Gephebase

Gephebase Search Results

This Summary Table shows only the major fields for each entry. If you are interested in other fields (gene synonyms, GO terms, molecular details of the mutation, comments, etc.), please export the .csv file, which contains the complete data for each entry. Please click on a GepheID if you want to see all information regarding a particular entry.

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Your research retrieved 71 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
ABCA1	Coloration (feathers) Cholesterol metabolism	Coding, SNP N	Gallus gallus chicken - (species) D	Domesticated	Linkage Mapping	Attie AD; Hamon Y; Brooks-Wilson AR ; et al. (2002) Identification and functional analysis of a naturally occurring E89K mutation in the ABCA1 gene of t[...]	GP00001682	Abca1 P41233	Morphology; Physiology Morphology; Physiology	amino acid substitution at a residue that is conserved in the ABCA1 gene between human; mouse; chicken; and Takifugu rubripes. Generation of a mouse ABCA1 protein with the mutation disrupts protein function. N	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	ABCA1	Gallus gallus chicken - (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
AHR	Xenobiotic resistance (dioxins; polycyclic aromatic hydrocarbons; TCDD)	2 Mutations: Coding SNP	Sterna hirundo hirundo (subspecies) D	Intergeneric or Higher	Candidate Gene	Karchner SI; Franks DG; Kennedy SW ; et al. (2006) The molecular basis for differential dioxin sensitivity in birds: role of the aryl hydrocarbon recep[...] 1 Additional References Head JA; Hahn ME; Kennedy SW (2008) Key amino acids in the aryl hydrocarbon receptor predict dioxin sensitivity in avian species.	GP00001811	Ahr P30561	Physiology	2 mutations	Gallus gallus chicken - (species)	Sterna hirundo hirundo (subspecies) D	AHR	Sterna hirundo hirundo (subspecies)	Published - Accepted by Curator
ameloblastin (AMBN)	Tooth absence (no enamel production)	Gene Loss, Deletion N	Gallus gallus chicken - (species) D	Intergeneric or Higher	Candidate Gene	Sire JY; Delgado SC; Girondot M (2008) Hen's teeth with enamel cap: from dream to impossibility.	GP00001934	AMBN Q9NP70	Physiology	synteny of the corresponding region - the gene has been likely deleted from the chicken genome as a consequence of intrachromosomal rearrangements which have probably occurred in the lineage that led to the last common ancestor of modern birds N	Paleosuchus palpebrosus Cuvier's dwarf caiman - (species)	Gallus gallus chicken - (species) D	ameloblastin (AMBN)	Gallus gallus chicken - (species)	Published - Accepted by Curator
amelogenin (AMEL)	Tooth absence (no enamel production)	3 Mutations: Coding N	Gallus gallus chicken - (species) D	Intergeneric or Higher	Candidate Gene	Sire JY; Delgado SC; Girondot M (2008) Hen's teeth with enamel cap: from dream to impossibility.	GP00001933	Amelx P63277	Physiology	3 mutations	Paleosuchus palpebrosus Cuvier's dwarf caiman - (species)	Gallus gallus chicken - (species) D	amelogenin (AMEL)	Gallus gallus chicken - (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
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
BTN1A1	Pathogen resistance (virus)	Coding, SNP N	Gallus gallus chicken - (species)	Domesticated	Linkage Mapping	Elleder D; Stepanets V; Melder DC ; et al. (2005) The receptor for the subgroup C avian sarcoma and leukosis viruses, Tvc, is related to mammalian but[...]	GP00002160	BTN1A1 Q13410	Physiology	g.808011C>A c.165C>A p.C55* N	Gallus gallus chicken - (species)	Gallus gallus chicken - (species)	BTN1A1	Gallus gallus chicken - (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
