hayashi T; Nii M ; et al. (2010) Fine mapping of quantitative trait loci for meat color on Sus scrofa chromosome 6: analysis of the s[...] 1 Additional References Taniguchi M; Hayashi T; Nii M (2010) Overexpression of NUDT7, a candidate quantitative trait locus for pork color, downregulates heme bio[...]	GP00000741	Nudt7 Q99P30	Physiology	unknown	Sus scrofa pig - (species)	Sus scrofa domesticus domestic pig - (subspecies)	NUDT7	Sus scrofa domesticus domestic pig - (subspecies)	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 Han J; Kraft P; Nan H (2008) A genome-wide association study identifies novel alleles associated with hair color and skin pigment[...] Visser M; Kayser M; Palstra RJ (2012) HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long[...] Beleza S; Johnson NA; Candille SI (2013) Genetic architecture of skin and eye color in an African-European admixed population. Crawford NG; Kelly DE; Hansen MEB (2017) Loci associated with skin pigmentation identified in African populations. Lona-Durazo F; Hernandez-Pacheco N; Fan S (2019) Meta-analysis of GWA studies provides new insights on the genetic architecture of skin pigmentation [...]	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
ODORANT1 [pseudo-replication between 2 ODO1 entries due to possible homology between alleles]	Fragrance	Cis-regulatory, Unknown	Petunia exserta (species)	Interspecific	Linkage Mapping	Klahre U; Gurba A; Hermann K ; et al. (2011) Pollinator choice in Petunia depends on two major genetic Loci for floral scent production.	GP00000750	ODO1 Q50EX6	Physiology	Not identified; but probably homologous to P. hybrida Mitchell x R27 promoter variation since these P. hybrida accessions are derived from a P. axillaris x P. integrifolia cross	Petunia axillaris (species)	Petunia exserta (species)	ODORANT1 [pseudo-replication between 2 ODO1 entries due to possible homology between alleles]	Petunia exserta (species)	Published - Accepted by Curator
ODORANT1 [pseudo-replication between 2 ODO1 entries due to possible homology between alleles]	Fragrance	Cis-regulatory, SNP	Petunia x hybrida (species)	Domesticated	Linkage Mapping	Van Moerkercke A; Haring MA; Schuurink RC (2011) The transcription factor EMISSION OF BENZENOIDS II activates the MYB ODORANT1 promoter at a MYB bind[...]	GP00000751	ODO1 Q50EX6	Physiology	C/T substitution in enhancer region MYB-TF binding site	Petunia x hybrida (species)	Petunia x hybrida (species)	ODORANT1 [pseudo-replication between 2 ODO1 entries due to possible homology between alleles]	Petunia x hybrida (species)	Published - Accepted by Curator
opaque2 (O2)	Lysine content (endosperm)	Cis-regulatory, Insertion	Zea mays (species) D	Domesticated	Linkage Mapping	Schmidt RJ; Burr FA; Burr B (1987) Transposon tagging and molecular analysis of the maize regulatory locus opaque-2.	GP00000754	O2 P12959	Physiology	insertion of a non-autonomous rbg transposable element in the untranslated leader sequence of the O2 gene	Zea mays (species)	Zea mays (species) D	opaque2 (O2)	Zea mays (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 Hines HM; Counterman BA; Papa R (2011) Wing patterning gene redefines the mimetic history of Heliconius butterflies.	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 Hines HM; Counterman BA; Papa R (2011) Wing patterning gene redefines the mimetic history of Heliconius butterflies.	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 Hines HM; Counterman BA; Papa R (2011) Wing patterning gene redefines the mimetic history of Heliconius butterflies.	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 Hines HM; Counterman BA; Papa R (2011) Wing patterning gene redefines the mimetic history of Heliconius butterflies.	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
ORGANIC CATION TRANSPORTER 1	Root growth (root length response to exogenous cadaverine)	Cis-regulatory, Unknown	Arabidopsis thaliana thale cress - (species)	Intraspecific	Linkage Mapping	Strohm AK; Vaughn LM; Masson PH (2015) Natural variation in the expression of ORGANIC CATION TRANSPORTER 1 affects root length responses to[...]	GP00001279	OCT1 Q9CAT6	Physiology	unknown	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species)	ORGANIC CATION TRANSPORTER 1	Arabidopsis thaliana thale cress - (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
OsGA20ox1	Seedling vigor	Cis-regulatory, Unknown	Oryza sativa rice - (species)	Domesticated	Linkage Mapping	Abe A; Takagi H; Fujibe T ; et al. (2012) OsGA20ox1, a candidate gene for a major QTL controlling seedling vigor in rice.	GP00000810	GA20OX1 P93771	Physiology	unknown ; no coding variation	Oryza sativa rice - (species)	Oryza sativa rice - (species)	OsGA20ox1	Oryza sativa rice - (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
