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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	Date of Sent Email
ABCA2	Xenobiotic resistance (insecticide; Bt Cry2Ab toxin)	Coding, Insertion N	Helicoverpa armigera cotton bollworm - (species) D	Intraspecific	Candidate Gene	Tay WT; Mahon RJ; Heckel DG ; et al. (2015) Insect Resistance to Bacillus thuringiensis Toxin Cry2Ab Is Conferred by Mutations in an ABC Transpo[...]	GP00000004	ABCA2 A0A0S0G7V0	Physiology	5bp (GAATA) nucleotide duplication inducing a frameshift N	Helicoverpa armigera cotton bollworm - (species)	Helicoverpa armigera cotton bollworm - (species) D	ABCA2	Helicoverpa armigera cotton bollworm - (species)	Published - Accepted by Curator
ABCA2	Xenobiotic resistance (insecticide; Bt Cry2Ab toxin)	Coding, Insertion N	Trichoplusia ni cabbage looper - (species) D	Intraspecific	Linkage Mapping	Yang X; Chen W; Song X ; et al. (2019) Mutation of ABC transporter ABCA2 confers resistance to Bt toxin Cry2Ab in Trichoplusia ni.	GP00002054	ABCA2 A0A0S0G7V0	Physiology	insertion of a transposon Tntransib (2581 bp) in ABCA2 which changes splicing sites in the transcript and lead to an indel in the coding region: change of 1551VETLAHALGFLRHLDKR1567 into 1551AHWGK- LYGSNTQN1563 N	Trichoplusia ni cabbage looper - (species)	Trichoplusia ni cabbage looper - (species) D	ABCA2	Trichoplusia ni cabbage looper - (species)	Published - Accepted by Curator
ABCA2	Xenobiotic resistance (insecticide; Bt Cry2Ab toxin)	Coding, Insertion N	Pectinophora gossypiella pink bollworm - (species) D	Intraspecific	Candidate Gene	Mathew LG; Ponnuraj J; Mallappa B ; et al. (2018) ABC transporter mis-splicing associated with resistance to Bt toxin Cry2Ab in laboratory- and field-[...]	GP00002057	ABCA2 A0A0S0G7V0	Physiology	loss of exon 6 caused by alternative splicing N	Pectinophora gossypiella pink bollworm - (species)	Pectinophora gossypiella pink bollworm - (species) D	ABCA2	Pectinophora gossypiella pink bollworm - (species)	Published - Accepted by Curator
ABCA2	Xenobiotic resistance (insecticide; Bt Cry2Ab)	Coding, Insertion N	Trichoplusia ni cabbage looper - (species) D	Intraspecific	Linkage Mapping	Yang X; Chen W; Song X ; et al. (2019) Mutation of ABC transporter ABCA2 confers resistance to Bt toxin Cry2Ab in Trichoplusia ni.	GP00002467	ABCA2 Q9BZC7	Physiology	insertion of a 2581-bp transposon Tntransib in ABCA2. This insertion disrupts splicing sites and leads to indels in the protein sequence. CRISPR ABCA2 mutants are highly resistant to Cry2Ab. N	Trichoplusia ni cabbage looper - (species)	Trichoplusia ni cabbage looper - (species) D	ABCA2	Trichoplusia ni cabbage looper - (species)	Published - Accepted by Curator
ABCB1	Plant size (dwarfism)	Coding, Insertion N	Sorghum bicolor sorghum - (species)	Domesticated	Candidate Gene	Multani DS; Briggs SP; Chamberlin MA ; et al. (2003) Loss of an MDR transporter in compact stalks of maize br2 and sorghum dw3 mutants.	GP00000007	ABCB1 Q9ZR72	Morphology	882bp direct duplication in exon 5 of the dw3 allele driving loss-of-function N	Sorghum bicolor sorghum - (species)	Sorghum bicolor sorghum - (species)	ABCB1	Sorghum bicolor sorghum - (species)	Published - Accepted by Curator
ABCB4	Xenobiotic resistance (insecticide)	Gene Amplification, Insertion	Aedes aegypti yellow fever mosquito - (species) D	Intraspecific	Candidate Gene	Bariami V; Jones CM; Poupardin R ; et al. (2012) Gene amplification, ABC transporters and cytochrome P450s: unraveling the molecular basis of pyrethr[...]	GP00002607	Abcb4 P21440	Physiology	ABCB4 gene amplified about 6–7 times	Aedes aegypti yellow fever mosquito - (species)	Aedes aegypti yellow fever mosquito - (species) D	ABCB4	Aedes aegypti yellow fever mosquito - (species)	Published - Accepted by Curator
ABCC2	Xenobiotic resistance (insecticide)	Coding, Insertion	Bombyx mori domestic silkworm - (species) D	Domesticated	Linkage Mapping	Atsumi S; Miyamoto K; Yamamoto K ; et al. (2012) Single amino acid mutation in an ATP-binding cassette transporter gene causes resistance to Bt toxin[...]	GP00000011	ABCC2 A0A0E3ZDK3	Physiology	1a.a. insertion at codon 234 (Tyr)	Bombyx mori domestic silkworm - (species)	Bombyx mori domestic silkworm - (species) D	ABCC2	Bombyx mori domestic silkworm - (species)	Published - Accepted by Curator
ABO histo blood group glycosyltransferase	ABO antigen blood type	Coding, Insertion N	Homo sapiens human - (species) D	Intraspecific	Candidate Gene	Hosseini-Maaf B; Irshaid NM; Hellberg A ; et al. (2005) New and unusual O alleles at the ABO locus are implicated in unexpected blood group phenotypes. 1 Additional References Yazer MH; Hosseini-Maaf B; Olsson ML (2008) Blood grouping discrepancies between ABO genotype and phenotype caused by O alleles.	GP00000021	ABO P16442	Physiology	1bp insertion resulting in premature stop codon N	Homo sapiens human - (species)	Homo sapiens human - (species) D	ABO histo blood group glycosyltransferase	Homo sapiens human - (species)	Published - Accepted by Curator
Acetylcholinesterase (Ace-1)	Xenobiotic resistance (insecticide)	3 Mutations:	Aphis gossypii cotton aphid - (species)	Intraspecific	Candidate Gene	Shang Q; Pan Y; Fang K ; et al. (2014) Extensive Ace2 duplication and multiple mutations on Ace1 and Ace2 are related with high level of or[...] 4 Additional References Andrews MC; Callaghan A; Field LM (2004) Identification of mutations conferring insecticide-insensitive AChE in the cotton-melon aphid, Aphis[...] Carletto J; Martin T; Vanlerberghe-Masutti F (2010) Insecticide resistance traits differ among and within host races in Aphis gossypii. Benting J; Nauen R (2004) Biochemical evidence that an S431F mutation in acetylcholinesterase-1 of Aphis gossypii mediates res[...] Toda S; Komazaki S; Tomita T (2004) Two amino acid substitutions in acetylcholinesterase associated with pirimicarb and organophosphorou[...]	GP00000036	Ace P07140	Physiology	3 mutations	Aphis gossypii cotton aphid - (species)	Aphis gossypii cotton aphid - (species)	Acetylcholinesterase (Ace-1)	Aphis gossypii cotton aphid - (species)	Published - Accepted by Curator
Acetylcholinesterase (Ace-1)	Xenobiotic resistance (insecticide)	Gene Amplification, Insertion	Anopheles gambiae African malaria mosquito - (species) D	Intraspecific	Candidate Gene	Assogba BS; Milesi P; Djogbénou LS ; et al. (2016) The ace-1 Locus Is Amplified in All Resistant Anopheles gambiae Mosquitoes: Fitness Consequences of [...] 1 Additional References Assogba BS; Djogbénou LS; Milesi P (2015) An ace-1 gene duplication resorbs the fitness cost associated with resistance in Anopheles gambiae, [...]	GP00001372	Ace P07140	Physiology	Strict tandem duplication of 203kb encompassing 12 genes ; ace1 heterogeneous gene duplication (susceptible G119 and resistant S119 copies)	Anopheles gambiae African malaria mosquito - (species)	Anopheles gambiae African malaria mosquito - (species) D	Acetylcholinesterase (Ace-1)	Anopheles gambiae African malaria mosquito - (species)	Published - Accepted by Curator
Acetylcholinesterase (Ace-1)	Xenobiotic resistance (insecticide)	Gene Amplification, Insertion	Anopheles gambiae African malaria mosquito - (species)	Intraspecific	Candidate Gene	Assogba BS; Milesi P; Djogbénou LS ; et al. (2016) The ace-1 Locus Is Amplified in All Resistant Anopheles gambiae Mosquitoes: Fitness Consequences of [...]	GP00001373	Ace P07140	Physiology	Strict tandem 3 times duplication of 203kb encompassing 12 genes with partial internal deletion of 97kb in the third copy - ace1 homogeneous gene duplications (all 3 copies S119 resistant)	Anopheles gambiae African malaria mosquito - (species)	Anopheles gambiae African malaria mosquito - (species)	Acetylcholinesterase (Ace-1)	Anopheles gambiae African malaria mosquito - (species)	Published - Accepted by Curator
Acetylcholinesterase (Ace-1)	Xenobiotic resistance (insecticide)	Gene Amplification, Insertion	Anopheles gambiae African malaria mosquito - (species) D	Intraspecific	Candidate Gene	Assogba BS; Milesi P; Djogbénou LS ; et al. (2016) The ace-1 Locus Is Amplified in All Resistant Anopheles gambiae Mosquitoes: Fitness Consequences of [...]	GP00001374	Ace P07140	Physiology	Strict tandem 5 times duplication of 203kb encompassing 12 genes - ace1 homogeneous gene duplications (all 5 copies S119 resistant)	Anopheles gambiae African malaria mosquito - (species)	Anopheles gambiae African malaria mosquito - (species) D	Acetylcholinesterase (Ace-1)	Anopheles gambiae African malaria mosquito - (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
aggrecan	Body size (dwarfism)	Coding, Insertion N	Bos taurus cattle - (species) D	Domesticated	Linkage Mapping	Cavanagh JA; Tammen I; Windsor PA ; et al. (2007) Bulldog dwarfism in Dexter cattle is caused by mutations in ACAN.	GP00002140	ACAN P16112	Morphology	2266_2267insGGCA mutation introduces a frameshift and a premature termination codon into exon 11; the frameshift occurs at amino acid position 756 ; the termination codon occurs at position 914 compared to the normal aggrecan product of 2327 amino acids N	Bos taurus cattle - (species)	Bos taurus cattle - (species) D	aggrecan	Bos taurus cattle - (species)	Published - Accepted by Curator
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)	Gene Amplification, Insertion	Coturnix japonica Japanese quail - (species) D	Domesticated	Linkage Mapping	Robic A; Morisson M; Leroux S ; et al. (2019) Two new structural mutations in the 5' region of the ASIP gene cause diluted feather color phenotype[...]	GP00001973	Asip Q03288	Morphology	71-kb tandem duplication that comprises one unchanged copy of ASIP and one copy present in the ITCH-ASIP fusion gene which leads to a transcript coding for a normal ASIP protein	Coturnix japonica Japanese quail - (species)	Coturnix japonica Japanese quail - (species) D	Agouti	Coturnix japonica Japanese quail - (species)	Published - Accepted by Curator
Agouti	Coloration (coat)	Cis-regulatory, Insertion	Mus musculus molossinus Japanese wild mouse - (subspecies) D	Intraspecific	Candidate Gene	Tanave A; Imai Y; Koide T (2019) Nested retrotransposition in the East Asian mouse genome causes the classical nonagouti mutation.	GP00002386	Asip Q03288	Morphology		Mus musculus molossinus Japanese wild mouse - (subspecies)	Mus musculus molossinus Japanese wild mouse - (subspecies) D	Agouti	Mus musculus molossinus Japanese wild mouse - (subspecies)	Published - Accepted by Curator
Agouti (ASIP)	Coloration (coat)	Gene Amplification, Insertion	Ovis aries sheep - (species) D	Domesticated	Candidate Gene	Norris BJ; Whan VA (2008) A gene duplication affecting expression of the ovine ASIP gene is responsible for white and black sh[...] 1 Additional References Hepp D; Gonçalves GL; Moreira GR (2016) Epistatic Interaction of the Melanocortin 1 Receptor and Agouti Signaling Protein Genes Modulates Wo[...]	GP00001324	Asip Q03288	Morphology	~190kb gene duplication causing dominant white phenotype. Duplication was facilitated by homologous recombination between two non-LTR SINE sequences flanking the duplicated segment ; possible involvement of gene conversion.	Ovis aries sheep - (species)	Ovis aries sheep - (species) D	Agouti (ASIP)	Ovis aries sheep - (species)	Published - Accepted by Curator
Agouti (ASIP)	Coloration (coat)	Cis-regulatory, 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)	Coding, Insertion N	Oryctolagus cuniculus rabbit - (species) D	Domesticated	Candidate Gene	Fontanesi L; Forestier L; Allain D ; et al. (2010) Characterization of the rabbit agouti signaling protein (ASIP) gene: transcripts and phylogenetic an[...] 1 Additional References Sakuma Y; Matsunami M; Takada T (2019) Multiple Conserved Elements Structuring Inverted Repeats in the Mammalian Coat Color-Related Gene As[...]	GP00001968	Asip Q03288	Morphology	an insertion in exon 2 of the black nonagouti allele = c.5_6insA mutation which causes a frameshift and a predicted truncated protein of only 21 amino acids N	Oryctolagus cuniculus rabbit - (species)	Oryctolagus cuniculus rabbit - (species) D	Agouti (ASIP)	Oryctolagus cuniculus rabbit - (species)	Published - Accepted by Curator
Agouti (ASIP)	Coloration (coat)	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 (coat)	Cis-regulatory, Insertion	Bubalus bubalis water buffalo - (species) D	Domesticated	Association Mapping	Liang D; Zhao P; Si J ; et al. (2021) Genomic Analysis Revealed a Convergent Evolution of LINE-1 in Coat Color: A Case Study in Water Buff[...]	GP00002370	Asip Q03288	Morphology	"2,809-bp-long LINE-1 insertion in the ASIP (agouti signaling protein) gene is the causative mutation for the white coat phenotype in swamp buffalo (Bubalus bubalis). This LINE-1 insertion (3′ truncated and containing only 5′ UTR) functions as a strong proximal promoter that leads to a 10-fold increase in the transcription of ASIP in white buffalo skin. The 165 bp of 5′ UTR transcribed from the LINE-1 is spliced into the first coding exon of ASIP, resulting in a chimeric transcript. The increased expression of ASIP prevents melanocyte maturation, leading to the absence of pigment in white buffalo skin and hairs. Phylogenetic analyses indicate that the white buffalo-specific ASIP allele originated from a recent genetic transposition event in swamp buffalo. Interestingly, as a similar LINE-1 insertion has been identified in the cattle ASIP gene, we discuss the convergent mechanism of coat color evolution in the Bovini tribe."	Bubalus bubalis water buffalo - (species)	Bubalus bubalis water buffalo - (species) D	Agouti (ASIP)	Bubalus bubalis water buffalo - (species)	Published - Accepted by Curator