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
dentin sialophosphoprotein (DSPP)	Tooth absence (no enamel production)	Coding, Deletion N	Gallus gallus chicken - (species) D	Intergeneric or Higher	Candidate Gene	Sire JY; Delgado SC; Girondot M (2008) Hen's teeth with enamel cap: from dream to impossibility.	GP00001936	DSPP Q9NZW4	Physiology	synteny of the corresponding region - only the N-terminal region of DSPP is present in the genome - 1-bp deletion in exon one leading to a reading frame shift were this sequence to be translated N	Paleosuchus palpebrosus Cuvier's dwarf caiman - (species)	Gallus gallus chicken - (species) D	dentin sialophosphoprotein (DSPP)	Gallus gallus chicken - (species)	Published - Accepted by Curator
EDN3	Coloration (hyperpigmentation)	Gene Amplification, Complex Change	Gallus gallus chicken - (species) D	Domesticated	Linkage Mapping	Dorshorst B; Molin AM; Rubin CJ ; et al. (2011) A complex genomic rearrangement involving the endothelin 3 locus causes dermal hyperpigmentation in [...] 3 Additional References Johansson AM; Nelson RM (2015) Characterization of genetic diversity and gene mapping in two Swedish local chicken breeds. Han R; Yang P; Tian Y (2014) Identification and functional characterization of copy number variations in diverse chicken breeds. Dharmayanthi AB; Terai Y; Sulandari S (2017) The origin and evolution of fibromelanosis in domesticated chickens: Genomic comparison of Indonesia[...]	GP00000258	EDN3 P14138	Morphology	Large duplication	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	EDN3	Gallus gallus chicken - (species)	Published - Accepted by Curator
enamelin (ENAM)	Tooth absence (no enamel production)	Gene Loss, Deletion N	Gallus gallus chicken - (species) D	Intergeneric or Higher	Candidate Gene	Sire JY; Delgado SC; Girondot M (2008) Hen's teeth with enamel cap: from dream to impossibility.	GP00001935	ENAM Q9NRM1	Physiology	synteny of the corresponding region - the gene has been likely deleted from the chicken genome as a consequence of intrachromosomal rearrangements which have probably occurred in the lineage that led to the last common ancestor of modern birds N	Paleosuchus palpebrosus Cuvier's dwarf caiman - (species)	Gallus gallus chicken - (species) D	enamelin (ENAM)	Gallus gallus chicken - (species)	Published - Accepted by Curator
Endothelin receptor B2	Coloration (feathers)	Coding, SNP	Gallus gallus chicken - (species) D	Domesticated	Linkage Mapping	Kinoshita K; Akiyama T; Mizutani M ; et al. (2014) Endothelin receptor B2 (EDNRB2) is responsible for the tyrosinase-independent recessive white (mo(w)[...]	GP00001360	EDNRB2 W8VUK4	Morphology	c.1008G>T p.Cys244Phe	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	Endothelin receptor B2	Gallus gallus chicken - (species)	Published - Accepted by Curator
Endothelin receptor B2	Coloration (feathers)	Coding, SNP	Gallus gallus chicken - (species) D	Domesticated	Linkage Mapping	Kinoshita K; Akiyama T; Mizutani M ; et al. (2014) Endothelin receptor B2 (EDNRB2) is responsible for the tyrosinase-independent recessive white (mo(w)[...]	GP00001361	EDNRB2 W8VUK4	Morphology	c.G1272A p.Arg332His	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	Endothelin receptor B2	Gallus gallus chicken - (species)	Published - Accepted by Curator
EOMES (eomesodermin)	Bird head comb (reduced)	Gene Amplification, Insertion	Gallus gallus chicken - (species) D	Domesticated	Linkage Mapping	Dorshorst B; Harun-Or-Rashid M; Bagherpoor AJ ; et al. (2015) A genomic duplication is associated with ectopic eomesodermin expression in the embryonic chicken co[...]	GP00000271	Eomes O54839	Morphology	a 20 Kb tandem duplication containing several conserved putative regulatory elements located 200 Kb upstream of the eomesodermin gene	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	EOMES (eomesodermin)	Gallus gallus chicken - (species)	Published - Accepted by Curator