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 Miura K; Ikeda M; Matsubara A (2010) OsSPL14 promotes panicle branching and higher grain productivity in rice.	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 Wang S; Li S; Liu Q (2015) The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and [...]	GP00000814	SPL16 L0AP48	Morphology Morphology	Promoter variation	Oryza sativa rice - (species)	Oryza sativa rice - (species)	OsSPL16	Oryza sativa rice - (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 Gautier M; Yamaguchi J; Foucaud J (2018) The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird. Ando T; Niimi T (2019) Development and evolution of color patterns in ladybird beetles: A case study in Harmonia axyridis.	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 Gautier M; Yamaguchi J; Foucaud J (2018) The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird. Ando T; Niimi T (2019) Development and evolution of color patterns in ladybird beetles: A case study in Harmonia axyridis.	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 Gautier M; Yamaguchi J; Foucaud J (2018) The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird. Ando T; Niimi T (2019) Development and evolution of color patterns in ladybird beetles: A case study in Harmonia axyridis.	GP00001707	pnr P52168	Morphology	exact mutation(s) unknown	Harmonia axyridis (species)	Harmonia axyridis (species)	pannier	Harmonia axyridis (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 Hu Y; Albertson RC (2014) Hedgehog signaling mediates adaptive variation in a dynamic functional system in the cichlid feeding[...]	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
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
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 (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
phosphoenolpyruvate carboxylase (PEPC)	C3-C4 photosynthesis (enzymatic properties)	Cis-regulatory, Insertion	Flaveria trinervia (species) D	Interspecific	Candidate Gene	Akyildiz M; Gowik U; Engelmann S ; et al. (2007) Evolution and function of a cis-regulatory module for mesophyll-specific gene expression in the C4 d[...]	GP00000868	PPCA P30694	Physiology	insertion of tetranucleotide CACT	Flaveria pringlei (species)	Flaveria trinervia (species) D	phosphoenolpyruvate carboxylase (PEPC)	Flaveria trinervia (species)	Published - Accepted by Curator
phosphoenolpyruvate carboxylase (PEPC)	C3-C4 photosynthesis (enzymatic properties)	Cis-regulatory, SNP	Flaveria trinervia (species)	Interspecific	Candidate Gene	Akyildiz M; Gowik U; Engelmann S ; et al. (2007) Evolution and function of a cis-regulatory module for mesophyll-specific gene expression in the C4 d[...]	GP00000869	PPCA P30694	Physiology	G->A	Flaveria pringlei (species)	Flaveria trinervia (species)	phosphoenolpyruvate carboxylase (PEPC)	Flaveria trinervia (species)	Published - Accepted by Curator
Pit	Pathogen resistance (rice blast disease; fungal pathogen; Magnaporthe grisea)	Cis-regulatory, Insertion	Oryza sativa rice - (species) D	Domesticated	Linkage Mapping	Hayashi K; Yoshida H (2009) Refunctionalization of the ancient rice blast disease resistance gene Pit by the recruitment of a re[...]	GP00002052	Pit B9A1G4	Physiology	insertion of a 5.5-kb LTR retrotransposon Renovator upstream of the gene (256‐bp upstream of the predicted start codon for NBSt2K59; in the same orientation as the gene)	Oryza sativa rice - (species)	Oryza sativa rice - (species) D	Pit	Oryza sativa rice - (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 Chan YF; Marks ME; Jones FC (2010) Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer.	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 Chan YF; Marks ME; Jones FC (2010) Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer.	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 Chan YF; Marks ME; Jones FC (2010) Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer.	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 Chan YF; Marks ME; Jones FC (2010) Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer.	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 Chan YF; Marks ME; Jones FC (2010) Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer.	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 Chan YF; Marks ME; Jones FC (2010) Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer.	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 Chan YF; Marks ME; Jones FC (2010) Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer.	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 Chan YF; Marks ME; Jones FC (2010) Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer.	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 Chan YF; Marks ME; Jones FC (2010) Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer.	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 (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)	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 Varga L; Lénárt X; Zenke P (2020) Being Merle: The Molecular Genetic Background of the Canine Merle Mutation.	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 Varga L; Lénárt X; Zenke P (2020) Being Merle: The Molecular Genetic Background of the Canine Merle Mutation.	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 Varga L; Lénárt X; Zenke P (2020) Being Merle: The Molecular Genetic Background of the Canine Merle Mutation.	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 Varga L; Lénárt X; Zenke P (2020) Being Merle: The Molecular Genetic Background of the Canine Merle Mutation.	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 Varga L; Lénárt X; Zenke P (2020) Being Merle: The Molecular Genetic Background of the Canine Merle Mutation.	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
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 Allais-Bonnet A; Grohs C; Medugorac I (2013) Novel insights into the bovine polled phenotype and horn ontogenesis in Bovidae. Wiedemar N; Tetens J; Jagannathan V (2014) Independent polled mutations leading to complex gene expression differences in cattle.	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 Allais-Bonnet A; Grohs C; Medugorac I (2013) Novel insights into the bovine polled phenotype and horn ontogenesis in Bovidae. Wiedemar N; Tetens J; Jagannathan V (2014) Independent polled mutations leading to complex gene expression differences in cattle. Rothammer S; Capitan A; Mullaart E (2014) The 80-kb DNA duplication on BTA1 is the only remaining candidate mutation for the polled phenotype [...]	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