Agouti (ASIP)	Coloration (coat; dorso-ventral)	Coding, Insertion N	Oryctolagus cuniculus rabbit - (species) D	Domesticated	Candidate Gene	Letko A; Ammann B; Jagannathan V ; et al. (2020) A deletion spanning the promoter and first exon of the hair cycle-specific ASIP transcript isoform i[...]	GP00002373	Asip Q03288	Morphology	"The structural variant represented an approximately 11 kb deletion (NC_013672.1:g.5,455,408_5,466,123del; Fig. 2). In rabbit, there are currently two ASIP transcript isoforms annotated (NCBI annotation release 102). The deletion removes the entire first 5′-untranslated exon of one of these transcripts (NM_001122939.1). (...) he deletion removed the transcription start site and the first untranslated exon of the presumably hair cycle-specific transcript isoform, suggesting that this is the most likely causative variant for the black and tan phenotype." N	Oryctolagus cuniculus rabbit - (species)	Oryctolagus cuniculus rabbit - (species) D	Agouti (ASIP)	Oryctolagus cuniculus rabbit - (species)	Published - Accepted by Curator
Agouti (ASIP)	Coloration	Gene Amplification, Insertion	Capra hircus goat - (species) D	Domesticated	Association Mapping	Guo J; Sun X; Mao A ; et al. (2022) A 13.42-kb tandem duplication at the ASIP locus is strongly associated with the depigmentation pheno[...]	GP00002380	Asip Q03288	Morphology	"We confirmed that a genomic region harboring the ASIP gene is a major locus affecting the coat color phenotype of Swiss markings in goats. Although the molecular genetic mechanisms remain unsolved, the 13,420-bp duplication upstream of ASIP is a necessary but not sufficient condition for this phenotype in goats. Moreover, the variations in the copy number of the duplication across different goat breeds do not lead to phenotypic heterogeneity."	Capra hircus goat - (species)	Capra hircus goat - (species) D	Agouti (ASIP)	Capra hircus goat - (species)	Published - Accepted by Curator
Agouti (ASIP)	Coloration (coat)	Gene Amplification, Insertion	Capra hircus goat - (species) D	Domesticated	Candidate Gene	Henkel J; Dubacher A; Bangerter E ; et al. (2021) Introgression of ASIP and TYRP1 Alleles Explains Coat Color Variation in Valais Goats.	GP00002381	Asip Q03288	Morphology	"The white Capra Sempione carried one copy of the AWt allele, which is commonly found in Saanen and Appenzell goats. AWt involves a triplication of ~155 kb comprising the coding sequence of the ASIP, AHCY and ITCH genes (Fontanesi et al. 2009; Henkel et al. 2019). Closer inspection of the short-read alignments revealed that the sequenced Capra Sempione had acquired additional smaller structural alterations compared to the original AWt allele, which comprised a duplication of 1053 bp inserted into a 10 194 bp deletion of the original AWt CNV allele (Supplementary Figure S1)."	Capra hircus goat - (species)	Capra hircus goat - (species) D	Agouti (ASIP)	Capra hircus goat - (species)	Published - Accepted by Curator
Agouti (ASIP)	Coloration (coat)	Gene Amplification, Insertion	Capra hircus goat - (species) D	Domesticated	Candidate Gene	Henkel J; Dubacher A; Bangerter E ; et al. (2021) Introgression of ASIP and TYRP1 Alleles Explains Coat Color Variation in Valais Goats.	GP00002382	Asip Q03288	Morphology	"The greyish Grüenochte goat carried one copy of the Apc allele, which causes the characteristic black and white pattern of Swiss Peacock goats (Henkel et al. 2019). The Apc allele consists of a central quadruplication of ~45 kb with triplicated adjacent flanking regions comprising ~28 kb and ~42 kb, respectively."	Capra hircus goat - (species)	Capra hircus goat - (species) D	Agouti (ASIP)	Capra hircus goat - (species)	Published - Accepted by Curator
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)	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
alcohol dehydrogenase (Adh)	Xenobiotic resistance (alcohol)	Coding, Insertion N	Drosophila melanogaster fruit fly - (species) D	Intraspecific	Candidate Gene	Freeth AL; Gibson JB; Wilks AV (1990) Aberrant splicing of a naturally occurring alcohol dehydrogenase null activity allele in Drosophila [...] 1 Additional References Gibson JB; Wilks AV; Agrotis A (1992) Molecular relationships between alcohol dehydrogenase null-activity alleles from natural populations[...]	GP00001990	Adh P00334	Physiology	eight extra nucleotides (in two groups of four) in the second intron commencing six bases 3' from the 5' splice site. A stop codon was also found in exon 2. S1 nuclease protection experiments have shown that the insertions in intron 2 disrupt the correct splicing of intron 2. The null allele produces a transcript approximately 100 bases longer than the normal mature adult transcript, and the amount of the null allele transcript is only about 10% of the normal level. N	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species) D	alcohol dehydrogenase (Adh)	Drosophila melanogaster fruit fly - (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
amylase	Starch processing	Gene Amplification, Insertion	Mus musculus house mouse - (species) D	Domesticated	Candidate Gene	Pajic P; Pavlidis P; Dean K ; et al. (2019) Independent amylase gene copy number bursts correlate with dietary preferences in mammals.	GP00001867	Amy1 P00687	Physiology	Copy Number Variation	Mus musculus house mouse - (species)	Mus musculus house mouse - (species) D	amylase	Mus musculus house mouse - (species)	Published - Accepted by Curator
amylase	Starch processing	Gene Amplification, Insertion	Rattus norvegicus Norway rat - (species) D	Domesticated	Candidate Gene	Pajic P; Pavlidis P; Dean K ; et al. (2019) Independent amylase gene copy number bursts correlate with dietary preferences in mammals.	GP00001868	Amy1 P00687	Physiology	Copy Number Variation	Rattus norvegicus Norway rat - (species)	Rattus norvegicus Norway rat - (species) D	amylase	Rattus norvegicus Norway rat - (species)	Published - Accepted by Curator
amylase	Starch processing	Gene Amplification, Insertion	Sus scrofa pig - (species) D	Domesticated	Candidate Gene	Pajic P; Pavlidis P; Dean K ; et al. (2019) Independent amylase gene copy number bursts correlate with dietary preferences in mammals.	GP00001869	Amy1 P00687	Physiology	Copy Number Variation	Sus scrofa pig - (species)	Sus scrofa pig - (species) D	amylase	Sus scrofa pig - (species)	Published - Accepted by Curator
amylase	Starch processing	Gene Amplification, Insertion	Cebus capucinus white-faced sapajou - (species) D	Intergeneric or Higher	Candidate Gene	Pajic P; Pavlidis P; Dean K ; et al. (2019) Independent amylase gene copy number bursts correlate with dietary preferences in mammals.	GP00001870	Amy1 P00687	Physiology	3-4 copies of the amylase gene; which coincides with increased levels of amylase activity in saliva	Aotus trivirgatus douroucouli - (species) Callithrix jacchus white-tufted-ear marmoset - (species)	Cebus capucinus white-faced sapajou - (species) D	amylase	Cebus capucinus white-faced sapajou - (species)	Published - Accepted by Curator
amylase	Starch processing	Gene Amplification, Insertion	Papio anubis olive baboon - (species) D	Intergeneric or Higher	Candidate Gene	Pajic P; Pavlidis P; Dean K ; et al. (2019) Independent amylase gene copy number bursts correlate with dietary preferences in mammals.	GP00001871	Amy1 P00687	Physiology	3-4 copies of the amylase gene; which coincides with increased levels of amylase activity in saliva	Cercocebus atys sooty mangabey - (species) Macaca mulatta Rhesus monkey - (species)	Papio anubis olive baboon - (species) D	amylase	Papio anubis olive baboon - (species)	Published - Accepted by Curator
amylase	Starch processing	Gene Amplification, Insertion	Meles leucurus Asian badger - (species) D	Intraspecific	Candidate Gene	Abduriyim Shamshidin; Nishita Yoshinori; Abramov AV ; et al. (2019 ) Variation in pancreatic amylase gene copy number among Eurasian badgers (Carnivora, Mustelidae, Mele[...]	GP00001907	Amy1 P00687	Physiology	Copy Number Variation varies between one and four in this species	Meles leucurus Asian badger - (species)	Meles leucurus Asian badger - (species) D	amylase	Meles leucurus Asian badger - (species)	Published - Accepted by Curator
amylase 1 (AMY1)	Starch processing	Gene Amplification, Insertion	Homo sapiens human - (species) D	Intraspecific	Candidate Gene	Perry GH; Dominy NJ; Claw KG ; et al. (2007) Diet and the evolution of human amylase gene copy number variation. 2 Additional References Falchi M; El-Sayed Moustafa JS; Takousis P (2014) Low copy number of the salivary amylase gene predisposes to obesity. Pajic P; Pavlidis P; Dean K (2019) Independent amylase gene copy number bursts correlate with dietary preferences in mammals.	GP00000085	AMY1A P04745	Physiology	Probably gene duplication	Homo sapiens human - (species)	Homo sapiens human - (species) D	amylase 1 (AMY1)	Homo sapiens human - (species)	Published - Accepted by Curator
amylase 2B (AMY2B)	Starch processing	Gene Amplification, Insertion	Canis lupus familiaris dog - (subspecies) D	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. 4 Additional References Arendt M; Cairns KM; Ballard JW (2016) Diet adaptation in dog reflects spread of prehistoric agriculture. Arendt M; Fall T; Lindblad-Toh K (2014) Amylase activity is associated with AMY2B copy numbers in dog: implications for dog domestication, d[...] Tonoike A; Hori Y; Inoue-Murayama M (2015) Copy number variations in the amylase gene (AMY2B) in Japanese native dog breeds. Pajic P; Pavlidis P; Dean K (2019) Independent amylase gene copy number bursts correlate with dietary preferences in mammals.	GP00000086	LOC479922 L7N0N6	Physiology	Copy Number Variation	Canis lupus gray wolf - (species)	Canis lupus familiaris dog - (subspecies) D	amylase 2B (AMY2B)	Canis lupus familiaris dog - (subspecies)	Published - Accepted by Curator
anthocyanin2 (an2)	Coloration (flowers)	Coding, Insertion N	Petunia axillaris (species) D	Intraspecific	Candidate Gene	Quattrocchio F; Wing J; van der Woude K ; et al. (1999) Molecular analysis of the anthocyanin2 gene of petunia and its role in the evolution of flower color[...]	GP00000090	AN2 A4GRU8	Morphology	4bp insertion at a.a. 127; premature stop N	Petunia integrifolia (species)	Petunia axillaris (species) D	anthocyanin2 (an2)	Petunia axillaris (species)	Published - Accepted by Curator
anthocyanin2 (an2)	Coloration (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
AtGA20ox1 (=GA5=Sd1)	Plant size (dwarfism)	Coding, Insertion N	Arabidopsis thaliana thale cress - (species) D	Domesticated	Linkage Mapping	Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013) Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]	GP00000113	GA20OX1 Q39110	Morphology	+1bp "G" at +256 N	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species) D	AtGA20ox1 (=GA5=Sd1)	Arabidopsis thaliana thale cress - (species)	Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)	Plant size (dwarfism)	Coding, Insertion N	Arabidopsis thaliana thale cress - (species) D	Domesticated	Linkage Mapping	Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013) Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]	GP00000114	GA20OX1 Q39110	Morphology	+7bp "G" at +961 N	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species) D	AtGA20ox1 (=GA5=Sd1)	Arabidopsis thaliana thale cress - (species)	Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)	Plant size (dwarfism)	Coding, Insertion N	Arabidopsis thaliana thale cress - (species) D	Domesticated	Linkage Mapping	Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013) Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]	GP00000115	GA20OX1 Q39110	Morphology	+1bp at +1270 N	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species) D	AtGA20ox1 (=GA5=Sd1)	Arabidopsis thaliana thale cress - (species)	Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)	Plant size (dwarfism)	Coding, Insertion N	Arabidopsis thaliana thale cress - (species) D	Domesticated	Linkage Mapping	Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013) Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]	GP00000116	GA20OX1 Q39110	Morphology	Transposon insertion at +1355 N	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species) D	AtGA20ox1 (=GA5=Sd1)	Arabidopsis thaliana thale cress - (species)	Published - Accepted by Curator
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