FGF20	Organ loss (feathers ; scales)	Coding, SNP N	Gallus gallus chicken - (species) D	Domesticated	Association Mapping	Wells KL; Hadad Y; Ben-Avraham D ; et al. (2012) Genome-wide SNP scan of pooled DNA reveals nonsense mutation in FGF20 in the scaleless line of feath[...]	GP00002171	FGF20 Q9NP95	Morphology	g.62878803A>T c.535A>T p.R179* N	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	FGF20	Gallus gallus chicken - (species)	Published - Accepted by Curator
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
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
Growth Hormone Receptor (GHR)	Body size (dwarfism)	Coding, Deletion N	Gallus gallus chicken - (species) D	Domesticated	Association Mapping	Agarwal SK; Cogburn LA; Burnside J (1994) Dysfunctional growth hormone receptor in a strain of sex-linked dwarf chicken: evidence for a mutati[...]	GP00002189	GHR P10912	Morphology	deletion of 1773 bp in the 3' end of the coding region N	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	Growth Hormone Receptor (GHR)	Gallus gallus chicken - (species)	Published - Accepted by Curator
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
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
HTR2C serotonin receptor	Immune response (complement activation)	Unknown, Unknown	Gallus gallus chicken - (species)	Domesticated	Association Mapping	Biscarini F; Bovenhuis H; van Arendonk JA ; et al. (2010) Across-line SNP association study of innate and adaptive immune response in laying hens.	GP00001595	HTR2C F1N989	Physiology	unknown	Gallus gallus chicken - (species)	Gallus gallus chicken - (species)	HTR2C serotonin receptor	Gallus gallus chicken - (species)	Published - Accepted by Curator
HTR3A serotonin receptor	Immune response (antibody titre)	Unknown, Unknown	Gallus gallus chicken - (species)	Domesticated	Association Mapping	Biscarini F; Bovenhuis H; van Arendonk JA ; et al. (2010) Across-line SNP association study of innate and adaptive immune response in laying hens.	GP00001596	HTR3A A0A1D5P8L2	Physiology	unknown	Gallus gallus chicken - (species)	Gallus gallus chicken - (species)	HTR3A serotonin receptor	Gallus gallus chicken - (species)	Published - Accepted by Curator
Indian hedgehog (IHH)	Limb size (legs)	Gene Loss, Deletion N	Gallus gallus chicken - (species) D	Domesticated	Association Mapping	Jin S; Zhu F; Wang Y ; et al. (2016) Deletion of Indian hedgehog gene causes dominant semi-lethal Creeper trait in chicken.	GP00002194	IHH Q98938	Morphology	11,896 bp large deletion region (chr7: 21,798,705-21,810,600) covering the entire Indian hedgehog (IHH) gene N	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	Indian hedgehog (IHH)	Gallus gallus chicken - (species)	Published - Accepted by Curator
Interleukin 10 (IL10)	Immune response (antibody titre and complement activation)	Unknown, Unknown	Gallus gallus chicken - (species)	Domesticated	Association Mapping	Biscarini F; Bovenhuis H; van Arendonk JA ; et al. (2010) Across-line SNP association study of innate and adaptive immune response in laying hens.	GP00001597	IL10 Q6A2H4	Physiology	unknown	Gallus gallus chicken - (species)	Gallus gallus chicken - (species)	Interleukin 10 (IL10)	Gallus gallus chicken - (species)	Published - Accepted by Curator