PPAR-gamma	Fertility	Cis-regulatory, SNP	Drosophila melanogaster fruit fly - (species)	Intraspecific	Association Mapping	Hoedjes KM; Kostic H; Flatt T ; et al. (2023) A Single Nucleotide Variant in the PPARγ-homolog Eip75B Affects Fecundity in Drosophila.	GP00002664	Eip75B P17672	Physiology	This SNP is biallelic with the “T” variant being more common in the late-reproducing long-lived populations (average frequency: 0.84 “T” / 0.16 “G”) as compared to the early-reproducing populations (average frequency: 0.52 “T” / 0.48 “G”).	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species)	PPAR-gamma	Drosophila melanogaster fruit fly - (species)	Published - Accepted by Curator
prodynorphin (PDYN)	Neuroendocronological homeostasis	Cis-regulatory, SNP	Homo sapiens human - (species)	Interspecific	Candidate Gene	Rockman MV; Hahn MW; Soranzo N ; et al. (2005) Ancient and recent positive selection transformed opioid cis-regulation in humans. 1 Additional References Babbitt CC; Silverman JS; Haygood R (2010) Multiple Functional Variants in cis Modulate PDYN Expression.	GP00000924	PDYN P01213	Physiology	up to 5 polymorphisms in 5' regulatory region	Primates (order)	Homo sapiens human - (species)	prodynorphin (PDYN)	Homo sapiens human - (species)	Published - Accepted by Curator
Prolactin (deciduous Prolactin; dPRL)	Gene expression change (quantitative; increase)	Cis-regulatory, SNP	Homininae (subfamily)	Intergeneric or Higher	Candidate Gene	Emera D; Wagner GP (2012) Transformation of a transposon into a derived prolactin promoter with function during human pregnanc[...]	GP00000926	PRL P01236	Physiology	Acquisition of enhancer activity in transposons via several base-pair substitutions	Primates (order)	Homininae (subfamily)	Prolactin (deciduous Prolactin; dPRL)	Homininae (subfamily)	Published - Accepted by Curator
Prolactin receptor	Fertility	Cis-regulatory, Insertion	Sus scrofa domesticus domestic pig - (subspecies) D	Domesticated	Linkage Mapping	Sironen A; Fischer D; Laiho A ; et al. (2014) A recent L1 insertion within SPEF2 gene is associated with changes in PRLR expression in sow reprodu[...] 1 Additional References Sironen A; Uimari P; Iso-Touru T (2012) L1 insertion within SPEF2 gene is associated with increased litter size in the Finnish Yorkshire pop[...]	GP00002339	PRLR P16471	Physiology	L1 insertion in sperm-factor SPEF2 gene causes sperm defect but also downregulation of PRLR	Sus scrofa domesticus domestic pig - (subspecies)	Sus scrofa domesticus domestic pig - (subspecies) D	Prolactin receptor	Sus scrofa domesticus domestic pig - (subspecies)	Published - Accepted by Curator
Prolactin releasing hormone receptor (Prlhr/GPR10)	Body size (weight)	Cis-regulatory, Unknown	Mus musculus house mouse - (species)	Domesticated	Association Mapping	Chan YF; Jones FC; McConnell E ; et al. (2012) Parallel selection mapping using artificially selected mice reveals body weight control loci.	GP00000928	PRLHR P49683	Physiology	unknown	Mus musculus house mouse - (species)	Mus musculus house mouse - (species)	Prolactin releasing hormone receptor (Prlhr/GPR10)	Mus musculus house mouse - (species)	Published - Accepted by Curator
Proline specific permease PUT4	Nitrogen use (growth rate on proline)	Cis-regulatory, Unknown	Saccharomyces cerevisiae baker's yeast - (species) D	Intraspecific	Linkage Mapping	Ibstedt S; Stenberg S; Bagés S ; et al. (2015) Concerted evolution of life stage performances signals recent selection on yeast nitrogen use.	GP00001501	PUT4 P15380	Physiology	several synonymous and promoter mutations	Saccharomyces cerevisiae baker's yeast - (species)	Saccharomyces cerevisiae baker's yeast - (species) D	Proline specific permease PUT4	Saccharomyces cerevisiae baker's yeast - (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
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
qSH1	Seed shattering	Cis-regulatory, SNP	Oryza sativa rice - (species)	Domesticated	Linkage Mapping	Konishi S; Izawa T; Lin SY ; et al. (2006) An SNP caused loss of seed shattering during rice domestication.	GP00000942	qSH1 Q941S9	Physiology	1bp change	Oryza sativa rice - (species)	Oryza sativa rice - (species)	qSH1	Oryza sativa rice - (species)	Published - Accepted by Curator
qSH1 (REPLUMLESS)	Seed shattering	Cis-regulatory, SNP	Brassicaceae mustard family - (family)	Interspecific	Candidate Gene	Arnaud N; Lawrenson T; Østergaard L ; et al. (2011) The same regulatory point mutation changed seed-dispersal structures in evolution and domestication.	GP00000943	qSH1 Q941S9	Physiology	1bp change	Brassicaceae mustard family - (family)	Brassicaceae mustard family - (family)	qSH1 (REPLUMLESS)	Brassicaceae mustard family - (family)	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
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
Rap2.7 (vgt1)	Flowering time	Cis-regulatory, Unknown	Zea mays (species)	Domesticated	Linkage Mapping	Salvi S; Sponza G; Morgante M ; et al. (2007) Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in m[...] 1 Additional References Buckler ES; Holland JB; Bradbury PJ (2009) The genetic architecture of maize flowering time.	GP00000951	RAP2-7 Q9SK03	Physiology	2kb-sequence located 70kb upstream of the Vg1 transcription start site - insertion of a miniature transposon (MITE) belonging to the Tourist family	Zea mays (species)	Zea mays (species)	Rap2.7 (vgt1)	Zea mays (species)	Published - Accepted by Curator