BADH2	Fragrance	Coding, Insertion N	Oryza sativa rice - (species) D	Domesticated	Candidate Gene	Kovach MJ; Calingacion MN; Fitzgerald MA ; et al. (2009) The origin and evolution of fragrance in rice (Oryza sativa L.).	GP00001774	BADH2 Q84LK3	Physiology	insertion of 1 bp (T) in exon 10 N	Oryza sativa rice - (species)	Oryza sativa rice - (species) D	BADH2	Oryza sativa rice - (species)	Published - Accepted by Curator
BADH2	Fragrance	Coding, Insertion N	Oryza sativa rice - (species) D	Domesticated	Candidate Gene	Kovach MJ; Calingacion MN; Fitzgerald MA ; et al. (2009) The origin and evolution of fragrance in rice (Oryza sativa L.).	GP00001779	BADH2 Q84LK3	Physiology	1-bp insertion (G) in exon 14 N	Oryza sativa rice - (species)	Oryza sativa rice - (species) D	BADH2	Oryza sativa rice - (species)	Published - Accepted by Curator
BADH2	Fragrance	Coding, Insertion N	Oryza sativa rice - (species) D	Domesticated	Candidate Gene	Kovach MJ; Calingacion MN; Fitzgerald MA ; et al. (2009) The origin and evolution of fragrance in rice (Oryza sativa L.).	GP00001780	BADH2 Q84LK3	Physiology	3-bp insertion (TAT) in exon 13 - causes a frameshift N	Oryza sativa rice - (species)	Oryza sativa rice - (species) D	BADH2	Oryza sativa rice - (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
BCMA	Glucosinolate content Herbivore resistance	3 Mutations:	Boechera stricta (species)	Intraspecific	Linkage Mapping	Prasad KV; Song BH; Olson-Manning C ; et al. (2012) A gain-of-function polymorphism controlling complex traits and fitness in nature.	GP00000136	J9QWI9	Physiology Physiology	3 mutations	Boechera stricta (species)	Boechera stricta (species)	BCMA	Boechera stricta (species)	Published - Accepted by Curator
beta-tubulin (ben-1)	Xenobiotic resistance (benzimidazole)	Coding, Insertion N	Caenorhabditis elegans (species) D	Intraspecific	Association Mapping	Hahnel SR; Zdraljevic S; Rodriguez BC ; et al. (2018) Extreme allelic heterogeneity at a Caenorhabditis elegans beta-tubulin locus explains natural resist[...]	GP00001833	TUB2 P02557	Physiology	Trans_3538426_3538832 – insertion of a transposable element = a cut and paste DNA transposon Tc5B - which is part of the TcMar-Tc4 transposon superfamily– 406bp of the reference sequence seem to be disrupted- Steffen Hahnel comment : Since we didn't re-amplify the insertion by PCR; we don't know its exact location; sequence and size. Its identification is only based on the illumina reads of genome sequencing of JU3125. N	Caenorhabditis elegans (species)	Caenorhabditis elegans (species) D	beta-tubulin (ben-1)	Caenorhabditis elegans (species)	Published - Accepted by Curator
beta-tubulin (ben-1)	Xenobiotic resistance (benzimidazole)	Coding, Insertion N	Caenorhabditis elegans (species) D	Intraspecific	Association Mapping	Hahnel SR; Zdraljevic S; Rodriguez BC ; et al. (2018) Extreme allelic heterogeneity at a Caenorhabditis elegans beta-tubulin locus explains natural resist[...]	GP00001842	TUB2 P02557	Physiology	Ins_3539575_3539576 – Steffen Hahnel comment: 1 bp insertion in coding exon 4 N	Caenorhabditis elegans (species)	Caenorhabditis elegans (species) D	beta-tubulin (ben-1)	Caenorhabditis elegans (species)	Published - Accepted by Curator
beta-tubulin (ben-1)	Xenobiotic resistance (benzimidazole)	Coding, Insertion N	Caenorhabditis elegans (species) D	Intraspecific	Association Mapping	Hahnel SR; Zdraljevic S; Rodriguez BC ; et al. (2018) Extreme allelic heterogeneity at a Caenorhabditis elegans beta-tubulin locus explains natural resist[...]	GP00001857	TUB2 P02557	Physiology	Ins_3541547_3541548 – 1 bp insertion in first coding exon N	Caenorhabditis elegans (species)	Caenorhabditis elegans (species) D	beta-tubulin (ben-1)	Caenorhabditis elegans (species)	Published - Accepted by Curator
bHLH2	Coloration (flower; seed)	Coding, Insertion N	Ipomoea purpurea common morning-glory - (species) D	Domesticated	Candidate Gene	Park KI; Ishikawa N; Morita Y ; et al. (2007) A bHLH regulatory gene in the common morning glory, Ipomoea purpurea, controls anthocyanin biosynthe[...]	GP00002078	BHLH2 Q9CAD0	Morphology	two copies of 3.9-kb Tip100 integrated into bHLH2 exon 7 and intron 2 N	Ipomoea purpurea common morning-glory - (species)	Ipomoea purpurea common morning-glory - (species) D	bHLH2	Ipomoea purpurea common morning-glory - (species)	Published - Accepted by Curator
bHLH2	Coloration (flower; seed)	Coding, Insertion N	Ipomoea purpurea common morning-glory - (species) D	Domesticated	Candidate Gene	Park KI; Ishikawa N; Morita Y ; et al. (2007) A bHLH regulatory gene in the common morning glory, Ipomoea purpurea, controls anthocyanin biosynthe[...]	GP00002085	BHLH2 Q9CAD0	Morphology	only one copy of Tip100 in exon 7 and no apparent footprint of Tip100 in intron 2 N	Ipomoea purpurea common morning-glory - (species)	Ipomoea purpurea common morning-glory - (species) D	bHLH2	Ipomoea purpurea common morning-glory - (species)	Published - Accepted by Curator
bHLH2	Coloration (flower; seed)	Coding, Insertion N	Ipomoea purpurea common morning-glory - (species) D	Domesticated	Candidate Gene	Park KI; Ishikawa N; Morita Y ; et al. (2007) A bHLH regulatory gene in the common morning glory, Ipomoea purpurea, controls anthocyanin biosynthe[...]	GP00002086	BHLH2 Q9CAD0	Morphology	insertion of 838 bp IpMu1 in exon 2 N	Ipomoea purpurea common morning-glory - (species)	Ipomoea purpurea common morning-glory - (species) D	bHLH2	Ipomoea purpurea common morning-glory - (species)	Published - Accepted by Curator
bHLH2	Coloration (flowers; seeds)	Coding, Insertion N	Ipomoea tricolor (species) D	Domesticated	Candidate Gene	Park KI; Choi JD; Hoshino A ; et al. (2004) An intragenic tandem duplication in a transcriptional regulatory gene for anthocyanin biosynthesis c[...]	GP00002091	BHLH2 Q9CAD0	Morphology	intragenic tandem duplication of 3.3 kbp of the bHLH2 gene. Each of the tandem repeats is flanked by a 3-bp sequence AAT; indicating that the 3-bp microhomology is used to generate the tandem duplication. The transcripts in the pale-blue flower buds of the mutant contain an internal 583-bp tandem duplication that results in the production of a truncated polypeptide lacking the bHLH domain. The mRNA accumulation of most of the structural genes encoding enzymes for anthocyanin biosynthesis in the flower buds of the mutant was significantly reduced. The transcripts identical to the wild-type mRNAs for the transcriptional activator were present abundantly in blue spots of the variegated flowers whereas the transcripts containing the 583-bp tandem duplication were predominant in the pale-blue background of the same flowers. The flower and seed variegations studied here are likely to be caused by somatic homologous recombination between an intragenic tandem duplication in the gene encoding a bHLH transcriptional activator for anthocyanin biosynthesis. N	Ipomoea tricolor (species)	Ipomoea tricolor (species) D	bHLH2	Ipomoea tricolor (species)	Published - Accepted by Curator
bHLH2	Coloration (flowers)	Coding, Insertion N	Petunia axillaris (species) D	Domesticated	Candidate Gene	Spelt C; Quattrocchio F; Mol J ; et al. (2002) ANTHOCYANIN1 of petunia controls pigment synthesis, vacuolar pH, and seed coat development by geneti[...]	GP00002092	BHLH2 Q9CAD0	Morphology	insertion of a dTph1 transposon in the AN1 gene N	Petunia axillaris (species)	Petunia axillaris (species) D	bHLH2	Petunia axillaris (species)	Published - Accepted by Curator
BMP15	Fertility (increased ovulation rate)	Coding, Insertion N	Ovis aries sheep - (species) D	Domesticated	Candidate Gene	Lassoued N; Benkhlil Z; Woloszyn F ; et al. (2017) FecX a Novel BMP15 mutation responsible for prolificacy and female sterility in Tunisian Barbarine [...]	GP00002159	Bmp15 Q9Z0L4	Physiology	C insertion (c.310insC) in the ovine BMP15 cDNA leading to a frame shift at protein position 101 N	Ovis aries sheep - (species)	Ovis aries sheep - (species) D	BMP15	Ovis aries sheep - (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
cadherin	Xenobiotic resistance (insecticide)	Coding, Insertion N	Heliothis virescens tobacco budworm - (species) D	Intraspecific	Linkage Mapping	Gahan LJ; Gould F; Heckel DG (2001) Identification of a gene associated with Bt resistance in Heliothis virescens.	GP00000161	BtR Q19KJ3	Physiology	Insertion of retrotransposon N	Heliothis virescens tobacco budworm - (species)	Heliothis virescens tobacco budworm - (species) D	cadherin	Heliothis virescens tobacco budworm - (species)	Published - Accepted by Curator
cadherin	Xenobiotic resistance (insecticide; Bt Cry2Ab toxin)	Coding, Insertion N	Pectinophora gossypiella pink bollworm - (species) D	Experimental Evolution	Candidate Gene	Morin S; Biggs RW; Sisterson MS ; et al. (2003) Three cadherin alleles associated with resistance to Bacillus thuringiensis in pink bollworm. 1 Additional References Fabrick JA; Mathew LG; Tabashnik BE (2011) Insertion of an intact CR1 retrotransposon in a cadherin gene linked with Bt resistance in the pink [...]	GP00002449	A0A1B0RHM4	Physiology	insertion into PgCad1 of an active chicken repeat (CR1) retrotransposon designated CR1-1_Pg. Unlike most other CR1 elements CR1-1_Pg is intact and transcribed by a flanking promoter. It contains target site duplications and has a relatively low number of copies. Examination of transcripts from the PgCad1 locus revealed that CR1-1_Pg disrupts both the cadherin protein and a long noncoding RNA of unknown function. N	Pectinophora gossypiella pink bollworm - (species)	Pectinophora gossypiella pink bollworm - (species) D	cadherin	Pectinophora gossypiella pink bollworm - (species)	Published - Accepted by Curator
cardinal	Coloration (eyes)	Coding, Insertion N	Tribolium castaneum red flour beetle - (species) D	Domesticated	Candidate Gene	Shirai Y; Daimon T (2020) Mutations in cardinal are responsible for the red-1 and peach eye color mutants of the red flour bee[...]	GP00002665	cd Q9VCW2	Morphology	A fragment of a transposable element (about 5 kb - 99% identical in amino acids to a putative retrotransposon (XP_015838217)) is inserted into exon 6. This insertion introduced a premature stop codon just after the insertion site. Amino acid residues near the C-terminal end of the haem peroxidase domain are thus disrupted. N	Tribolium castaneum red flour beetle - (species)	Tribolium castaneum red flour beetle - (species) D	cardinal	Tribolium castaneum red flour beetle - (species)	Published - Accepted by Curator
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
Chalcone synthase D (CHS-D)	Coloration (flower)	Unknown, Insertion	Ipomoea purpurea common morning-glory - (species) D	Intraspecific	Candidate Gene	Habu Y; Hisatomi Y; Iida S (1998) Molecular characterization of the mutable flaked allele for flower variegation in the common morning[...]	GP00001459	CHSD O22045	Morphology	insertion of a 3.9kb long transposable element Tip100 in intron	Ipomoea purpurea common morning-glory - (species)	Ipomoea purpurea common morning-glory - (species) D	Chalcone synthase D (CHS-D)	Ipomoea purpurea common morning-glory - (species)	Published - Accepted by Curator
Chalcone synthase D (CHS-D)	Coloration (flower)	Unknown, Insertion	Ipomoea purpurea common morning-glory - (species) D	Intraspecific	Candidate Gene	Habu Y; Hisatomi Y; Iida S (1998) Molecular characterization of the mutable flaked allele for flower variegation in the common morning[...]	GP00001460	CHSD O22045	Morphology	2 insertions of Tip100 in opposite orientation at different sites within the same intron	Ipomoea purpurea common morning-glory - (species)	Ipomoea purpurea common morning-glory - (species) D	Chalcone synthase D (CHS-D)	Ipomoea purpurea common morning-glory - (species)	Published - Accepted by Curator
CHKov1	Pathogen resistance Xenobiotic resistance (insecticide)	Coding, Insertion	Drosophila melanogaster fruit fly - (species) D	Intraspecific	Linkage Mapping	Magwire MM; Bayer F; Webster CL ; et al. (2011) Successive increases in the resistance of Drosophila to viral infection through a transposon inserti[...] 1 Additional References Aminetzach YT; Macpherson JM; Petrov DA (2005) Pesticide resistance via transposition-mediated adaptive gene truncation in Drosophila.	GP00000182	CHKov1 Q961V7	Physiology Physiology	Insertion of a Doc TE element resulting in novel; seemingly functional short protein	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species) D	CHKov1	Drosophila melanogaster fruit fly - (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
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, 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