Interleukin 12B (IL12B)	Immune response (antibody titre)	Unknown, Unknown	Gallus gallus chicken - (species)	Domesticated	Association Mapping	Biscarini F; Bovenhuis H; van Arendonk JA ; et al. (2010) Across-line SNP association study of innate and adaptive immune response in laying hens.	GP00001594	IL-12B Q6X0K9	Physiology	unknown	Gallus gallus chicken - (species)	Gallus gallus chicken - (species)	Interleukin 12B (IL12B)	Gallus gallus chicken - (species)	Published - Accepted by Curator
Interleukin 17A (IL17A)	Immune response (antibody titre and complement activation)	Unknown, Unknown	Gallus gallus chicken - (species)	Domesticated	Association Mapping	Biscarini F; Bovenhuis H; van Arendonk JA ; et al. (2010) Across-line SNP association study of innate and adaptive immune response in laying hens.	GP00001593	IL17A B4ER12	Physiology	unknown	Gallus gallus chicken - (species)	Gallus gallus chicken - (species)	Interleukin 17A (IL17A)	Gallus gallus chicken - (species)	Published - Accepted by Curator
KRT6A	Feathers	Coding, Deletion	Gallus gallus chicken - (species) D	Domesticated	Linkage Mapping	Ng CS; Wu P; Foley J ; et al. (2012) The chicken frizzle feather is due to an α-keratin (KRT75) mutation that causes a defective rachis.	GP00000527	Krt6a P50446	Morphology	69bp deletion partially overlapping with exon 5	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	KRT6A	Gallus gallus chicken - (species)	Published - Accepted by Curator
KRT75L4	Feathers	Coding, Deletion	Gallus gallus chicken - (species) D	Domesticated	Association Mapping	Guo X; Li YQ; Wang MS ; et al. (2018) A parallel mechanism underlying frizzle in domestic chickens.	GP00002334	KRT75L4 A0A1L1RKR4	Morphology	15bp deletion resulting in loss of 5 conserved amino-acids	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	KRT75L4	Gallus gallus chicken - (species)	Published - Accepted by Curator
MC1R	Coloration (feathers; eyes)	Coding, SNP	Gallus gallus chicken - (species)	Domesticated	Linkage Mapping	Takeuchi S; Suzuki H; Yabuuchi M ; et al. (1996) A possible involvement of melanocortin 1-receptor in regulating feather color pigmentation in the ch[...] 2 Additional References Kerje S; Lind J; Schütz K (2003) Melanocortin 1-receptor (MC1R) mutations are associated with plumage colour in chicken. Dávila SG; Gil MG; Resino-Talaván P (2014) Association between polymorphism in the melanocortin 1 receptor gene and E locus plumage color pheno[...]	GP00000605	MC1R Q01726	Morphology	E92K; constitutive activation	Gallus gallus chicken - (species)	Gallus gallus chicken - (species)	MC1R	Gallus gallus chicken - (species)	Published - Accepted by Curator
MC1R	Coloration (feathers)	Coding, SNP	Gallus gallus chicken - (species)	Domesticated	Candidate Gene	Takeuchi S; Suzuki H; Yabuuchi M ; et al. (1996) A possible involvement of melanocortin 1-receptor in regulating feather color pigmentation in the ch[...]	GP00000606	MC1R Q01726	Morphology	C33W	Gallus gallus chicken - (species)	Gallus gallus chicken - (species)	MC1R	Gallus gallus chicken - (species)	Published - Accepted by Curator
MC1R	Coloration (feathers)	Coding, SNP	Gallus gallus chicken - (species)	Domesticated	Candidate Gene	Takeuchi S; Suzuki H; Yabuuchi M ; et al. (1996) A possible involvement of melanocortin 1-receptor in regulating feather color pigmentation in the ch[...]	GP00000607	MC1R Q01726	Morphology	D37G	Gallus gallus chicken - (species)	Gallus gallus chicken - (species)	MC1R	Gallus gallus chicken - (species)	Published - Accepted by Curator
MC1R	Coloration (feathers)	Coding, SNP	Gallus gallus chicken - (species)	Domesticated	Candidate Gene	Takeuchi S; Suzuki H; Yabuuchi M ; et al. (1996) A possible involvement of melanocortin 1-receptor in regulating feather color pigmentation in the ch[...]	GP00000608	MC1R Q01726	Morphology	L244P	Gallus gallus chicken - (species)	Gallus gallus chicken - (species)	MC1R	Gallus gallus chicken - (species)	Published - Accepted by Curator