RAS2	Sporulation efficiency	Cis-regulatory, Insertion	Saccharomyces cerevisiae baker's yeast - (species) D	Domesticated	Linkage Mapping	Ben-Ari G; Zenvirth D; Sherman A ; et al. (2006) Four linked genes participate in controlling sporulation efficiency in budding yeast.	GP00000956	RAS2 P01120	Physiology	1bp insertion in promoter	Saccharomyces cerevisiae baker's yeast - (species)	Saccharomyces cerevisiae baker's yeast - (species) D	RAS2	Saccharomyces cerevisiae baker's yeast - (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
REC8	Recombination rate (male)	Cis-regulatory, SNP	Bos taurus cattle - (species)	Domesticated	Linkage Mapping	Sandor C; Li W; Coppieters W ; et al. (2012) Genetic variants in REC8, RNF212, and PRDM9 influence male recombination in cattle.	GP00001638	REC8 E1BL69	Physiology	A>G in intron 12 with reduction in Genome-wide recombination rate	Bos taurus cattle - (species)	Bos taurus cattle - (species)	REC8	Bos taurus cattle - (species)	Published - Accepted by Curator
Rhg1	Pathogen resistance (cyst nematode)	Cis-regulatory, Insertion	Glycine max soybean - (species) D	Intraspecific	Linkage Mapping	Bayless AM; Zapotocny RW; Han S ; et al. (2019) The rhg1-a (Rhg1 low-copy) nematode resistance source harbors a copia-family retrotransposon within [...]	GP00002049	rhg1s Q8L3Y5	Physiology	insertion of a copia retrotransposon within the gene Rhg1 Glyma.18G022500 (α-SNAP-encoding). This transposable element is intact and resides within intron 1; anti-sense to the rhg1-a α-SNAP open reading frame.	Glycine max soybean - (species)	Glycine max soybean - (species) D	Rhg1	Glycine max soybean - (species)	Published - Accepted by Curator
RHO2	Temperature tolerance / virulence	Cis-regulatory, Unknown	Saccharomyces cerevisiae baker's yeast - (species)	Intraspecific	Linkage Mapping	Steinmetz LM; Sinha H; Richards DR ; et al. (2002) Dissecting the architecture of a quantitative trait locus in yeast. 1 Additional References Sinha H; Nicholson BP; Steinmetz LM (2006) Complex genetic interactions in a quantitative trait locus.	GP00000986	RHO2 P06781	Physiology	3'UTR polymorphism	Saccharomyces cerevisiae baker's yeast - (species)	Saccharomyces cerevisiae baker's yeast - (species)	RHO2	Saccharomyces cerevisiae baker's yeast - (species)	Published - Accepted by Curator
RME1	Sporulation efficiency	Cis-regulatory, Deletion	Saccharomyces cerevisiae baker's yeast - (species) D	Domesticated	Linkage Mapping	Deutschbauer AM; Davis RW (2005) Quantitative trait loci mapped to single-nucleotide resolution in yeast.	GP00000994	RME1 P32338	Physiology	single nucleotide deletion in promoter region	Saccharomyces cerevisiae baker's yeast - (species)	Saccharomyces cerevisiae baker's yeast - (species) D	RME1	Saccharomyces cerevisiae baker's yeast - (species)	Published - Accepted by Curator
RME1 [possible pseudo-replicate of laboratory strain entry]	Sporulation efficiency	Cis-regulatory, Deletion	Saccharomyces cerevisiae baker's yeast - (species) D	Intraspecific	Linkage Mapping	Gerke J; Lorenz K; Cohen B (2009) Genetic interactions between transcription factors cause natural variation in yeast.	GP00000995	RME1 P32338	Physiology	single nucleotide deletion in promoter region	Saccharomyces cerevisiae baker's yeast - (species)	Saccharomyces cerevisiae baker's yeast - (species) D	RME1 [possible pseudo-replicate of laboratory strain entry]	Saccharomyces cerevisiae baker's yeast - (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
RTA1	Xenobiotic resistance (citrinin)	Cis-regulatory, Unknown	Saccharomyces paradoxus (species) D	Domesticated	Association Mapping	Naranjo S; Smith JD; Artieri CG ; et al. (2015) Dissecting the Genetic Basis of a Complex cis-Regulatory Adaptation.	GP00001312	RTA1 P53047	Physiology	unknown	Saccharomyces cerevisiae baker's yeast - (species)	Saccharomyces paradoxus (species) D	RTA1	Saccharomyces paradoxus (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
Rx1	Color vision (expression of SWS2b opsin)	Cis-regulatory, Indel	Tramitichromis intermedius (species)	Interspecific	Linkage Mapping	Schulte JE; O'Brien CS; Conte MA ; et al. (2014) Interspecific variation in Rx1 expression controls opsin expression and causes visual system diversi[...]	GP00001441	rx1 O42356	Physiology	413bp deletion located 2.5-kb upstream of the Rx1 translation start site correlating with decreased Rx1 expression	Aulonocara baenschi Nkhomo-benga peacock cichlid - (species)	Tramitichromis intermedius (species)	Rx1	Tramitichromis intermedius (species)	Published - Accepted by Curator
sage	Silk yield	Cis-regulatory, Unknown	Bombyx mori domestic silkworm - (species) D	Domesticated	Association Mapping	Xia Q; Guo Y; Zhang Z ; et al. (2009) Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx).	GP00002410	sage Q9VHG3	Physiology	Increased expression in high yield strains. The sage gene encodes a transcription factor that activates glue genes in salivary glands of Drosophila melanogaster.	Bombyx mori domestic silkworm - (species)	Bombyx mori domestic silkworm - (species) D	sage	Bombyx mori domestic silkworm - (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
