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.

Advanced Search

Field

Term

Summary Table

Your research retrieved 14 results.

Summary
Others

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
EphB2	Feathers (crest morphology)	Coding, SNP	Columba livia rock pigeon - (species) D	Domesticated	Association Mapping	Shapiro MD; Kronenberg Z; Li C ; et al. (2013) Genomic diversity and evolution of the head crest in the rock pigeon. 1 Additional References Vickrey AI; Domyan ET; Horvath MP (2015) Convergent Evolution of Head Crests in Two Domesticated Columbids Is Associated with Different Misse[...]	GP00000275	EPHB2 P28693	Morphology	Arg758Cys (C>T) p.R758C	Columba livia rock pigeon - (species)	Columba livia rock pigeon - (species) D	EphB2	Columba livia rock pigeon - (species)	Published - Accepted by Curator
MC1R	Coloration (feathers)	Coding, SNP	Columba livia rock pigeon - (species)	Domesticated	Candidate Gene	Guernsey MW; Ritscher L; Miller MA ; et al. (2013) A Val85Met mutation in melanocortin-1 receptor is associated with reductions in eumelanic pigmentati[...]	GP00000601	MC1R Q01726	Morphology	Val85Met (G253A)	Columba livia rock pigeon - (species)	Columba livia rock pigeon - (species)	MC1R	Columba livia rock pigeon - (species)	Published - Accepted by Curator
Mlana	Coloration (feathers ; white-spotting)	Gene Amplification, Complex Change	Columba livia rock pigeon - (species) D	Domesticated	Association Mapping	Bruders R; Van Hollebeke H; Osborne EJ ; et al. (2020) A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Col[...]	GP00002342	MLANA Q16655	Morphology	CNV with 7 copies of the outer 77-kb segment and 14 copies of the inner 25-kb segment in the genomes of female (ZStW) Almond pigeons	Columba livia rock pigeon - (species)	Columba livia rock pigeon - (species) D	Mlana	Columba livia rock pigeon - (species)	Published - Accepted by Curator
ndp (norrin)	Coloration (plumage)	Coding, SNP N	Columba livia rock pigeon - (species) D	Domesticated	Association Mapping	Vickrey AI; Bruders R; Kronenberg Z ; et al. (2018) Introgression of regulatory alleles and a missense coding mutation drive plumage pattern diversity i[...]	GP00002250	Ndp P48744	Morphology	Start-codon change predicted to truncate the amino terminus of the NDP protein by 11 amino acids thereby disrupting the 24-amino acid signal peptide sequence N	Columba livia rock pigeon - (species)	Columba livia rock pigeon - (species) D	ndp (norrin)	Columba livia rock pigeon - (species)	Published - Accepted by Curator
ndp (norrin)	Coloration (plumage)	Cis-regulatory, Insertion N	Columba livia rock pigeon - (species) D Columba guinea speckled pigeon - (species) D	Intraspecific	Association Mapping	Vickrey AI; Bruders R; Kronenberg Z ; et al. (2018) Introgression of regulatory alleles and a missense coding mutation drive plumage pattern diversity i[...]	GP00002251	Ndp P48744	Morphology	CNV driven by tandem repeats with one (bar) two (checker) or four (T-checker) copies per chromosome between approximative positions 1790000 and 1805600 N	Columba livia rock pigeon - (species)	Columba livia rock pigeon - (species) D Columba guinea speckled pigeon - (species) D	ndp (norrin)	Columba livia rock pigeon - (species) Columba guinea speckled pigeon - (species)	Published - Accepted by Curator
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
slc2a11b	Coloration (eyes)	Coding, SNP N	Columba livia rock pigeon - (species) D	Domesticated	Linkage Mapping	Maclary ET; Phillips B; Wauer R ; et al. (2021) Two Genomic Loci Control Three Eye Colors in the Domestic Pigeon (Columba livia). 2 Additional References Si S; Xu X; Zhuang Y (2021) The genetics and evolution of eye color in domestic pigeons (Columba livia). Andrade P; Gazda MA; Araújo PM (2021) Molecular parallelisms between pigmentation in the avian iris and the integument of ectothermic vert[...]	GP00002367	slc2a11b F6P601	Morphology	"The premature stop codon in pearl-eyed pigeons falls in exon 3 of SLC2A11B, and is predicted to severely truncate the resulting protein from 504 to 57 amino acids." "Based on genotypes at the two coding SNPs in the pearl eye haplotype, we found that gene expression in embryo head samples only shows changes associated with the pearl eye haplotype in SLC2A11B, and not in any other genes within 15 kb of the pearl eye haplotype, further supporting SLC2A11B as the primary candidate for the pearl eye phenotype (supplementary fig. S3A, Supplementary Material online). Embryo heads homozygous for the pearl allele show a significant reduction in SLC2A11B expression (P = 3.94 × 10−6, two-tailed t-test; supplementary fig. S3B, Supplementary Material online). Analysis of read distribution within the SLC2A11B gene shows a decrease in spliced reads specifically within the first three annotated exons, suggesting that alternative splicing or nonsense-mediated decay may be occurring (supplementary fig. S3D, Supplementary Material online)." N	Columba livia rock pigeon - (species)	Columba livia rock pigeon - (species) D	slc2a11b	Columba livia rock pigeon - (species)	Published - Accepted by Curator
SLC45A2=MATP	Coloration (feathers)	Coding, SNP	Columba livia rock pigeon - (species) D	Domesticated	Linkage Mapping	Domyan ET; Guernsey MW; Kronenberg Z ; et al. (2014) Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon.	GP00001062	SLC45A2 Q9UMX9	Morphology	His341Arg	Columba livia rock pigeon - (species)	Columba livia rock pigeon - (species) D	SLC45A2=MATP	Columba livia rock pigeon - (species)	Published - Accepted by Curator
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
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
tyrosinase-related protein 1 (TYRP1)	Coloration (feathers)	Coding, SNP	Columba livia rock pigeon - (species) D	Domesticated	Linkage Mapping	Domyan ET; Guernsey MW; Kronenberg Z ; et al. (2014) Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon.	GP00001149	Tyrp1 P07147	Morphology	Ala23Pro	Columba livia rock pigeon - (species)	Columba livia rock pigeon - (species) D	tyrosinase-related protein 1 (TYRP1)	Columba livia rock pigeon - (species)	Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)	Coloration (feathers)	Coding, SNP N	Columba livia rock pigeon - (species) D	Domesticated	Linkage Mapping	Domyan ET; Guernsey MW; Kronenberg Z ; et al. (2014) Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon.	GP00001150	Tyrp1 P07147	Morphology	Arg72* N	Columba livia rock pigeon - (species)	Columba livia rock pigeon - (species) D	tyrosinase-related protein 1 (TYRP1)	Columba livia rock pigeon - (species)	Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)	Coloration (feathers)	Coding, Deletion N	Columba livia rock pigeon - (species) D	Domesticated	Linkage Mapping	Domyan ET; Guernsey MW; Kronenberg Z ; et al. (2014) Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon.	GP00001151	Tyrp1 P07147	Morphology	7-bp deletion 411-418del resulting in null allele N	Columba livia rock pigeon - (species)	Columba livia rock pigeon - (species) D	tyrosinase-related protein 1 (TYRP1)	Columba livia rock pigeon - (species)	Published - Accepted by Curator