MC1R	Coloration (feathers)	Coding, SNP	Gallus gallus chicken - (species)	Domesticated	Candidate Gene	Kerje S; Lind J; Schütz K ; et al. (2003) Melanocortin 1-receptor (MC1R) mutations are associated with plumage colour in chicken. 1 Additional References Dávila SG; Gil MG; Resino-Talaván P (2014) Association between polymorphism in the melanocortin 1 receptor gene and E locus plumage color pheno[...]	GP00000609	MC1R Q01726	Morphology	H215P	Gallus gallus chicken - (species)	Gallus gallus chicken - (species)	MC1R	Gallus gallus chicken - (species)	Published - Accepted by Curator
MC1R	Coloration (feathers; eyes)	Coding, SNP	Gallus gallus chicken - (species)	Domesticated	Candidate Gene	Dávila SG; Gil MG; Resino-Talaván P ; et al. (2014) Association between polymorphism in the melanocortin 1 receptor gene and E locus plumage color pheno[...]	GP00002390	MC1R Q01726	Morphology	the Arg213Cys mutation may be the cause of the loss or the decrease of function of the receptor to produce eumelanin	Gallus gallus chicken - (species)	Gallus gallus chicken - (species)	MC1R	Gallus gallus chicken - (species)	Published - Accepted by Curator
Melanophilin (MLPH)	Coloration (coat)	Coding, SNP	Gallus gallus chicken - (species) D	Domesticated	Candidate Gene	Vaez M; Follett SA; Bed'hom B ; et al. (2008) A single point-mutation within the melanophilin gene causes the lavender plumage colour dilution phe[...]	GP00000645	Mlph Q91V27	Morphology	c.103C>T p.R35W	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	Melanophilin (MLPH)	Gallus gallus chicken - (species)	Published - Accepted by Curator
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
MNR2	Bird head comb Fertility (sperm motility)	Gene Amplification, Inversion	Gallus gallus chicken - (species) D	Domesticated	Linkage Mapping	Imsland F; Feng C; Boije H ; et al. (2012) The Rose-comb mutation in chickens constitutes a structural rearrangement causing both altered comb [...]	GP00000675	MNR2 Q9YHY8	Morphology Physiology	7.4Mb inversion (and secondary structural re-arrangement in some individuals)	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	MNR2	Gallus gallus chicken - (species)	Published - Accepted by Curator
MX1	Pathogen resistance (myxovirus)	Coding, SNP	Gallus gallus chicken - (species) D	Intraspecific		Ko JH; Jin HK; Asano A ; et al. (2002) Polymorphisms and the differential antiviral activity of the chicken Mx gene.	GP00002249	MX1 P20591	Physiology	c.1892G>A p.S631N	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	MX1	Gallus gallus chicken - (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
PMEL17	Coloration (feathers)	Coding, Deletion	Gallus gallus chicken - (species) D	Domesticated	Candidate Gene	Kerje S; Sharma P; Gunnarsson U ; et al. (2004) The Dominant white, Dun and Smoky color variants in chicken are associated with insertion/deletion p[...]	GP00000911	PMEL Q98917	Morphology	deletion of amino acids 731-735	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	PMEL17	Gallus gallus chicken - (species)	Published - Accepted by Curator
PMEL17	Coloration (feathers)	Coding, Deletion	Gallus gallus chicken - (species) D	Domesticated	Candidate Gene	Kerje S; Sharma P; Gunnarsson U ; et al. (2004) The Dominant white, Dun and Smoky color variants in chicken are associated with insertion/deletion p[...]	GP00000912	PMEL Q98917	Morphology	deletion of amino acids 280-284	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	PMEL17	Gallus gallus chicken - (species)	Published - Accepted by Curator