Cpm1	Xenobiotic resistance (insecticide; toxin produced by Bacillus sphaericus)	Coding, Insertion N	Culex pipiens northern house mosquito - (species) D	Intraspecific	Candidate Gene	Darboux I; Charles JF; Pauchet Y ; et al. (2007) Transposon-mediated resistance to Bacillus sphaericus in a field-evolved population of Culex pipiens[...]	GP00002103	Q95WY5	Physiology	Insertion of a 451-bpTE into the exon 2 of the toxin receptor gene. The insertion induces a new mRNA splicing event that creates a shorter transcript. This new transcript encodes an altered receptor unable to interact with the toxin resulting in resistance to this insecticide. The missing portion includes GPI-anchoring signals N	Culex pipiens northern house mosquito - (species)	Culex pipiens northern house mosquito - (species) D	Cpm1	Culex pipiens northern house mosquito - (species)	Published - Accepted by Curator
CPR	Xenobiotic resistance	Gene Amplification, Insertion	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 [...]	GP00002398	Cpr Q27597	Physiology	Pyflubumide resistant populations are estimated to harbor three CPR copies by two methods, whereas susceptible populations have a single CPR copy.	Tetranychus urticae two-spotted spider mite - (species)	Tetranychus urticae two-spotted spider mite - (species) D	CPR	Tetranychus urticae two-spotted spider mite - (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
CYP(T)	Flower morphology (style length)	Coding, Insertion N	Primula vulgaris (species) D	Intraspecific	Linkage Mapping	Li J; Cocker JM; Wright J ; et al. (2016) Genetic architecture and evolution of the S locus supergene in Primula vulgaris.	GP00001394	CYP734A1 O48786	Morphology	single base insertion in exon 2 introduces a disruptive premature stop codon N	Primula vulgaris (species)	Primula vulgaris (species) D	CYP(T)	Primula vulgaris (species)	Published - Accepted by Curator
Cyp12d1	Xenobiotic resistance (caffeine tolerance)	Gene Amplification, Insertion	Drosophila melanogaster fruit fly - (species)	Intraspecific	Linkage Mapping	Najarro MA; Hackett JL; Smith BR ; et al. (2015) Identifying Loci Contributing to Natural Variation in Xenobiotic Resistance in Drosophila.	GP00000198	Cyp12d1-d Q7KR10	Physiology	Copy number Variant	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species)	Cyp12d1	Drosophila melanogaster fruit fly - (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
Cyp28d1	Xenobiotic resistance (nicotine ; larval stage)	Gene Amplification, Insertion	Drosophila melanogaster fruit fly - (species) D	Intraspecific	Linkage Mapping	Chakraborty M; VanKuren NW; Zhao R ; et al. (2018) Hidden genetic variation shapes the structure of functional elements in Drosophila. 2 Additional References Marriage TN; King EG; Long AD (2014) Fine-mapping nicotine resistance loci in Drosophila using a multiparent advanced generation inter-cr[...] Chakraborty M; Emerson JJ; Macdonald SJ (2019) Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits.	GP00001407	Cyp28d1 Q9VMT5	Physiology	insertion of a partial 1.5kb Accord transposable element and a Cyp28d1 gene tandem duplication (CNV - 3754 bp) that may play complementary role in resistance levels	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species) D	Cyp28d1	Drosophila melanogaster fruit fly - (species)	Published - Accepted by Curator
Cyp28d1	Xenobiotic resistance (nicotine ; larval stage)	Coding, Insertion	Drosophila melanogaster fruit fly - (species) D	Intraspecific	Candidate Gene	Chakraborty M; Emerson JJ; Macdonald SJ ; et al. (2019) Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits.	GP00002113	Cyp28d1 Q9VMT5	Physiology	insertion of a FW element (4720 bp) into the coding region (exon) of the second copy of the Cyp28d1 (there is still another copy of the gene left due to a duplication). Associated with a decrease in Cyp28d2 gene expression and a decrease in nicotin resistance.	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species) D	Cyp28d1	Drosophila melanogaster fruit fly - (species)	Published - Accepted by Curator
Cyp28d1-Cyp28d2	Xenobiotic resistance (nicotine ; larval stage)	Gene Amplification, Insertion	Drosophila melanogaster fruit fly - (species) D	Intraspecific	Candidate Gene	Chakraborty M; Emerson JJ; Macdonald SJ ; et al. (2019) Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits.	GP00002112	Cyp28d1 Q9VMT5	Physiology	duplication of 6063 bp which includes genes Cyp28d1; Cyp28d2 and CG7742. Associated with increased expression of Cyp28d2 and increased resistance to nicotin	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species) D	Cyp28d1-Cyp28d2	Drosophila melanogaster fruit fly - (species)	Published - Accepted by Curator
Cyp28d1-Cyp28d2	Xenobiotic resistance (nicotine ; larval stage)	Gene Amplification, Insertion	Drosophila melanogaster fruit fly - (species) D	Intraspecific	Linkage Mapping	Chakraborty M; Emerson JJ; Macdonald SJ ; et al. (2019) Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits.	GP00002114	Cyp28d1 Q9VMT5	Physiology	duplication of a 15297-bp region; which encompasses 5 genes: Msp300 Cyp28d2 Cyp28d1 CG7742 and CG14034. Associated with increased expression of Cyp28d1 gene expression and increased nicotin resistance	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species) D	Cyp28d1-Cyp28d2	Drosophila melanogaster fruit fly - (species)	Published - Accepted by Curator
CYP337B3	Xenobiotic resistance (insecticide; pyrethroid)	Coding, Insertion	Helicoverpa zea corn earworm - (species) D	Intraspecific	Candidate Gene	Walsh TK; Joussen N; Tian K ; et al. (2018) Multiple recombination events between two cytochrome P450 loci contribute to global pyrethroid resis[...] 1 Additional References Valencia-Montoya WA; Elfekih S; North HL (2020) Adaptive Introgression across Semipermeable Species Boundaries between Local Helicoverpa zea and Inv[...]	GP00002485	CYP337B3 A0A0H3V333	Physiology	Introgression of the CYP337B3v2 resistant allele from Helicoverpa armigera	Helicoverpa zea corn earworm - (species)	Helicoverpa zea corn earworm - (species) D	CYP337B3	Helicoverpa zea corn earworm - (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
CYP6CY3-CYP6CY4	Xenobiotic resistance (insecticide; neonicotinoid; host plant)	Gene Amplification, 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. 3 Additional References Puinean AM; Foster SP; Oliphant L (2010) Amplification of a cytochrome P450 gene is associated with resistance to neonicotinoid insecticides [...] Bass C; Zimmer CT; Riveron JM (2013) Gene amplification and microsatellite polymorphism underlie a recent insect host shift. Singh KS; Troczka BJ; Duarte A (2020) The genetic architecture of a host shift: An adaptive walk protected an aphid and its endosymbiont f[...]	GP00001473	CYP6CY3 V5SQ25	Physiology	gene amplification (from 2 to 14-100 copies) - CYP6CY3 and neighboring gene CYP6CY4 are duplicated in M. p. nicotianae as a large amplicon of ~325 kb creating characteristic breakpoints identifying the region. CYP6CY4 and CYP6CY3 are highly effective at metabolizing nicotine to its nontoxic metabolite cotinine.	Myzus persicae green peach aphid - (species)	Myzus persicae green peach aphid - (species) D	CYP6CY3-CYP6CY4	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
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
CYP76AD1	Coloration	Coding, Insertion N	Beta vulgaris (species) D	Domesticated	Linkage Mapping	Hatlestad GJ; Sunnadeniya RM; Akhavan NA ; et al. (2012) The beet R locus encodes a new cytochrome P450 required for red betalain production.	GP00000210	CYP76AD1 I3PFJ5	Morphology	5bp insertion resulting in frameshift N	Beta vulgaris (species)	Beta vulgaris (species) D	CYP76AD1	Beta vulgaris (species)	Published - Accepted by Curator
CYP9A	Xenobiotic resistance (insecticide; deltamethrin)	Gene Amplification, Insertion	Spodoptera frugiperda fall armyworm - (species)	Intraspecific	Association Mapping	Gimenez S; Abdelgaffar H; Goff GL ; et al. (2020) Adaptation by copy number variation increases insecticide resistance in the fall armyworm.	GP00002476		Physiology	In sensitive alleles the gene cluster is composed of 12 CYP9A genes and two alcohol dehydrogenase genes. All 30 resistant alleles have two copies of this unit while 28 and 6 alleles of the sensitive individuals had one and two copies; respectively.	Spodoptera frugiperda fall armyworm - (species)	Spodoptera frugiperda fall armyworm - (species)	CYP9A	Spodoptera frugiperda fall armyworm - (species)	Published - Accepted by Curator
CYP9J26	Xenobiotic resistance (insecticide)	Gene Amplification, Insertion	Aedes aegypti yellow fever mosquito - (species) D	Intraspecific	Candidate Gene	Bariami V; Jones CM; Poupardin R ; et al. (2012) Gene amplification, ABC transporters and cytochrome P450s: unraveling the molecular basis of pyrethr[...]	GP00002606	CYP9J Q8T4S7	Physiology	CYP9J26 gene amplified about 6–7 times	Aedes aegypti yellow fever mosquito - (species)	Aedes aegypti yellow fever mosquito - (species) D	CYP9J26	Aedes aegypti yellow fever mosquito - (species)	Published - Accepted by Curator
CYP9M6	Xenobiotic resistance (insecticide)	Gene Amplification, Insertion	Aedes aegypti yellow fever mosquito - (species) D	Experimental Evolution	Candidate Gene	Kasai S; Komagata O; Itokawa K ; et al. (2014) Mechanisms of pyrethroid resistance in the dengue mosquito vector, Aedes aegypti: target site insens[...] 1 Additional References Smith LB; Kasai S; Scott JG (2016) Pyrethroid resistance in Aedes aegypti and Aedes albopictus: Important mosquito vectors of human dis[...]	GP00002448	CYP9M6 X5ICI6	Physiology	CYP9M6 has the capability to metabolize permethrin and is over expressed in the resistant strain partially due to gene amplification. The average copy number of the CYP9M9 gene is 4.6-fold more than the standard strain based on qPCR.	Aedes aegypti yellow fever mosquito - (species)	Aedes aegypti yellow fever mosquito - (species) D	CYP9M6	Aedes aegypti yellow fever mosquito - (species)	Published - Accepted by Curator
DCAR-032551	Carotenoid content	Coding, Insertion N	Daucus carota carrot - (species) D	Domesticated	Linkage Mapping	Iorizzo M; Ellison S; Senalik D ; et al. (2016) A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid[...]	GP00001568	DCAR_032551 A0A162A3G8	Morphology	A 212-nt insertion in exon 2 that creates a frameshift mutation N	Daucus carota carrot - (species)	Daucus carota carrot - (species) D	DCAR-032551	Daucus carota carrot - (species)	Published - Accepted by Curator
Delta-1-pyrroline-5-carboxylate synthase A	Drought response (drought-induced proline accumulation)	2 Mutations: Coding	Arabidopsis thaliana thale cress - (species) D	Intraspecific	Linkage Mapping	Kesari R; Lasky JR; Villamor JG ; et al. (2012) Intron-mediated alternative splicing of Arabidopsis P5CS1 and its association with natural variation[...]	GP00001280	P5CSA P54887	Physiology	2 mutations	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species) D	Delta-1-pyrroline-5-carboxylate synthase A	Arabidopsis thaliana thale cress - (species)	Published - Accepted by Curator
Dihydroflavonol 4 reductase (MlDfr)	Coloration (flower)	Coding, Insertion N	Erythranthe lewisii (species) D	Intraspecific	Candidate Gene	Wu CA; Streisfeld MA; Nutter LI ; et al. (2013) The genetic basis of a rare flower color polymorphism in Mimulus lewisii provides insight into the r[...]	GP00001457	DFRA P51102	Morphology	A 2 nt (TG) insertion at position 265 causing a frameshift and a greatly truncated protein of 106 aa only about one-fourth of its functional length N	Erythranthe lewisii (species)	Erythranthe lewisii (species) D	Dihydroflavonol 4 reductase (MlDfr)	Erythranthe lewisii (species)	Published - Accepted by Curator
Drosomycin-like 5	Pathogen resistance (fungi)	Gene Amplification, Insertion	Drosophila melanogaster fruit fly - (species) D	Intraspecific	Candidate Gene	Chakraborty M; Emerson JJ; Macdonald SJ ; et al. (2019) Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits.	GP00002111	Drsl5 Q9VZR2	Physiology	Duplication of the gene and insertion of a 4993-bp region (which comes from part of a neighboring gene). Associated with a >1000-fold expression increase of the gene.	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species) D	Drosomycin-like 5	Drosophila melanogaster fruit fly - (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)	Scales (loss) Femoral glands (absent) Tooth number	Coding, Insertion	Pogona vitticeps central bearded dragon - (species) D	Intraspecific	Candidate Gene	Di-Poï N; Milinkovitch MC (2016) The anatomical placode in reptile scale morphogenesis indicates shared ancestry among skin appendage[...]	GP00002040	Eda O54693	Morphology Morphology Morphology	5′688–bp insertion of a transposon of the LTR-Gypsy family which generates a new splice donor site (gt) 42 bases upstream of the wild-type donor site; thus generating a 14–amino acid deletion in the corresponding transcript	Pogona vitticeps central bearded dragon - (species)	Pogona vitticeps central bearded dragon - (species) D	Ectodysplasin (EDA)	Pogona vitticeps central bearded dragon - (species)	Published - Accepted by Curator