SAP-2	Xenobiotic resistance (insecticide; pyrethroid)	Cis-regulatory, Unknown	Anopheles gambiae African malaria mosquito - (species) D	Intraspecific	Association Mapping	Ingham VA; Anthousi A; Douris V ; et al. (2020) A sensory appendage protein protects malaria vectors from pyrethroids.	GP00002432	SAP-2 Q6H8Z3	Physiology	The gene is highly overexpressed in the appendages of pyrethroid-resistant mosquitoes and its expression is further induced by insecticide exposure. Silencing of SAP2 almost completely restored susceptibility to the pyrethroid deltamethrin and also significantly increased the susceptibility to the other two pyrethroids (permethrin and alpha-cypermethrin).	Anopheles gambiae African malaria mosquito - (species)	Anopheles gambiae African malaria mosquito - (species) D	SAP-2	Anopheles gambiae African malaria mosquito - (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
SELF PRUNING 5G (SP5G)	Flowering time	Cis-regulatory, Unknown	Solanum lycopersicum tomato - (species)	Domesticated	Linkage Mapping	Soyk S; Müller NA; Park SJ ; et al. (2017) Variation in the flowering gene SELF PRUNING 5G promotes day-neutrality and early yield in tomato.	GP00001564	SP5G Q84XK9	Physiology	several candidate SNPs and structural variants	Solanum pimpinellifolium (species)	Solanum lycopersicum tomato - (species)	SELF PRUNING 5G (SP5G)	Solanum lycopersicum tomato - (species)	Published - Accepted by Curator
shattering4 - sh4	Seed shattering	Cis-regulatory, Unknown	Oryza glaberrima African rice - (species) D	Domesticated	Association Mapping	Wang M; Yu Y; Haberer G ; et al. (2014) The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication.	GP00001045	sh4 Q1PIH9	Physiology	several candidate mutations: ten SNPs and five small insertion/deletions leading to reduced expression	Oryza barthii (species)	Oryza glaberrima African rice - (species) D	shattering4 - sh4	Oryza glaberrima African rice - (species)	Published - Accepted by Curator
shrunken-2 (Sh2) = endosperm ADP-glucose pyrophosphorylase large subunit	Feather	Cis-regulatory, Insertion	Zea mays (species) D	Domesticated	Linkage Mapping	Preiss J; Danner S; Summers PS ; et al. (1990) Molecular Characterization of the Brittle-2 Gene Effect on Maize Endosperm ADPglucose Pyrophosphoryl[...] 1 Additional References Bhave MR; Lawrence S; Barton C (1990) Identification and molecular characterization of shrunken-2 cDNA clones of maize.	GP00001050	SH2 P55241	Physiology	insertion of the transposable element Dissociation	Zea mays (species)	Zea mays (species) D	shrunken-2 (Sh2) = endosperm ADP-glucose pyrophosphorylase large subunit	Zea mays (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
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
slowpoke (slo)	Courtship song (sine song frequency)	Cis-regulatory, Insertion	Drosophila simulans (species) D	Intraspecific	Linkage Mapping	Ding Y; Berrocal A; Morita T ; et al. (2016) Natural courtship song variation caused by an intronic retroelement in an ion channel gene.	GP00001066	slo Q03720	Behavior	6.7kb "Shelder" retroelement insertion in slowpoke intron; with effect on splicing	Drosophila simulans (species)	Drosophila simulans (species) D	slowpoke (slo)	Drosophila simulans (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
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 Zhu T; Liu M; Peng S (2022) A Deletion Upstream of SOX10 Causes Light Yellow Plumage Colour in Chicken.	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
spineless (ss)	Color vision (eye; photoreceptor composition)	Cis-regulatory, Insertion	Drosophila melanogaster fruit fly - (species) D	Intraspecific	Candidate Gene	Anderson C; Reiss I; Zhou C ; et al. (2017) Natural variation in stochastic photoreceptor specification and color preference in Drosophila.	GP00001987	ss E1JIM6	Physiology	Single base insertion in the ss regulatory region upstream of the ss transcription start site. The insertion affects the stochastic on/off expression of the ss protein seen in the R7 photoreceptors: the presence of the insertion results in a significant decrease in the ratio of ss expressing to non-expressing R7 cells.	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species) D	spineless (ss)	Drosophila melanogaster fruit fly - (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
srx-43	Pheromone response (ascaroside)	Cis-regulatory, Unknown	Caenorhabditis elegans (species) D	Intraspecific	Linkage Mapping	Greene JS; Brown M; Dobosiewicz M ; et al. (2016) Balancing selection shapes density-dependent foraging behaviour. 1 Additional References Greene JS; Dobosiewicz M; Butcher RA (2016) Regulatory changes in two chemoreceptor genes contribute to a Caenorhabditis elegans QTL for foragin[...]	GP00001319	srx-43 O45767	Physiology	unknown	Caenorhabditis elegans (species)	Caenorhabditis elegans (species) D	srx-43	Caenorhabditis elegans (species)	Published - Accepted by Curator
srx-44	Pheromone response (ascaroside)	Cis-regulatory, Unknown	Caenorhabditis elegans (species) D	Intraspecific	Linkage Mapping	Greene JS; Dobosiewicz M; Butcher RA ; et al. (2016) Regulatory changes in two chemoreceptor genes contribute to a Caenorhabditis elegans QTL for foragin[...] 1 Additional References Greene JS; Brown M; Dobosiewicz M (2016) Balancing selection shapes density-dependent foraging behaviour.	GP00001504	srx-43 O45767	Physiology	Phenotypic change mapped to a small region located between 34bp and 72 bp upstream of the srx-44 start codon. This DNA region contains 9 changes between N2 strain and MY14 strain.	Caenorhabditis elegans (species)	Caenorhabditis elegans (species) D	srx-44	Caenorhabditis elegans (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
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
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 Preger-Ben Noon E; Davis FP; Stern DL (2016) Evolved Repression Overcomes Enhancer Robustness.	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 Sucena E; Delon I; Jones I (2003) Regulatory evolution of shavenbaby/ovo underlies multiple cases of morphological parallelism.	GP00001086	ovo P51521	Morphology	unknown	virilis group (species group)	Drosophila ezoana (species)	Svb/ovo	Drosophila ezoana (species)	Published - Accepted by Curator