PMEL17	Coloration (feathers)	Coding, Insertion	Gallus gallus chicken - (species) D	Domesticated	Linkage Mapping	Kerje S; Sharma P; Gunnarsson U ; et al. (2004) The Dominant white, Dun and Smoky color variants in chicken are associated with insertion/deletion p[...]	GP00000913	PMEL Q98917	Morphology	insertion of amino acid 723-725 due to a 9bp-insert in exon 10	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	PMEL17	Gallus gallus chicken - (species)	Published - Accepted by Curator
Prolactin receptor	Feather (slow-feathering ; delay)	Other, Insertion	Gallus gallus chicken - (species) D	Domesticated	Linkage Mapping	Elferink MG; Vallée AA; Jungerius AP ; et al. (2008) Partial duplication of the PRLR and SPEF2 genes at the late feathering locus in chicken. 1 Additional References Takenouchi A; Toshishige M; Ito N (2018) Endogenous viral gene ev21 is not responsible for the expression of late feathering in chickens.	GP00002280	PRLR P16471	Morphology	tandem duplication of 176324 basepairs resulting in a partially duplicated PRLR (dPRLR) gene nearly identical to the original PRLR ; except for its lack of a 149-amino acid C-terminal tail - which may titrate PRL ligands and act as a dominant-negative receptor	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	Prolactin receptor	Gallus gallus chicken - (species)	Published - Accepted by Curator
RB1	Body size (weight) Body size (bone length)	Unknown, Unknown	Gallus gallus chicken - (species)	Domesticated	Linkage Mapping	Zhang H; Liu SH; Zhang Q ; et al. (2011) Fine-mapping of quantitative trait loci for body weight and bone traits and positional cloning of th[...]	GP00000957		Morphology Morphology	unknown	Gallus gallus chicken - (species)	Gallus gallus chicken - (species)	RB1	Gallus gallus chicken - (species)	Published - Accepted by Curator
SCN9A (Nav1.7)	Xenobiotic resistance (TTX)	Coding, SNP	Chrysemys picta painted turtle - (species) D	Intergeneric or Higher	Candidate Gene	McGlothlin JW; Kobiela ME; Feldman CR ; et al. (2016) Historical Contingency in a Multigene Family Facilitates Adaptive Evolution of Toxin Resistance.	GP00001645	SCN9A Q15858	Physiology	D1393P (most probably E>P) in DIII domain (not tested)	Gallus gallus chicken - (species)	Chrysemys picta painted turtle - (species) D	SCN9A (Nav1.7)	Chrysemys picta painted turtle - (species)	Published - Accepted by Curator
SCN9A (Nav1.7)	Xenobiotic resistance (TTX)	Coding, SNP	Chrysemys picta painted turtle - (species) D	Interspecific	Candidate Gene	McGlothlin JW; Kobiela ME; Feldman CR ; et al. (2016) Historical Contingency in a Multigene Family Facilitates Adaptive Evolution of Toxin Resistance.	GP00001647	SCN9A Q15858	Physiology	A1681G in DIV domain (1.5x resistance)	Gallus gallus chicken - (species)	Chrysemys picta painted turtle - (species) D	SCN9A (Nav1.7)	Chrysemys picta painted turtle - (species)	Published - Accepted by Curator
SLC45A2=MATP	Coloration (feathers)	Coding, Deletion N	Gallus gallus chicken - (species) D	Domesticated	Linkage Mapping	Gunnarsson U; Hellström AR; Tixier-Boichard M ; et al. (2007) Mutations in SLC45A2 cause plumage color variation in chicken and Japanese quail.	GP00001059	SLC45A2 Q9UMX9	Morphology	1bp deletion at codon 36; resulting in frameshift and a premature stop codon in exon 1; the corresponding mRNA appears to be degraded by Nonsense-mediated mRNA decay. N	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	SLC45A2=MATP	Gallus gallus chicken - (species)	Published - Accepted by Curator