EDNRA	Coloration (coat ; white-spotting)	Gene Amplification, Insertion	Capra hircus goat - (species) D	Domesticated	Association Mapping	Menzi F; Keller I; Reber I ; et al. (2016) Genomic amplification of the caprine EDNRA locus might lead to a dose dependent loss of pigmentation[...]	GP00002170	Ednra Q61614	Morphology	1 Mb copy number variant (CNV) harboring 5 genes including EDNRA ; The duplicated EDNRA copies contain a missense variant (p.Tyr129His) predicted to increase the affinity of the encoded mutant receptor for endothelin 3. Menzi et al. proposed a hypothesis whereby ectopic overexpression of a mutant EDNRA scavenges EDN3 required for EDNRB signaling and normal melanocyte development and thus likely leads to an absence of melanocytes in the non-pigmented body areas of Boer goats (thanks to OMIA for the summary)	Capra hircus goat - (species)	Capra hircus goat - (species) D	EDNRA	Capra hircus goat - (species)	Published - Accepted by Curator
enamelin (ENAM)	Tooth composition (no enamel production)	3 Mutations: Coding N	Orycteropus afer aardvark - (species) D	Intergeneric or Higher	Candidate Gene	Meredith RW; Gatesy J; Murphy WJ ; et al. (2009) Molecular decay of the tooth gene Enamelin (ENAM) mirrors the loss of enamel in the fossil record of[...]	GP00001943	ENAM Q9NRM1	Physiology	3 mutations	Elephantulus rufescens East African long-eared elephant shrew - (species)	Orycteropus afer aardvark - (species) D	enamelin (ENAM)	Orycteropus afer aardvark - (species)	Published - Accepted by Curator
enamelysin (MMP20)	Tooth absence (no enamel production)	Coding, Insertion N	Balaenoptera physalus Fin whale - (species) D Balaena mysticetus bowhead whale - (species) D Megaptera novaeangliae humpback whale - (species) D	Intergeneric or Higher	Candidate Gene	Meredith RW; Gatesy J; Cheng J ; et al. (2011) Pseudogenization of the tooth gene enamelysin (MMP20) in the common ancestor of extant baleen whales[...]	GP00001940	MMP20 O60882	Physiology	insertion of a CHR-2 SINE retroposon in exon 2 of MMP20 which would result in premature truncation of the MMP20 protein owing to stop codons in all possible reading frames of the CHR-2 SINE. The length of the MMP20 SINE ranges from 302 bp (B. musculus) to 318 bp (B. physalus). This mutation is found in eight investigated species of baleen whales. Other inactivating mutations (nonsense and frameshift mutations) are found in various species N	Physeter catodon sperm whale - (species)	Balaenoptera physalus Fin whale - (species) D Balaena mysticetus bowhead whale - (species) D Megaptera novaeangliae humpback whale - (species) D	enamelysin (MMP20)	Balaenoptera physalus Fin whale - (species) Balaena mysticetus bowhead whale - (species) Megaptera novaeangliae humpback whale - (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
EPSPS	Xenobiotic resistance (herbicides; glyphosate)	Gene Amplification, Insertion	Amaranthus palmeri (species) D	Intraspecific	Candidate Gene	Gaines TA; Zhang W; Wang D ; et al. (2010) Gene amplification confers glyphosate resistance in Amaranthus palmeri.	GP00001883	At2g45300 P05466	Physiology	Genomes of resistant plants contain from 5-fold to more than 160-fold more copies of the EPSPS gene than did genomes of susceptible plants - the duplicated section of DNA including the 10 kb EPSPS gene is at least 30 kb long	Amaranthus palmeri (species)	Amaranthus palmeri (species) D	EPSPS	Amaranthus palmeri (species)	Published - Accepted by Curator
EPSPS	Xenobiotic resistance (herbicides; glyphosate)	Gene Amplification, Insertion	Amaranthus tuberculatus (species) D	Intraspecific	Candidate Gene	Tranel PJ; Riggins CW; Bell MS ; et al. (2011) Herbicide resistances in Amaranthus tuberculatus: a call for new options.	GP00001884	At2g45300 P05466	Physiology	4 copies of the EPSPS gene	Amaranthus tuberculatus (species)	Amaranthus tuberculatus (species) D	EPSPS	Amaranthus tuberculatus (species)	Published - Accepted by Curator
EPSPS	Xenobiotic resistance (herbicides; glyphosate)	Gene Amplification, Insertion	Lolium multiflorum Italian ryegrass - (species) D	Intraspecific	Candidate Gene	Salas RA; Dayan FE; Pan Z ; et al. (2012) EPSPS gene amplification in glyphosate-resistant Italian ryegrass (Lolium perenne ssp. multiflorum) [...]	GP00001885	At2g45300 P05466	Physiology	15-25 copies of the EPSPS gene	Lolium multiflorum Italian ryegrass - (species)	Lolium multiflorum Italian ryegrass - (species) D	EPSPS	Lolium multiflorum Italian ryegrass - (species)	Published - Accepted by Curator
EPSPS	Xenobiotic resistance (herbicides; glyphosate)	Gene Amplification, Insertion	Bassia scoparia (species) D	Intraspecific	Candidate Gene	Sammons RD; Gaines TA (2014) Glyphosate resistance: state of knowledge.	GP00001886	At2g45300 P05466	Physiology	15-25 copies of the EPSPS gene	Bassia scoparia (species)	Bassia scoparia (species) D	EPSPS	Bassia scoparia (species)	Published - Accepted by Curator
EPSPS	Xenobiotic resistance (herbicides; glyphosate)	Gene Amplification, Insertion	Amaranthus spinosus (species) D	Intraspecific	Candidate Gene	Sammons RD; Gaines TA (2014) Glyphosate resistance: state of knowledge.	GP00001887	At2g45300 P05466	Physiology	26-37 copies of the EPSPS gene	Amaranthus spinosus (species)	Amaranthus spinosus (species) D	EPSPS	Amaranthus spinosus (species)	Published - Accepted by Curator
ERG3	Xenobiotic resistance (drug)	Coding, Insertion N	Saccharomyces cerevisiae baker's yeast - (species) D	Experimental Evolution	Association Mapping	Gerstein AC; Lo DS; Otto SP (2012) Parallel genetic changes and nonparallel gene-environment interactions characterize the evolution of[...]	GP00001750	ERG3 P32353	Physiology	29-bp duplication in line 28 at nucleotide position 641 N	Saccharomyces cerevisiae baker's yeast - (species)	Saccharomyces cerevisiae baker's yeast - (species) D	ERG3	Saccharomyces cerevisiae baker's yeast - (species)	Published - Accepted by Curator
esterase A8 and B8	Xenobiotic resistance (insecticide)	Gene Amplification, Insertion	Culex pipiens northern house mosquito - (species) D	Intraspecific	Candidate Gene	Qiao CL; Marquine M; Pasteur N ; et al. (1998) A new esterase gene amplification involved in OP resistance in Culex pipiens mosquitoes from China.	GP00002641	B1 P16854	Physiology	coamplification of both esterase loci (Est-2 and Est-3)	Culex pipiens northern house mosquito - (species)	Culex pipiens northern house mosquito - (species) D	esterase A8 and B8	Culex pipiens northern house mosquito - (species)	Published - Accepted by Curator
esterase B4	Xenobiotic resistance (insecticide; chlorpyrifos)	Gene Amplification, Insertion	Culex pipiens northern house mosquito - (species) D	Intraspecific	Candidate Gene	Poirié M; Raymond M; Pasteur N (1992) Identification of two distinct amplifications of the esterase B locus in Culex pipiens (L.) mosquito[...]	GP00002639	B1 P16854	Physiology	The production of the esterase B is approximately 50- and 500-fold higher in mosquitoes from France and Cyprus (respectively) than in susceptible insects whereas the number of gene copies is about 25 and 250. Differences of about 7- and 95-fold were also found in the degree of chlorpyrifos resistance.	Culex pipiens northern house mosquito - (species)	Culex pipiens northern house mosquito - (species) D	esterase B4	Culex pipiens northern house mosquito - (species)	Published - Accepted by Curator
esterase B5	Xenobiotic resistance (insecticide; chlorpyrifos)	Gene Amplification, Insertion	Culex pipiens northern house mosquito - (species) D	Intraspecific	Candidate Gene	Poirié M; Raymond M; Pasteur N (1992) Identification of two distinct amplifications of the esterase B locus in Culex pipiens (L.) mosquito[...]	GP00002640	B1 P16854	Physiology	The production of the esterase B is approximately 50- and 500-fold higher in mosquitoes from France and Cyprus (respectively) than in susceptible insects whereas the number of gene copies is about 25 and 250. Differences of about 7- and 95-fold were also found in the degree of chlorpyrifos resistance.	Culex pipiens northern house mosquito - (species)	Culex pipiens northern house mosquito - (species) D	esterase B5	Culex pipiens northern house mosquito - (species)	Published - Accepted by Curator
esterase FE4	Xenobiotic resistance (insecticide)	Gene Amplification, Insertion	Myzus persicae green peach aphid - (species) D	Intraspecific	Candidate Gene	Blackman RL; Spence JM; Field LM ; et al. (1999 ) Variation in the chromosomal distribution of amplified esterase (FE4) genes in Greek field populatio[...] 2 Additional References Field LM; Blackman RL; Tyler-Smith C (1999) Relationship between amount of esterase and gene copy number in insecticide-resistant Myzus persicae[...] Bass C; Puinean AM; Zimmer CT (2014) The evolution of insecticide resistance in the peach potato aphid, Myzus persicae.	GP00002642	P35502	Physiology	Gene amplification	Myzus persicae green peach aphid - (species)	Myzus persicae green peach aphid - (species) D	esterase FE4	Myzus persicae green peach aphid - (species)	Published - Accepted by Curator
esterase NI-EST1	Xenobiotic resistance (organophosphorus insecticides)	Gene Amplification, Insertion	Nilaparvata lugens brown planthopper - (species) D	Intraspecific	Candidate Gene	Small GJ; Hemingway J (2000) Molecular characterization of the amplified carboxylesterase gene associated with organophosphorus i[...]	GP00002638	Ces1 Q8VCC2	Physiology	Southern analysis of genomic DNA from the Sri Lankan OP-resistant and susceptible strains suggests that the Nl-EST1 esterase gene is amplified in the resistant strain	Nilaparvata lugens brown planthopper - (species)	Nilaparvata lugens brown planthopper - (species) D	esterase NI-EST1	Nilaparvata lugens brown planthopper - (species)	Published - Accepted by Curator
esterase type I	Xenobiotic resistance (insecticide)	Gene Amplification, Insertion	Schizaphis graminum greenbug - (species) D	Intraspecific	Candidate Gene	Ono M; Swanson JJ; Field LM ; et al. (1999) Amplification and methylation of an esterase gene associated with insecticide-resistance in greenbug[...] 1 Additional References Vontas JG; Small GJ; Hemingway J (2000) Comparison of esterase gene amplification, gene expression and esterase activity in insecticide susc[...]	GP00002637	P35501	Physiology	The type I esterase is amplified 4- to 8-fold in resistant S. graminum and that the amplified sequences contain 5-methylcytosine at MspI/HpaII sites.	Schizaphis graminum greenbug - (species)	Schizaphis graminum greenbug - (species) D	esterase type I	Schizaphis graminum greenbug - (species)	Published - Accepted by Curator
FAD2 (BnaA.FAD2.a)	Oil composition Oil yield	Coding, Insertion N	Brassica napus rape - (species) D	Domesticated	Linkage Mapping	Yang Q; Fan C; Guo Z ; et al. (2012) Identification of FAD2 and FAD3 genes in Brassica napus genome and development of allele-specific ma[...]	GP00000302	FAD2 P46313	Physiology Physiology	4bp insertion resulting in frameshift and premature stop codon N	Brassica napus rape - (species)	Brassica napus rape - (species) D	FAD2 (BnaA.FAD2.a)	Brassica napus rape - (species)	Published - Accepted by Curator
FAD2B	Oil composition (oleate levels)	Coding, Insertion N	Arachis hypogaea peanut - (species) D	Domesticated	Candidate Gene	Patel M; Jung S; Moore K ; et al. (2004) High-oleate peanut mutants result from a MITE insertion into the FAD2 gene.	GP00002073	FAD2B Q9LKK6	Physiology	insertion of 205-bp miniature inverted-repeat transposable element (MITE) called ahMITE1 at position 665 near the center of the coding region in the case of MF; which causes a frameshift N	Arachis hypogaea peanut - (species)	Arachis hypogaea peanut - (species) D	FAD2B	Arachis hypogaea peanut - (species)	Published - Accepted by Curator
FAD2B	Oil composition (oleate levels)	Coding, Insertion N	Arachis hypogaea peanut - (species) D	Domesticated	Candidate Gene	Patel M; Jung S; Moore K ; et al. (2004) High-oleate peanut mutants result from a MITE insertion into the FAD2 gene.	GP00002074	FAD2B Q9LKK6	Physiology	insertion of 205-bp miniature inverted-repeat transposable element (MITE) called ahMITE1 at position 997 of the coding region; which causes a frameshift N	Arachis hypogaea peanut - (species)	Arachis hypogaea peanut - (species) D	FAD2B	Arachis hypogaea peanut - (species)	Published - Accepted by Curator
Fads2	Fatty acid metabolism (fatty acid desaturation)	Gene Amplification, Insertion	Gasterosteus aculeatus three-spined stickleback - (species) D	Interspecific	Linkage Mapping	Ishikawa A; Kabeya N; Ikeya K ; et al. (2019) A key metabolic gene for recurrent freshwater colonization and radiation in fishes.	GP00001959	fads2 Q9DEX7	Physiology	Fads2 locus is duplicated in G. aculeatus increasing DHA intake and the propensity to invade of freshwater environments. The ancestral copy is on linkage group 19 and the derived copy is on linkage group 12.	Gasterosteus nipponicus (species)	Gasterosteus aculeatus three-spined stickleback - (species) D	Fads2	Gasterosteus aculeatus three-spined stickleback - (species)	Published - Accepted by Curator