SWS2	Xenobiotic resistance (alcohol, ethanol)	Cis-regulatory, Unknown	Saccharomyces cerevisiae baker's yeast - (species)	Domesticated	Linkage Mapping	Swinnen S; Schaerlaekens K; Pais T ; et al. (2012) Identification of novel causative genes determining the complex trait of high ethanol tolerance in y[...]	GP00001088	SWS2 P53937	Physiology	unknown	Saccharomyces cerevisiae baker's yeast - (species)	Saccharomyces cerevisiae baker's yeast - (species)	SWS2	Saccharomyces cerevisiae baker's yeast - (species)	Published - Accepted by Curator
SWS2	Sporulation efficiency	Cis-regulatory, Unknown	Saccharomyces cerevisiae baker's yeast - (species)	Domesticated	Linkage Mapping	Ben-Ari G; Zenvirth D; Sherman A ; et al. (2006) Four linked genes participate in controlling sporulation efficiency in budding yeast.	GP00001089	SWS2 P53937	Physiology	unknown	Saccharomyces cerevisiae baker's yeast - (species)	Saccharomyces cerevisiae baker's yeast - (species)	SWS2	Saccharomyces cerevisiae baker's yeast - (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 Sundström E; Imsland F; Mikko S (2012) Copy number expansion of the STX17 duplication in melanoma tissue from Grey horses. Sundström E; Komisarczuk AZ; Jiang L (2012) Identification of a melanocyte-specific, microphthalmia-associated transcription factor-dependent re[...]	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
syntaxin1a	Eusociality	Cis-regulatory, Unknown	Lasioglossum albipes (species) D	Intraspecific	Association Mapping	Kocher SD; Mallarino R; Rubin BER ; et al. (2018) The genetic basis of a social polymorphism in halictid bees.	GP00002624	Syx1A Q24547	Behavior	Increased expression in eusocial individuals compared to solitary individuals	Lasioglossum albipes (species)	Lasioglossum albipes (species) D	syntaxin1a	Lasioglossum albipes (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 Rebeiz M; Ramos-Womack M; Jeong S (2009) Evolution of the tan locus contributed to pigment loss in Drosophila santomea: a response to Matute [...]	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 Rebeiz M; Ramos-Womack M; Jeong S (2009) Evolution of the tan locus contributed to pigment loss in Drosophila santomea: a response to Matute [...]	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 Rebeiz M; Ramos-Womack M; Jeong S (2009) Evolution of the tan locus contributed to pigment loss in Drosophila santomea: a response to Matute [...]	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 Dembeck LM; Huang W; Magwire MM (2015) Genetic Architecture of Abdominal Pigmentation in Drosophila melanogaster. Endler L; Betancourt AJ; Nolte V (2016) Reconciling Differences in Pool-GWAS Between Populations: A Case Study of Female Abdominal Pigmentat[...] Endler L; Gibert JM; Nolte V (2018) Pleiotropic effects of regulatory variation in tan result in correlation of two pigmentation traits [...]	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
TAO3	Sporulation efficiency	Cis-regulatory, SNP	Saccharomyces cerevisiae baker's yeast - (species)	Domesticated	Linkage Mapping	Deutschbauer AM; Davis RW (2005) Quantitative trait loci mapped to single-nucleotide resolution in yeast.	GP00001103	TAO3 P40468	Physiology	E1493Q	Saccharomyces cerevisiae baker's yeast - (species)	Saccharomyces cerevisiae baker's yeast - (species)	TAO3	Saccharomyces cerevisiae baker's yeast - (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
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 Studer A; Zhao Q; Ross-Ibarra J (2011) Identification of a functional transposon insertion in the maize domestication gene tb1. Studer AJ; Doebley JF (2012) Evidence for a natural allelic series at the maize domestication locus teosinte branched1.	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
TFL1/FvTFL1	Flowering time Seasonal growth	Cis-regulatory, Unknown	Fragaria vesca wild strawberry - (species)	Intraspecific	Linkage Mapping	Koskela EA; Mouhu K; Albani MC ; et al. (2012) Mutation in TERMINAL FLOWER1 reverses the photoperiodic requirement for flowering in the wild strawb[...]	GP00001120	TFL1 P93003	Physiology Physiology	unknown	Fragaria vesca wild strawberry - (species)	Fragaria vesca wild strawberry - (species)	TFL1/FvTFL1	Fragaria vesca wild strawberry - (species)	Published - Accepted by Curator
thyroid-stimulating hormone-beta-2	Metabolic rate Thyroid Hormone (plasma concentration)	Cis-regulatory, Unknown	Gasterosteus aculeatus three-spined stickleback - (species) D	Intraspecific	Candidate Gene	Kitano J; Lema SC; Luckenbach JA ; et al. (2010) Adaptive divergence in the thyroid hormone signaling pathway in the stickleback radiation.	GP00001288	tshba B3DJU0	Physiology Physiology	unknown	Gasterosteus aculeatus three-spined stickleback - (species)	Gasterosteus aculeatus three-spined stickleback - (species) D	thyroid-stimulating hormone-beta-2	Gasterosteus aculeatus three-spined stickleback - (species)	Published - Accepted by Curator
tra-2	Fertility (self-fertility; hermaphrodite spermatogenesis)	Cis-regulatory, Insertion	Caenorhabditis elegans (species)	Interspecific	Candidate Gene	Kuwabara PE (1996) Interspecies comparison reveals evolution of control regions in the nematode sex-determining gene tr[...] 2 Additional References Haag ES; Kimble J (2000) Regulatory elements required for development of caenorhabditis elegans hermaphrodites are conserved [...] Beadell AV; Liu Q; Johnson DM (2011) Independent recruitments of a translational regulator in the evolution of self-fertile nematodes.	GP00001132	tra-2 P34709	Physiology	Tandem duplication of GLD-1 binding sites in 3'UTR; see also fog-2 entry	Caenorhabditis briggsae (species)	Caenorhabditis elegans (species)	tra-2	Caenorhabditis elegans (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