SLC45A2=MATP	Coloration (feathers)	Coding, SNP N	Gallus gallus chicken - (species) D	Domesticated	Association Mapping	Gunnarsson U; Hellström AR; Tixier-Boichard M ; et al. (2007) Mutations in SLC45A2 cause plumage color variation in chicken and Japanese quail.	GP00002294	SLC45A2 Q9UMX9	Morphology	c.1039C>A p.L347M N	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	SLC45A2=MATP	Gallus gallus chicken - (species)	Published - Accepted by Curator
SLC45A2=MATP	Coloration (feathers)	Coding, SNP N	Gallus gallus chicken - (species) D	Domesticated	Association Mapping	Gunnarsson U; Hellström AR; Tixier-Boichard M ; et al. (2007) Mutations in SLC45A2 cause plumage color variation in chicken and Japanese quail.	GP00002295	SLC45A2 Q9UMX9	Morphology	c.830A>G p.Y277C N	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	SLC45A2=MATP	Gallus gallus chicken - (species)	Published - Accepted by Curator
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
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
TAS1R1	Taste sensitivity (sugar)	Coding, Unknown	Calypte anna Anna's hummingbird - (species) D	Interspecific	Candidate Gene	Baldwin MW; Toda Y; Nakagita T ; et al. (2014) Sensory biology. Evolution of sweet taste perception in hummingbirds by transformation of the ancest[...]	GP00001307	T1R1 A0A088DBT6	Physiology	unknown	Gallus gallus chicken - (species)	Calypte anna Anna's hummingbird - (species) D	TAS1R1	Calypte anna Anna's hummingbird - (species)	Published - Accepted by Curator
TAS1R3	Taste sensitivity (sugar)	Coding, SNP	Calypte anna Anna's hummingbird - (species) D	Interspecific	Candidate Gene	Baldwin MW; Toda Y; Nakagita T ; et al. (2014) Sensory biology. Evolution of sweet taste perception in hummingbirds by transformation of the ancest[...]	GP00001306	T1R3 A0A088DCH0	Physiology	19 nonconsecutive amino acids confer sugar responsiveness and they are confined to three different regions of the protein - change(s) in all 3 regions are required for the acquisition of sugar binding- The exact effect of each single amino acid change has not been tested	Gallus gallus chicken - (species)	Calypte anna Anna's hummingbird - (species) D	TAS1R3	Calypte anna Anna's hummingbird - (species)	Published - Accepted by Curator
Thyroid stimulating hormone receptor	Metabolism	Coding, SNP	Gallus gallus chicken - (species)	Domesticated	Association Mapping	Rubin CJ; Zody MC; Eriksson J ; et al. (2010) Whole-genome resequencing reveals loci under selection during chicken domestication. 1 Additional References Girdland Flink L; Allen R; Barnett R (2014) Establishing the validity of domestication genes using DNA from ancient chickens.	GP00001127	TSHR P16473	Physiology	Gly558Arg	Gallus gallus chicken - (species)	Gallus gallus chicken - (species)	Thyroid stimulating hormone receptor	Gallus gallus chicken - (species)	Published - Accepted by Curator
TMEM263	Body size (dwarfism)	Coding, SNP N	Gallus gallus chicken - (species) D	Domesticated	Linkage Mapping	Wu Z; Derks MFL; Dibbits B ; et al. (2018) A Novel Loss-of-Function Variant in Transmembrane Protein 263 (TMEM263) of Autosomal Dwarfism in Chi[...]	GP00002161		Physiology	g.53688583C>T c.433G>A p.Trp59∗ N	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	TMEM263	Gallus gallus chicken - (species)	Published - Accepted by Curator
Tva	Pathogen resistance (virus)	Coding, SNP	Gallus gallus chicken - (species) D	Intraspecific	Candidate Gene	Elleder D; Melder DC; Trejbalova K ; et al. (2004) Two different molecular defects in the Tva receptor gene explain the resistance of two tvar lines of[...]	GP00002256	tva Q6JBY7	Physiology	c.120C>G p.C40W	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	Tva	Gallus gallus chicken - (species)	Published - Accepted by Curator