Fads2	Fatty acid metabolism (fatty acid desaturation)	Gene Amplification, Insertion	Pungitius tymensis Sakhalin sticlkeback - (species) D Pungitius kaibarae (species) D	Interspecific	Candidate Gene	Ishikawa A; Kabeya N; Ikeya K ; et al. (2019) A key metabolic gene for recurrent freshwater colonization and radiation in fishes.	GP00002053	fads2 Q9DEX7	Physiology	higher number of copies of Fads2.	Pungitius pungitius ninespine stickleback - (species)	Pungitius tymensis Sakhalin sticlkeback - (species) D Pungitius kaibarae (species) D	Fads2	Pungitius tymensis Sakhalin sticlkeback - (species) Pungitius kaibarae (species)	Published - Accepted by Curator
FGF4 retrogene	Limb size	Unknown, Insertion	Canis lupus familiaris dog - (subspecies) D	Domesticated	Association Mapping	Parker HG; VonHoldt BM; Quignon P ; et al. (2009) An expressed fgf4 retrogene is associated with breed-defining chondrodysplasia in domestic dogs.	GP00000309	FGF4 J9P3I7	Morphology	Gene retroposition : 5kb insertion containing a FGF4 retrogene; 25Mb away from the complete (original) FGF4 gene	Canis lupus gray wolf - (species)	Canis lupus familiaris dog - (subspecies) D	FGF4 retrogene	Canis lupus familiaris dog - (subspecies)	Published - Accepted by Curator
FGF5	Hair length (length)	Coding, Insertion N	Felis catus domestic cat - (species) D	Domesticated	Candidate Gene	Drögemüller C; Rüfenacht S; Wichert B ; et al. (2007) Mutations within the FGF5 gene are associated with hair length in cats. 1 Additional References Kehler JS; David VA; Schäffer AA (2007 Sep-Oct) Four independent mutations in the feline fibroblast growth factor 5 gene determine the long-haired p[...]	GP00002172	Fgf5 P15656	Morphology	c.ins356T resulting in frameshift N	Felis catus domestic cat - (species)	Felis catus domestic cat - (species) D	FGF5	Felis catus domestic cat - (species)	Published - Accepted by Curator
FGF5	Hair length	Coding, Insertion	Canis lupus familiaris dog - (subspecies) D	Domesticated	Candidate Gene	Dierks C; Mömke S; Philipp U ; et al. (2013) Allelic heterogeneity of FGF5 mutations causes the long-hair phenotype in dogs. 1 Additional References Cadieu E; Neff MW; Quignon P (2009) Coat variation in the domestic dog is governed by variants in three genes.	GP00002176	Fgf5 P15656	Morphology	c.559_560dupGG p.R188Afs*73	Canis lupus gray wolf - (species)	Canis lupus familiaris dog - (subspecies) D	FGF5	Canis lupus familiaris dog - (subspecies)	Published - Accepted by Curator
flavonoid 3'-hydroxylase (F3'H)	Coloration (flowers)	Cis-regulatory, Insertion	Glycine max soybean - (species) D	Domesticated	Candidate Gene	Zabala G; Vodkin LO (2005) The wp mutation of Glycine max carries a gene-fragment-rich transposon of the CACTA superfamily.	GP00000318	CYP75B1 Q9SD85	Morphology	Transposon insertion in intron 2	Glycine max soybean - (species)	Glycine max soybean - (species) D	flavonoid 3'-hydroxylase (F3'H)	Glycine max soybean - (species)	Published - Accepted by Curator
flavonoid 3'-hydroxylase (F3'H)	Coloration (flowers)	Coding, Insertion N	Ipomoea purpurea common morning-glory - (species) D	Domesticated	Candidate Gene	Zufall RA; Rausher MD (2003 Nov-Dec) The genetic basis of a flower color polymorphism in the common morning glory (Ipomoea purpurea). 3 Additional References Hoshino A; Morita Y; Choi JD (2003) Spontaneous mutations of the flavonoid 3'-hydroxylase gene conferring reddish flowers in the three m[...] Zufall RA; Rausher MD (2004) Genetic changes associated with floral adaptation restrict future evolutionary potential. Des Marais DL; Rausher MD (2010) Parallel evolution at multiple levels in the origin of hummingbird pollinated flowers in Ipomoea.	GP00000319	CYP75B1 Q9SD85	Morphology	insertion of the 0.55-kb DNA transposable element Tip201 belonging to the Ac/Ds superfamily. No excision of Tip201 from the F3'H gene could be detected. Both splicing and polyadenylation patterns of the F3'H transcripts were affected by the Tip201 integration. N	Ipomoea purpurea common morning-glory - (species)	Ipomoea purpurea common morning-glory - (species) D	flavonoid 3'-hydroxylase (F3'H)	Ipomoea purpurea common morning-glory - (species)	Published - Accepted by Curator
flavonoid 3'-hydroxylase (F3'H)	Coloration (flowers)	Coding, Insertion N	Ipomoea tricolor (species) D	Domesticated	Candidate Gene	Hoshino A; Morita Y; Choi JD ; et al. (2003) Spontaneous mutations of the flavonoid 3'-hydroxylase gene conferring reddish flowers in the three m[...]	GP00002088	CYP75B1 Q9SD85	Morphology	a single T insertion generating the stop codon TAG. The accumulation of the F3'H transcripts is drastically reduced by the nonsense-mediated RNA decay. N	Ipomoea tricolor (species)	Ipomoea tricolor (species) D	flavonoid 3'-hydroxylase (F3'H)	Ipomoea tricolor (species)	Published - Accepted by Curator
flavonoid 3';5'-hydroxylase (F3'5'H)	Coloration (flowers; pubescence; seeds)	Coding, Insertion N	Glycine soja (species) D	Intraspecific	Candidate Gene	Guo Y; Qiu LJ (2013) Allele-specific marker development and selection efficiencies for both flavonoid 3'-hydroxylase and [...]	GP00000322	CYP75A2 P37120	Morphology	53bp insertion at +1352 N	Glycine max soybean - (species)	Glycine soja (species) D	flavonoid 3';5'-hydroxylase (F3'5'H)	Glycine soja (species)	Published - Accepted by Curator
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
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
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
follistatin	Limb morphology (wing dimorphism) Flight behavior (wing dimorphism)	Gene Amplification, Insertion	Acyrthosiphon pisum pea aphid - (species) D	Intraspecific	Linkage Mapping	Li B; Bickel RD; Parker BJ ; et al. (2020) A large genomic insertion containing a duplicated follistatin gene is linked to the pea aphid male w[...]	GP00002138	Fs Q86NV3	Morphology Behavior	the api allele from winged males is a 120kb insertion that includes a copy of the follistatin gene	Acyrthosiphon pisum pea aphid - (species)	Acyrthosiphon pisum pea aphid - (species) D	follistatin	Acyrthosiphon pisum pea aphid - (species)	Published - Accepted by Curator	February 9, 2021 22:00
FOXI3	Hair (hypotrichosis)	Coding, Insertion N	Canis lupus familiaris dog - (subspecies) D	Domesticated	Association Mapping	Drögemüller C; Karlsson EK; Hytönen MK ; et al. (2008) A mutation in hairless dogs implicates FOXI3 in ectodermal development.	GP00000351	FOXI3 B5RHS5	Morphology	Frameshift; 7-bp duplication within exon 1 N	Canis lupus gray wolf - (species)	Canis lupus familiaris dog - (subspecies) D	FOXI3	Canis lupus familiaris dog - (subspecies)	Published - Accepted by Curator
FPN2	Metal tolerance	Coding, Insertion N	Arabidopsis thaliana thale cress - (species) D	Intraspecific	Linkage Mapping	Morrissey J; Baxter IR; Lee J ; et al. (2009) The ferroportin metal efflux proteins function in iron and cobalt homeostasis in Arabidopsis.	GP00000354	IREG2 F4KGN5	Physiology	1bp insertion resulting in frameshift N	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species) D	FPN2	Arabidopsis thaliana thale cress - (species)	Published - Accepted by Curator
Frigida (FRI)	Flowering time	Coding, Insertion N	Arabidopsis thaliana thale cress - (species) D	Intraspecific	Candidate Gene	Le Corre V; Roux F; Reboud X (2002) DNA polymorphism at the FRIGIDA gene in Arabidopsis thaliana: extensive nonsynonymous variation is c[...]	GP00000361	FRI P0DH90	Physiology	1bp insertion at 766 N	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species) D	Frigida (FRI)	Arabidopsis thaliana thale cress - (species)	Published - Accepted by Curator
Frigida (FRI)	Flowering time	Coding, Insertion N	Arabidopsis thaliana thale cress - (species) D	Intraspecific	Candidate Gene	Le Corre V; Roux F; Reboud X (2002) DNA polymorphism at the FRIGIDA gene in Arabidopsis thaliana: extensive nonsynonymous variation is c[...] 1 Additional References Shindo C; Aranzana MJ; Lister C (2005) Role of FRIGIDA and FLOWERING LOCUS C in determining variation in flowering time of Arabidopsis.	GP00000362	FRI P0DH90	Physiology	Insertion 1 bp at 1454 in exon 1 N	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species) D	Frigida (FRI)	Arabidopsis thaliana thale cress - (species)	Published - Accepted by Curator
Frigida (FRI)	Flowering time	Coding, Insertion N	Arabidopsis thaliana thale cress - (species) D	Intraspecific	Candidate Gene	Shindo C; Aranzana MJ; Lister C ; et al. (2005) Role of FRIGIDA and FLOWERING LOCUS C in determining variation in flowering time of Arabidopsis.	GP00000371	FRI P0DH90	Physiology	insertion; I490* N	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species) D	Frigida (FRI)	Arabidopsis thaliana thale cress - (species)	Published - Accepted by Curator
Frigida (FRI)	Flowering time	Coding, Insertion N	Arabidopsis thaliana thale cress - (species) D	Intraspecific	Candidate Gene	Shindo C; Aranzana MJ; Lister C ; et al. (2005) Role of FRIGIDA and FLOWERING LOCUS C in determining variation in flowering time of Arabidopsis.	GP00000372	FRI P0DH90	Physiology	insertion; T258* N	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species) D	Frigida (FRI)	Arabidopsis thaliana thale cress - (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
GLABROUS1	Trichome density (leaf)	Coding, Insertion N	Arabidopsis thaliana thale cress - (species)	Intraspecific	Candidate Gene	Hauser MT; Harr B; Schlötterer C (2001) Trichome distribution in Arabidopsis thaliana and its close relative Arabidopsis lyrata: molecular a[...] 1 Additional References Hauser MT; Harr B; Schlötterer C (2001) Trichome distribution in Arabidopsis thaliana and its close relative Arabidopsis lyrata: molecular a[...]	GP00001240	GL1 P27900	Morphology	+1bp at position 352 causing premature stop N	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species)	GLABROUS1	Arabidopsis thaliana thale cress - (species)	Published - Accepted by Curator
GLO(T)	Flower morphology (anther elevation)	Coding, Insertion N	Primula vulgaris (species) D	Intraspecific	Linkage Mapping	Li J; Cocker JM; Wright J ; et al. (2016) Genetic architecture and evolution of the S locus supergene in Primula vulgaris.	GP00001393	GLO Q03378	Morphology	A 2.5 kb retrotransposon in exon 2 severely truncates the protein N	Primula vulgaris (species)	Primula vulgaris (species) D	GLO(T)	Primula vulgaris (species)	Published - Accepted by Curator
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
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
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
GPRC6A	Cell signaling (membrane receptor activity)	Coding, Insertion	Homo sapiens human - (species) D	Intraspecific	Candidate Gene	Jørgensen S; Have CT; Underwood CR ; et al. (2017) Genetic Variations in the Human G Protein-coupled Receptor Class C, Group 6, Member A (GPRC6A) Contr[...]	GP00001669	GPRC6A Q5T6X5	Physiology	insertion of KL (6 bp) resulting in sequence KGKKLY in the third intracellular loop (ICL3) with surface expression and function greatly reduced	Homo sapiens human - (species)	Homo sapiens human - (species) D	GPRC6A	Homo sapiens human - (species)	Published - Accepted by Curator
GSS (glutathione synthetase)	Xenobiotic resistance (arsenic)	Gene Amplification, Insertion	Drosophila melanogaster fruit fly - (species) D	Intraspecific	Candidate Gene	Chakraborty M; Emerson JJ; Macdonald SJ ; et al. (2019) Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits. 1 Additional References Ortiz JG; Opoka R; Kane D (2009) Investigating arsenic susceptibility from a genetic perspective in Drosophila reveals a key role for[...]	GP00002115	Gss2 Q86B44	Physiology	tandem duplication creating the Gss1/Gss2 gene pair. Associated with increased expression of Gss1.	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species) D	GSS (glutathione synthetase)	Drosophila melanogaster fruit fly - (species)	Published - Accepted by Curator
GST	Xenobiotic resistance (pyrethroid)	Gene Amplification, Insertion	Nilaparvata lugens brown planthopper - (species) D	Intraspecific	Candidate Gene	Vontas JG; Small GJ; Nikou DC ; et al. (2002) Purification, molecular cloning and heterologous expression of a glutathione S-transferase involved [...]	GP00002643	GstD1 P20432	Physiology	nlgst1-1 is overexpressed in resistant insects. Southern analysis of genomic DNA from the resistant and susceptible strains indicated that GST-based insecticide resistance may be associated with gene amplification in N. lugens.	Nilaparvata lugens brown planthopper - (species)	Nilaparvata lugens brown planthopper - (species) D	GST	Nilaparvata lugens brown planthopper - (species)	Published - Accepted by Curator
GW2	Grain size	Coding, Insertion N	Triticum aestivum bread wheat - (species) D	Domesticated	Linkage Mapping	Yang Z; Bai Z; Li X ; et al. (2012) SNP identification and allelic-specific PCR markers development for TaGW2, a gene linked to wheat ke[...]	GP00000425	GW2 A4GWX9	Morphology	1bp insertion resulting in premature stop codon N	Triticum aestivum bread wheat - (species)	Triticum aestivum bread wheat - (species) D	GW2	Triticum aestivum bread wheat - (species)	Published - Accepted by Curator