Tret1-like	Diapause	Cis-regulatory, Unknown	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[...]	GP00002402	Tret1-1 A1Z8N1	Physiology	The expression level of BmTret1-like in homozygotes (pnd/pnd) is significantly lower (p < 0.01, t test) than that in heterozygotes (pnd/+). CRISPR BmTret1-like knockout lines generate non-diapause eggs. A 747 bp deletion is present in the 3′-untranslated region (3′-UTR) of BmTret1-like in pnd homozygotes	Bombyx mori domestic silkworm - (species)	Bombyx mori domestic silkworm - (species) D	Tret1-like	Bombyx mori domestic silkworm - (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 Pruvost M; Bellone R; Benecke N (2011) Genotypes of predomestic horses match phenotypes painted in Paleolithic works of cave art. Bellone RR; Holl H; Setaluri V (2013) Evidence for a retroviral insertion in TRPM1 as the cause of congenital stationary night blindness a[...] Druml T; Grilz-Seger G; Neuditschko M (2017) Phenotypic and Genetic Analysis of the Leopard Complex Spotting in Noriker Horses.	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
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 Rothammer S; Kunz E; Krebs S (2018) Remapping of the belted phenotype in cattle on BTA3 identifies a multiplication event as the candida[...] Drögemüller C; Demmel S; Engensteiner M (2010) A shared 336 kb haplotype associated with the belt pattern in three divergent cattle breeds.	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-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
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
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
VRN1	Flowering time	Cis-regulatory, Indel	Lolium perenne (species)	Intraspecific	Candidate Gene	Asp T; Byrne S; Gundlach H ; et al. (2011) Comparative sequence analysis of VRN1 alleles of Lolium perenne with the co-linear regions in barley[...]	GP00001183	VRN1 Q8L3W1	Physiology	8.6kb indel in first intron	Lolium perenne (species)	Lolium perenne (species)	VRN1	Lolium perenne (species)	Published - Accepted by Curator
VRN1	Flowering time	Cis-regulatory, Deletion	Triticum aestivum bread wheat - (species) D	Domesticated	Linkage Mapping	Trevaskis B; Bagnall DJ; Ellis MH ; et al. (2003) MADS box genes control vernalization-induced flowering in cereals.	GP00001184	VRN1 Q8L3W1	Physiology	Deletion	Triticum aestivum bread wheat - (species)	Triticum aestivum bread wheat - (species) D	VRN1	Triticum aestivum bread wheat - (species)	Published - Accepted by Curator
VRN1	Flowering time	Cis-regulatory, Unknown	Triticum monococcum (species)	Domesticated	Linkage Mapping	Yan L; Loukoianov A; Tranquilli G ; et al. (2003) Positional cloning of the wheat vernalization gene VRN1.	GP00001185	VRN1 Q8L3W1	Physiology	Not identified	Triticum monococcum (species)	Triticum monococcum (species)	VRN1	Triticum monococcum (species)	Published - Accepted by Curator
VRN1	Flowering time	Cis-regulatory, Insertion	Triticum turgidum (species) D	Domesticated	Linkage Mapping	Chu CG; Tan CT; Yu GT ; et al. (2011) A Novel Retrotransposon Inserted in the Dominant Vrn-B1 Allele Confers Spring Growth Habit in Tetrap[...]	GP00002105	VRN1 Q8L3W1	Physiology	5463-bp insertion in the 5'-UTR region of the Vrn-B1 allele. This insertion is a novel retrotransposon (designated as retrotrans_VRN), which is flanked by a 5-bp target site duplication and contains primer binding site and polypurine tract motifs; a 325-bp long terminal repeat and an open reading frame encoding 1231 amino acids. The insertion of retrotrans_VRN results in expression of Vrn-B1 without vernalization.	Triticum turgidum (species)	Triticum turgidum (species) D	VRN1	Triticum turgidum (species)	Published - Accepted by Curator
VTE3(1)	Vitamin-E synthesis	Cis-regulatory, Epigenetic Change	Solanum lycopersicum tomato - (species)	Domesticated	Linkage Mapping	Quadrana L; Almeida J; Asís R ; et al. (2014) Natural occurring epialleles determine vitamin E accumulation in tomato fruits.	GP00001684	VTE3 Q9LY74	Physiology		Solanum lycopersicum tomato - (species)	Solanum lycopersicum tomato - (species)	VTE3(1)	Solanum lycopersicum tomato - (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)	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 Migliaro D; Crespan Manna; Muñoz‐Organero G (2014 ) Structural dynamics at the berry colour locus in V itis vinifera L. somatic variants	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
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
Waxy /GBSS	Amylose content	Cis-regulatory, Deletion	Hordeum vulgare (species) D	Domesticated	Linkage Mapping	Domon E; Fuijita M; Ishikawa N (2002) The insertion/deletion polymorphisms in the waxy gene of barley genetic resources from East Asia.	GP00001197	waxy Q8L699	Physiology	403-bp deletion spanning from position –129 bp to position +274 relative to the deduced starting point of transcription in the barley waxy gene and	Hordeum vulgare (species)	Hordeum vulgare (species) D	Waxy /GBSS	Hordeum vulgare (species)	Published - Accepted by Curator