Tva	Pathogen resistance (virus)	Coding, Insertion N	Gallus gallus chicken - (species) D	Intraspecific	Candidate Gene	Elleder D; Melder DC; Trejbalova K ; et al. (2004) Two different molecular defects in the Tva receptor gene explain the resistance of two tvar lines of[...]	GP00002257	tva Q6JBY7	Physiology	c.48insCTCG N	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	Tva	Gallus gallus chicken - (species)	Published - Accepted by Curator
Tva	Pathogen resistance (virus)	Coding, Deletion N	Gallus gallus chicken - (species) D	Intraspecific	Candidate Gene	Chen W; Liu Y; Li H ; et al. (2015) Intronic deletions of tva receptor gene decrease the susceptibility to infection by avian sarcoma an[...]	GP00002258	tva Q6JBY7	Physiology	c.502_511delCGCTCACCCC N	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	Tva	Gallus gallus chicken - (species)	Published - Accepted by Curator
Tva	Pathogen resistance (virus)	Coding, Deletion N	Gallus gallus chicken - (species) D	Intraspecific	Candidate Gene	Chen W; Liu Y; Li H ; et al. (2015) Intronic deletions of tva receptor gene decrease the susceptibility to infection by avian sarcoma an[...]	GP00002259	tva Q6JBY7	Physiology	c.502_516delCGCTCACCCCGCCCC N	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	Tva	Gallus gallus chicken - (species)	Published - Accepted by Curator
Tva	Pathogen resistance (virus)	Coding, Deletion N	Gallus gallus chicken - (species) D	Intraspecific	Candidate Gene	Reinišová M; Plachý J; Trejbalová K ; et al. (2012) Intronic deletions that disrupt mRNA splicing of the tva receptor gene result in decreased susceptib[...]	GP00002260	tva Q6JBY7	Physiology	c.506-515del10 ; splicing N	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	Tva	Gallus gallus chicken - (species)	Published - Accepted by Curator
Tva	Pathogen resistance (virus)	Coding, Deletion N	Gallus gallus chicken - (species) D	Intraspecific	Candidate Gene	Reinišová M; Plachý J; Trejbalová K ; et al. (2012) Intronic deletions that disrupt mRNA splicing of the tva receptor gene result in decreased susceptib[...]	GP00002261	tva Q6JBY7	Physiology	c.507-511del5 ; splicing N	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	Tva	Gallus gallus chicken - (species)	Published - Accepted by Curator
tyrosinase (TYR)	Coloration (feathers)	Coding, Deletion	Gallus gallus chicken - (species) D	Domesticated	Candidate Gene	Tobita-Teramoto T; Jang GY; Kino K ; et al. (2000) Autosomal albino chicken mutation (ca/ca) deletes hexanucleotide (-deltaGACTGG817) at a copper-bindi[...]	GP00002308	Tyr P11344	Morphology	c.817_822del6 p.237-238delDW	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	tyrosinase (TYR)	Gallus gallus chicken - (species)	Published - Accepted by Curator
tyrosinase (TYR)	Coloration (feathers)	Coding, Insertion	Gallus gallus chicken - (species) D	Domesticated	Candidate Gene	Chang CM; Coville JL; Coquerelle G ; et al. (2006) Complete association between a retroviral insertion in the tyrosinase gene and the recessive white m[...]	GP00002309	Tyr P11344	Morphology	insertion of a complete avian retroviral sequence in intron 4 causes aberrant transcripts lacking exon 5	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	tyrosinase (TYR)	Gallus gallus chicken - (species)	Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)	Coloration (feathers)	Coding, SNP	Gallus gallus chicken - (species)	Domesticated	Linkage Mapping	Li J; Bed'hom B; Marthey S ; et al. (2019) A missense mutation in TYRP1 causes the chocolate plumage color in chicken and alters melanosome str[...]	GP00002126	Tyrp1 P07147	Morphology	g.30830367C>A c.640C>A p.His214Asn	Gallus gallus chicken - (species)	Gallus gallus chicken - (species)	tyrosinase-related protein 1 (TYRP1)	Gallus gallus chicken - (species)	Published - Accepted by Curator