Ha_BtR	Xenobiotic resistance (insecticide; Bt Cry1Ac toxin)	Coding, Insertion N	Helicoverpa armigera cotton bollworm - (species) D	Intraspecific	Candidate Gene	Yang Y; Chen H; Wu S ; et al. (2006) Identification and molecular detection of a deletion mutation responsible for a truncated cadherin o[...] 1 Additional References Zhao J; Jin L; Yang Y (2010) Diverse cadherin mutations conferring resistance to Bacillus thuringiensis toxin Cry1Ac in Helicover[...]	GP00000428	ABCA2 A0A0S0G7V0	Physiology	Insertion of a LTR retrotransposon N	Helicoverpa armigera cotton bollworm - (species)	Helicoverpa armigera cotton bollworm - (species) D	Ha_BtR	Helicoverpa armigera cotton bollworm - (species)	Published - Accepted by Curator
Ha_BtR	Xenobiotic resistance (insecticide; Bt Cry1Ac toxin)	Coding, Insertion N	Helicoverpa armigera cotton bollworm - (species) D	Intraspecific	Candidate Gene	Yang Y; Chen H; Wu S ; et al. (2006) Identification and molecular detection of a deletion mutation responsible for a truncated cadherin o[...] 1 Additional References Zhao J; Jin L; Yang Y (2010) Diverse cadherin mutations conferring resistance to Bacillus thuringiensis toxin Cry1Ac in Helicover[...]	GP00000429	ABCA2 A0A0S0G7V0	Physiology	Insertion of a LTR retrotransposon N	Helicoverpa armigera cotton bollworm - (species)	Helicoverpa armigera cotton bollworm - (species) D	Ha_BtR	Helicoverpa armigera cotton bollworm - (species)	Published - Accepted by Curator
Ha_BtR	Xenobiotic resistance (insecticide; Bt Cry1Ac toxin)	Coding, Insertion N	Helicoverpa armigera cotton bollworm - (species) D	Intraspecific	Candidate Gene	Zhao J; Jin L; Yang Y ; et al. (2010) Diverse cadherin mutations conferring resistance to Bacillus thuringiensis toxin Cry1Ac in Helicover[...] 1 Additional References Yang Y; Chen H; Wu S (2006) Identification and molecular detection of a deletion mutation responsible for a truncated cadherin o[...]	GP00000430	ABCA2 A0A0S0G7V0	Physiology	Insertion of an incomplete RNA transposon (1498bp) N	Helicoverpa armigera cotton bollworm - (species)	Helicoverpa armigera cotton bollworm - (species) D	Ha_BtR	Helicoverpa armigera cotton bollworm - (species)	Published - Accepted by Curator
Ha_BtR	Xenobiotic resistance (insecticide; Bt Cry1Ac toxin)	Coding, Insertion N	Helicoverpa armigera cotton bollworm - (species) D	Intraspecific	Candidate Gene	Zhao J; Jin L; Yang Y ; et al. (2010) Diverse cadherin mutations conferring resistance to Bacillus thuringiensis toxin Cry1Ac in Helicover[...] 1 Additional References Yang Y; Chen H; Wu S (2006) Identification and molecular detection of a deletion mutation responsible for a truncated cadherin o[...]	GP00000431	ABCA2 A0A0S0G7V0	Physiology	Insertion of a DNA transposon N	Helicoverpa armigera cotton bollworm - (species)	Helicoverpa armigera cotton bollworm - (species) D	Ha_BtR	Helicoverpa armigera cotton bollworm - (species)	Published - Accepted by Curator
Ha_BtR	Xenobiotic resistance (insecticide; Bt Cry1Ac toxin)	Coding, Insertion N	Helicoverpa armigera cotton bollworm - (species) D	Intraspecific	Candidate Gene	Zhao J; Jin L; Yang Y ; et al. (2010) Diverse cadherin mutations conferring resistance to Bacillus thuringiensis toxin Cry1Ac in Helicover[...] 1 Additional References Yang Y; Chen H; Wu S (2006) Identification and molecular detection of a deletion mutation responsible for a truncated cadherin o[...]	GP00000432	ABCA2 A0A0S0G7V0	Physiology	Insertion of a LTR retrotransposon N	Helicoverpa armigera cotton bollworm - (species)	Helicoverpa armigera cotton bollworm - (species) D	Ha_BtR	Helicoverpa armigera cotton bollworm - (species)	Published - Accepted by Curator
Ha_BtR	Xenobiotic resistance (insecticide; Bt Cry1Ac toxin)	Coding, Insertion N	Helicoverpa armigera cotton bollworm - (species) D	Intraspecific	Candidate Gene	Zhao J; Jin L; Yang Y ; et al. (2010) Diverse cadherin mutations conferring resistance to Bacillus thuringiensis toxin Cry1Ac in Helicover[...] 1 Additional References Yang Y; Chen H; Wu S (2006) Identification and molecular detection of a deletion mutation responsible for a truncated cadherin o[...]	GP00000433	ABCA2 A0A0S0G7V0	Physiology	Insertion of a LTR retrotransposon N	Helicoverpa armigera cotton bollworm - (species)	Helicoverpa armigera cotton bollworm - (species) D	Ha_BtR	Helicoverpa armigera cotton bollworm - (species)	Published - Accepted by Curator
Hd1	Flowering time	Coding, Insertion N	Oryza sativa rice - (species) D	Domesticated	Candidate Gene	Doi K; Izawa T; Fuse T ; et al. (2004) Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-[...]	GP00000439	HD1 Q9FDX8	Physiology	Retro-element-like inserted in exon 2 N	Oryza glaberrima African rice - (species)	Oryza sativa rice - (species) D	Hd1	Oryza sativa rice - (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
HM1 = HC toxin reductase (HCTR) [possible pseudo-replicate from other Maize entry]	Pathogen resistance	Coding, Insertion N	Zea mays (species) D	Domesticated	Linkage Mapping	Johal GS; Briggs SP (1992) Reductase activity encoded by the HM1 disease resistance gene in maize. 1 Additional References Multani DS; Meeley RB; Paterson AH (1998) Plant-pathogen microevolution: molecular basis for the origin of a fungal disease in maize.	GP00000481	hm1 O49163	Physiology	256-bp transposable element insertion in exon 4 N	Zea mays (species)	Zea mays (species) D	HM1 = HC toxin reductase (HCTR) [possible pseudo-replicate from other Maize entry]	Zea mays (species)	Published - Accepted by Curator
HM2 = HC toxin reductase (HCTR)	Pathogen resistance	Coding, Insertion N	Zea mays (species) D	Domesticated	Candidate Gene	Chintamanani S; Multani DS; Ruess H ; et al. (2008) Distinct mechanisms govern the dosage-dependent and developmentally regulated resistance conferred b[...]	GP00000483	hm2 B8QWA3	Physiology	8-bp insertion in exon 1 that disrupt the reading frame and introduces a stop codon shortly after the beginning of the gene N	Zea mays (species)	Zea mays (species) D	HM2 = HC toxin reductase (HCTR)	Zea mays (species)	Published - Accepted by Curator
HMX1	Organ size (ear; cropped)	Cis-regulatory, Insertion	Bos taurus cattle - (species) D	Domesticated	Association Mapping	Koch CT; Bruggmann R; Tetens J ; et al. (2013) A non-coding genomic duplication at the HMX1 locus is associated with crop ears in highland cattle.	GP00002191	HMX1 Q9NP08	Morphology	76bp duplication in an ultra-conserved enhancer located 148 kb apart of the coding region of HMX1	Bos taurus cattle - (species)	Bos taurus cattle - (species) D	HMX1	Bos taurus cattle - (species)	Published - Accepted by Curator
Hooded	Flower morphology	Cis-regulatory, Insertion	Hordeum vulgare (species) D	Domesticated	Linkage Mapping	Müller KJ; Romano N; Gerstner O ; et al. (1995) The barley Hooded mutation caused by a duplication in a homeobox gene intron.	GP00000488	KNOX3 Q43484	Morphology	305bp duplication in intron 4	Hordeum vulgare (species)	Hordeum vulgare (species) D	Hooded	Hordeum vulgare (species)	Published - Accepted by Curator
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
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
HSP90	Developmental time	Unknown, Insertion	Locusta migratoria migratory locust - (species) D	Intraspecific	Candidate Gene	Chen B; Zhang B; Xu L ; et al. (2017) Transposable Element-Mediated Balancing Selection at Hsp90 Underlies Embryo Developmental Variation.	GP00002437	daf-21 Q18688	Physiology	an Lm1 SINE insertion in the third exon of the Hsp90 gene produces an alternative splicing form associated with faster development and higher developmental synchrony. Found by scanning Lm1 insertions in natural locust populations.	Locusta migratoria migratory locust - (species)	Locusta migratoria migratory locust - (species) D	HSP90	Locusta migratoria migratory locust - (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
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
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	Coloration (coat ; white-spotting)	Coding, Insertion N	Canis lupus familiaris dog - (subspecies) D	Domesticated	Candidate Gene	Wong AK; Ruhe AL; Robertson KR ; et al. (2013) A de novo mutation in KIT causes white spotting in a subpopulation of German Shepherd dogs.	GP00002228	Kit P05532	Morphology	a 1-bp insertion of an adenine 70 bases downstream of the beginning of exon 2 resulting in frameshift N	Canis lupus gray wolf - (species)	Canis lupus familiaris dog - (subspecies) D	Kit	Canis lupus familiaris dog - (subspecies)	Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)	Coloration (coat)	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)	2 Mutations:	Sus scrofa domesticus domestic pig - (subspecies) D	Domesticated	Linkage Mapping	Marklund S; Kijas J; Rodriguez-Martinez H ; et al. (1998) Molecular basis for the dominant white phenotype in the domestic pig. 3 Additional References Rubin CJ; Megens HJ; Martinez Barrio A (2012) Strong signatures of selection in the domestic pig genome. Sun G; Liang X; Qin K (2020) Functional Analysis of KIT Gene Structural Mutations Causing the Porcine Dominant White Phenotype Us[...] Pielberg G; Day AE; Plastow GS (2003) A sensitive method for detecting variation in copy numbers of duplicated genes.	GP00000520	Kit P05532	Morphology	2 mutations	Sus scrofa pig - (species)	Sus scrofa domesticus domestic pig - (subspecies) D	Kit (type III receptor protein-tyrosine kinase)	Sus scrofa domesticus domestic pig - (subspecies)	Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)	Coloration (coat)	Cis-regulatory, 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
L6	Pathogen resistance	Coding, Insertion N	Linum usitatissimum flax - (species)	Intraspecific	Linkage Mapping	Lawrence GJ; Finnegan EJ; Ayliffe MA ; et al. (1995) The L6 gene for flax rust resistance is related to the Arabidopsis bacterial resistance gene RPS2 an[...]	GP00000528	L6 Q40253	Physiology	Truncated protein due to insertion of a transposable element. Reversion to resistance among descendants of mutant X75 was associated with excision of the newly transposable element Ac. N	Linum usitatissimum flax - (species)	Linum usitatissimum flax - (species)	L6	Linum usitatissimum flax - (species)	Published - Accepted by Curator
Lethal Hybrid rescue	Hybrid incompatibility (F1 male lethality)	Coding, Insertion	Drosophila simulans (species) D	Interspecific	Linkage Mapping	Brideau NJ; Flores HA; Wang J ; et al. (2006) Two Dobzhansky-Muller genes interact to cause hybrid lethality in Drosophila. 2 Additional References Nolte V; Weigel D; Schlötterer C (2008) The impact of shared ancestral variation on hybrid male lethality--a 16 codon indel in the Drosophil[...] Maheshwari S; Barbash DA (2012) An indel polymorphism in the hybrid incompatibility gene lethal hybrid rescue of Drosophila is funct[...]	GP00000540	Lhr Q95RV3	Physiology	16a.a. insertion with effect in sensitive background only (Maheshwari and Barbash 2012)	Drosophila melanogaster fruit fly - (species)	Drosophila simulans (species) D	Lethal Hybrid rescue	Drosophila simulans (species)	Published - Accepted by Curator
LOC105383139	Courtship behavior	Other, Insertion	Lepidoptera butterflies and moths - (order) D	Intergeneric or Higher	Association Mapping	Li Y; Liu Z; Liu C ; et al. (2022) HGT is widespread in insects and contributes to male courtship in lepidopterans.	GP00002412		Behavior	Horizontal Gene Transfer from Listeria bacteria to Lepidoptera of an entire gene coding region. The gene contains an alcohol dehydrogenase domain and a zinc-binding dehydrogenase domain.	Trichoptera caddisflies - (order)	Lepidoptera butterflies and moths - (order) D	LOC105383139	Lepidoptera butterflies and moths - (order)	Published - Accepted by Curator
Low-density lipoprotein receptor-related protein 2	Organ size (eye; enlarged)	3 Mutations: Coding N	Carassius auratus goldfish - (species) D	Domesticated	Association Mapping	Kon T; Omori Y; Fukuta K ; et al. (2020) The Genetic Basis of Morphological Diversity in Domesticated Goldfish.	GP00002349	LRP2 P98164	Morphology	3 mutations	Carassius auratus goldfish - (species)	Carassius auratus goldfish - (species) D	Low-density lipoprotein receptor-related protein 2	Carassius auratus goldfish - (species)	Published - Accepted by Curator
Lysine histidine transporter 1	Pathogen resistance	Coding, Insertion N	Zea mays (species) D	Domesticated	Linkage Mapping	Zhao Y; Lu X; Liu C ; et al. (2012) Identification and fine mapping of rhm1 locus for resistance to Southern corn leaf blight in maize.	GP00000555	LHT1 Q9FKS8	Physiology	354bp insertioin resulting in premature stop codon N	Zea mays (species)	Zea mays (species) D	Lysine histidine transporter 1	Zea mays (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
MC1R	Coloration (skin)	Coding, Insertion N	Sus scrofa domesticus domestic pig - (subspecies) D	Domesticated	Linkage Mapping	Kijas JM; Moller M; Plastow G ; et al. (2001) A frameshift mutation in MC1R and a high frequency of somatic reversions cause black spotting in pig[...] 1 Additional References Liu R; Jin L; Long K (2016) Detection of genetic diversity and selection at the coding region of the melanocortin receptor 1 (MC[...]	GP00000631	MC1R Q01726	Morphology	2bp insertion at 23 generates early stop @ 56 & D"121"N ? N	Sus scrofa pig - (species)	Sus scrofa domesticus domestic pig - (subspecies) D	MC1R	Sus scrofa domesticus domestic pig - (subspecies)	Published - Accepted by Curator