Waxy /GBSS	Amylose content	Cis-regulatory, Insertion	Setaria italica foxtail millet - (species) D	Domesticated	Candidate Gene	Kawase M; Fukunaga K; Kato K (2005) Diverse origins of waxy foxtail millet crops in East and Southeast Asia mediated by multiple transpo[...]	GP00001198	waxy Q8L699	Physiology	Transposon insertion TSI-11 (Intron 12)	Setaria italica foxtail millet - (species)	Setaria italica foxtail millet - (species) D	Waxy /GBSS	Setaria italica foxtail millet - (species)	Published - Accepted by Curator
Waxy /GBSS	Amylose content	Cis-regulatory, Insertion	Setaria italica foxtail millet - (species) D	Domesticated	Linkage Mapping	Kawase M; Fukunaga K; Kato K (2005) Diverse origins of waxy foxtail millet crops in East and Southeast Asia mediated by multiple transpo[...]	GP00001199	waxy Q8L699	Physiology	Transposon insertion TSI-2 (intron 1)	Setaria italica foxtail millet - (species)	Setaria italica foxtail millet - (species) D	Waxy /GBSS	Setaria italica foxtail millet - (species)	Published - Accepted by Curator
Waxy /GBSS	Amylose content	Cis-regulatory, Insertion	Setaria italica foxtail millet - (species) D	Domesticated	Candidate Gene	Kawase M; Fukunaga K; Kato K (2005) Diverse origins of waxy foxtail millet crops in East and Southeast Asia mediated by multiple transpo[...]	GP00001200	waxy Q8L699	Physiology	Transposon insertion TSI-10 (Intron 12)	Setaria italica foxtail millet - (species)	Setaria italica foxtail millet - (species) D	Waxy /GBSS	Setaria italica foxtail millet - (species)	Published - Accepted by Curator
Waxy /GBSS	Amylose content	Cis-regulatory, Deletion	Setaria italica foxtail millet - (species) D	Domesticated	Candidate Gene	Kawase M; Fukunaga K; Kato K (2005) Diverse origins of waxy foxtail millet crops in East and Southeast Asia mediated by multiple transpo[...]	GP00001203	waxy Q8L699	Physiology	2.4kb deletion (intron 1)	Setaria italica foxtail millet - (species)	Setaria italica foxtail millet - (species) D	Waxy /GBSS	Setaria italica foxtail millet - (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 Werner T; Koshikawa S; Williams TM (2010) Generation of a novel wing colour pattern by the Wingless morphogen.	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 Edayoshi M; Yamaguchi J; Fujiwara H (2015) Protruding structures on caterpillars are controlled by ectopic Wnt1 expression. Tong X; Han MJ; Lu K (2022) High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecologic[...]	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 Martin A; Papa R; Nadeau NJ (2012) Diversification of complex butterfly wing patterns by repeated regulatory evolution of a Wnt ligand.	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 Gallant JR; Imhoff VE; Martin A (2014) Ancient homology underlies adaptive mimetic diversity across butterflies.	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
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 Yeh SD; Liou SR; True JR (2006) Genetics of divergence in male wing pigmentation and courtship behavior between Drosophila elegans a[...]	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 (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
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 Inoue Y; Saga T; Aikawa T (2017) Complete fusion of a transposon and herpesvirus created the Teratorn mobile element in medaka fish.	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
ZmCCT	Flowering time	Cis-regulatory, Insertion	Zea mays (species) D	Domesticated	Linkage Mapping	Ducrocq S; Giauffret C; Madur D ; et al. (2009) Fine mapping and haplotype structure analysis of a major flowering time quantitative trait locus on [...] 2 Additional References Hung HY; Shannon LM; Tian F (2012) ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maiz[...] Yang Q; Li Z; Li W (2013) CACTA-like transposable element in ZmCCT attenuated photoperiod sensitivity and accelerated the post[...]	GP00001227	GHD7 E5RQA1	Physiology	insertion of a CACTA-like transposon into the promoter of ZmCCT. This insertion suppresses ZmCCT expression through methylation and reduces maize sensitivity to photoperiod.	Zea mays (species)	Zea mays (species) D	ZmCCT	Zea mays (species)	Published - Accepted by Curator
ZmNAC111	Drought tolerance	Cis-regulatory, Insertion N	Zea mays (species) D	Domesticated	Association Mapping	Yang Q; Li Z; Li W ; et al. (2013) CACTA-like transposable element in ZmCCT attenuated photoperiod sensitivity and accelerated the post[...]	GP00002084		Morphology; Physiology	MITE insertion within the ZmCCT promoter which results in histone hypermethylation and represses the expression of NAC; resulting in a higher drought tolerance. N	Zea mays (species)	Zea mays (species) D	ZmNAC111	Zea mays (species)	Published - Accepted by Curator
Zmr1	Xenobiotic resistance (fungicide) Melanin content	2 Mutations: Cis-regulatory	Zymoseptoria tritici (species)	Intraspecific	Linkage Mapping	Krishnan P; Meile L; Plissonneau C ; et al. (2018) Transposable element insertions shape gene regulation and melanin production in a fungal pathogen of[...]	GP00001715	CMR1 Q06F33	Physiology Physiology	2 mutations	Zymoseptoria tritici (species)	Zymoseptoria tritici (species)	Zmr1	Zymoseptoria tritici (species)	Published - Accepted by Curator
ZmVPP1	Drought tolerance	Cis-regulatory, Insertion	Zea mays (species)	Intraspecific	Association Mapping	Wang X; Wang H; Liu S ; et al. (2016) Genetic variation in ZmVPP1 contributes to drought tolerance in maize seedlings.	GP00001567	GRMZM2G170927 A0A172DSU8	Physiology	A 366-bp insertion in the promoter containing 3 MYB cis elements confers drought-inducible expression of ZmVPP1 in drought-tolerant genotypes	Zea mays (species)	Zea mays (species)	ZmVPP1	Zea mays (species)	Published - Accepted by Curator