MCO	Metal tolerance (copper)	Gene Amplification, Insertion	Erythranthe guttata spotted monkey flower - (species) D	Intraspecific	Linkage Mapping	Wright KM; Lloyd D; Lowry DB ; et al. (2013) Indirect evolution of hybrid lethality due to linkage with selected locus in Mimulus guttatus. 1 Additional References Wright Kevin M; Hellsten Uffe; Xu Chenling (2015 ) Adaptation to heavy-metal contaminated environments proceeds via selection on pre-existing genetic v[...]	GP00001814	LPR2 Q949X9	Physiology	several recent tandem duplications of this gene are responsible for the 12x increase in expression observed in copper tolerant lines - 6X fold enrichment of aligned reads at MCO	Erythranthe guttata spotted monkey flower - (species)	Erythranthe guttata spotted monkey flower - (species) D	MCO	Erythranthe guttata spotted monkey flower - (species)	Published - Accepted by Curator
Melanophilin (MLPH)	Coloration (coat)	Coding, Insertion N	Canis lupus familiaris dog - (subspecies) D	Domesticated	Candidate Gene	Van Buren SL; Minor KM; Grahn RA ; et al. (2020) A Third MLPH Variant Causing Coat Color Dilution in Dogs.	GP00002331	Mlph Q91V27	Morphology	c.667_668insC p.(His223Profs*41) N	Canis lupus gray wolf - (species)	Canis lupus familiaris dog - (subspecies) D	Melanophilin (MLPH)	Canis lupus familiaris dog - (subspecies)	Published - Accepted by Curator
MFSD12	Coloration (coat)	Coding, Insertion N	Equus caballus horse - (species) D	Domesticated	Association Mapping	Tanaka J; Leeb T; Rushton J ; et al. (2019) Frameshift Variant in MFSD12 Explains the Mushroom Coat Color Dilution in Shetland Ponies.	GP00002243	MFSD12 Q6NUT3	Morphology	p.(Asp201fs) due to c.600Cins N	Equus caballus horse - (species)	Equus caballus horse - (species) D	MFSD12	Equus caballus horse - (species)	Published - Accepted by Curator
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
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
MLO	Pathogen resistance	Gene Amplification, Insertion	Hordeum vulgare (species) D	Domesticated	Linkage Mapping	Piffanelli P; Ramsay L; Waugh R ; et al. (2004) A barley cultivation-associated polymorphism conveys resistance to powdery mildew.	GP00000672	MLO P93766	Physiology	Tandem array duplication including promoter and partial CDS; resulting in loss-of-function by transcriptional interference	Hordeum vulgare (species)	Hordeum vulgare (species) D	MLO	Hordeum vulgare (species)	Published - Accepted by Curator
Molybdenum transporter1 (MOT1)	Metal tolerance	Gene Amplification, Insertion	Arabidopsis thaliana thale cress - (species) D	Intraspecific	Association Mapping	Forsberg SK; Andreatta ME; Huang XY ; et al. (2015) The Multi-allelic Genetic Architecture of a Variance-Heterogeneity Locus for Molybdenum Concentratio[...]	GP00000677	MOT1 Q9SL95	Physiology	330bp duplication followed by minor indels	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species) D	Molybdenum transporter1 (MOT1)	Arabidopsis thaliana thale cress - (species)	Published - Accepted by Curator
MTH1	Low-glucose adaptation (experimental evolution)	Coding, Insertion N	Saccharomyces cerevisiae baker's yeast - (species) D	Experimental Evolution	Association Mapping	Gresham D; Desai MM; Tucker CM ; et al. (2008) The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments [...]	GP00000680	CUP1-1 P0CX80	Physiology	Ty retrotranposition resulting in a coding frameshift N	Saccharomyces cerevisiae baker's yeast - (species)	Saccharomyces cerevisiae baker's yeast - (species) D	MTH1	Saccharomyces cerevisiae baker's yeast - (species)	Published - Accepted by Curator
mucilage-modified 2 (mum2)	Mucilage (seeds)	Coding, Insertion N	Arabidopsis thaliana thale cress - (species)	Intraspecific	Candidate Gene	Saez-Aguayo S; Rondeau-Mouro C; Macquet A ; et al. (2014) Local evolution of seed flotation in Arabidopsis.	GP00001277	BGAL6 Q9FFN4	Physiology	TACA insertion @position 4906 causing frame shift + Stop N	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species)	mucilage-modified 2 (mum2)	Arabidopsis thaliana thale cress - (species)	Published - Accepted by Curator
Multidrug resistance protein 1 (pvmdr1)	Xenobiotic resistance (mefloquine)	Gene Amplification, Insertion	Plasmodium vivax malaria parasite P. vivax - (species) D	Intraspecific	Association Mapping	Pearson RD; Amato R; Auburn S ; et al. (2016) Genomic analysis of local variation and recent evolution in Plasmodium vivax.	GP00001482	B7STB0	Physiology	37 kb duplication on chromosome 10 that includes pvmdr1	Plasmodium vivax malaria parasite P. vivax - (species)	Plasmodium vivax malaria parasite P. vivax - (species) D	Multidrug resistance protein 1 (pvmdr1)	Plasmodium vivax malaria parasite P. vivax - (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
Myostatin (MSTN = GDF8)	Muscular mass (double muscling)	Coding, Insertion N	Ovis aries sheep - (species) D	Domesticated	Candidate Gene	Boman IA; Våge DI (2009) An insertion in the coding region of the myostatin (MSTN) gene affects carcass conformation and fatn[...]	GP00000694	MSTN O14793	Morphology	1bp insertion resulting in premature stop codon at position 49 N	Ovis aries sheep - (species)	Ovis aries sheep - (species) D	Myostatin (MSTN = GDF8)	Ovis aries sheep - (species)	Published - Accepted by Curator
Myostatin (MSTN = GDF8)	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
NAM-B1 (=Gpc-B1)	Grain content Senescence (grain)	Coding, Insertion N	Triticum turgidum (species) D	Domesticated	Linkage Mapping	Uauy C; Distelfeld A; Fahima T ; et al. (2006) A NAC Gene regulating senescence improves grain protein, zinc, and iron content in wheat.	GP00000717	NAM-B1 A0SPJ4	Physiology Physiology	1bp insertion resulting in frameshift N	Triticum turgidum (species)	Triticum turgidum (species) D	NAM-B1 (=Gpc-B1)	Triticum turgidum (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
Oca2	Coloration (albinism)	Coding, Insertion N	Pantherophis guttatus (species) D	Intraspecific	Linkage Mapping	Saenko SV; Lamichhaney S; Martinez Barrio A ; et al. (2015) Amelanism in the corn snake is associated with the insertion of an LTR-retrotransposon in the OCA2 g[...]	GP00001619	OCA2 Q04671	Morphology	insertion of an LTR-retrotransposon (5832-bp) in the 11th intron resulting after splicing in an additional 397-bp fragment constituted of 3 new exons inserted between exons 11 and 12. Generates truncated protein with two stop codons N	Pantherophis guttatus (species)	Pantherophis guttatus (species) D	Oca2	Pantherophis guttatus (species)	Published - Accepted by Curator
Oca2	Coloration (albinism)	Coding, Insertion N	Carassius auratus goldfish - (species) D	Domesticated	Candidate Gene	Kon T; Omori Y; Fukuta K ; et al. (2020) The Genetic Basis of Morphological Diversity in Domesticated Goldfish.	GP00002351	Oca2 Q62052	Morphology	1-bp insert creating a frameshift and a truncated protein (470 amino acids instead of 805). In oca2L ohnolog on chromosome LG6. N	Carassius auratus goldfish - (species)	Carassius auratus goldfish - (species) D	Oca2	Carassius auratus goldfish - (species)	Published - Accepted by Curator
OCYMENE SYNTHASE (OS)	Fragrance (floral terpenoid volatiles; E- beta-ocimene)	Coding, Insertion N	Erythranthe bicolor (species) D	Interspecific	Candidate Gene	Peng F; Byers KJRP; Bradshaw HD (2017) Less is more: Independent loss-of-function OCIMENE SYNTHASE alleles parallel pollination syndrome di[...]	GP00001763	TPS02 P0CJ43	Physiology	2-bp insertion in the second exon, producing a frameshift mutation and premature termination N	Erythranthe lewisii (species)	Erythranthe bicolor (species) D	OCYMENE SYNTHASE (OS)	Erythranthe bicolor (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
opsin - rhodopsin (LWS)	Color vision	Coding, Insertion N	Mesoplodon bidens Sowerby's beaked whale - (species) D	Intergeneric or Higher	Candidate Gene	Meredith RW; Gatesy J; Emerling CA ; et al. (2013) Rod monochromacy and the coevolution of cetacean retinal opsins.	GP00000774	OPN1LW P04000	Physiology	4bp frameshift insertion in exon 2 of LWS N	Cetacea whales - (order)	Mesoplodon bidens Sowerby's beaked whale - (species) D	opsin - rhodopsin (LWS)	Mesoplodon bidens Sowerby's beaked whale - (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
P2RY5	Hair type (woolly)	Coding, Insertion N	Homo sapiens human - (species) D	Intraspecific	Association Mapping	Shimomura Y; Wajid M; Ishii Y ; et al. (2008) Disruption of P2RY5, an orphan G protein-coupled receptor, underlies autosomal recessive woolly hair[...]	GP00000817	LPAR6 P43657	Morphology	at position 69 insertion of 4bp CATG - causes frameshift at codon 24 (PTC +29) N	Homo sapiens human - (species)	Homo sapiens human - (species) D	P2RY5	Homo sapiens human - (species)	Published - Accepted by Curator
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
PHO5	Low-phosphate adaptation (experimental evolution)	Gene Amplification, Insertion	Saccharomyces cerevisiae baker's yeast - (species)	Experimental Evolution	Association Mapping	Gresham D; Desai MM; Tucker CM ; et al. (2008) The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments [...]	GP00000864	PHO5 P00635	Physiology	Gene duplication. Out of 8 lines; 2 distinct lines evolved structural variation at PHO5. (Interestingly; one was a deletion and another one was a gene amplification)	Saccharomyces cerevisiae baker's yeast - (species)	Saccharomyces cerevisiae baker's yeast - (species)	PHO5	Saccharomyces cerevisiae baker's yeast - (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
phytochrome A (PHYA)	Light sensitivity High-altitude adaptation	Coding, Insertion N	Glycine max soybean - (species) D	Domesticated	Candidate Gene	Liu B; Kanazawa A; Matsumura H ; et al. (2008) Genetic redundancy in soybean photoresponses associated with duplication of the phytochrome A gene. 1 Additional References Kanazawa A; Liu B; Kong F (2009) Adaptive evolution involving gene duplication and insertion of a novel Ty1/copia-like retrotransposo[...]	GP00002104	PHYA P14712	Physiology Physiology	insertion of a retrotransposon in exon 1 - The transposable element is SORE-1 = a novel Ty1/copia-like retrotransposon in soybean N	Glycine max soybean - (species)	Glycine max soybean - (species) D	phytochrome A (PHYA)	Glycine max soybean - (species)	Published - Accepted by Curator
phytoene synthase	Carotenoid content (fruit)	Coding, Insertion N	Solanum lycopersicum tomato - (species) D	Domesticated	Linkage Mapping	Fray RG; Grierson D (1993) Identification and genetic analysis of normal and mutant phytoene synthase genes of tomato by sequen[...] 1 Additional References Gilbert C; Feschotte C (2018) Horizontal acquisition of transposable elements and viral sequences: patterns and consequences.	GP00001718	PSY1 P49085	Physiology	insertion of a Rider transposable element within the coding region N	Solanum lycopersicum tomato - (species)	Solanum lycopersicum tomato - (species) D	phytoene synthase	Solanum lycopersicum tomato - (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
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
plg-1	Copulatory plug	Coding, Insertion N	Caenorhabditis elegans (species) D	Intraspecific	Linkage Mapping	Palopoli MF; Rockman MV; TinMaung A ; et al. (2008) Molecular basis of the copulatory plug polymorphism in Caenorhabditis elegans.	GP00000898		Physiology	insertion of transposable element in an exon N	Caenorhabditis elegans (species)	Caenorhabditis elegans (species) D	plg-1	Caenorhabditis elegans (species)	Published - Accepted by Curator
PMEI6	Mucilage (seeds)	Coding, Insertion N	Arabidopsis thaliana thale cress - (species)	Intraspecific	Linkage Mapping	Saez-Aguayo S; Rondeau-Mouro C; Macquet A ; et al. (2014) Local evolution of seed flotation in Arabidopsis. 1 Additional References Saez-Aguayo S; Ralet MC; Berger A (2013) PECTIN METHYLESTERASE INHIBITOR6 promotes Arabidopsis mucilage release by limiting methylesterificat[...]	GP00001272	AXX17_At2g45450 A0A178VVA1	Physiology	frameshift mutation due to a 1-bp insertion 581 bp after the ATG codon that changed amino acids 194 to 205 followed by the introduction of a stop codon N	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species)	PMEI6	Arabidopsis thaliana thale cress - (species)	Published - Accepted by Curator
PMEL17	Coloration (feathers)	Coding, Insertion	Gallus gallus chicken - (species) D	Domesticated	Linkage Mapping	Kerje S; Sharma P; Gunnarsson U ; et al. (2004) The Dominant white, Dun and Smoky color variants in chicken are associated with insertion/deletion p[...]	GP00000913	PMEL Q98917	Morphology	insertion of amino acid 723-725 due to a 9bp-insert in exon 10	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	PMEL17	Gallus gallus chicken - (species)	Published - Accepted by Curator
PMEL17	Coloration (coat)	Cis-regulatory, Insertion	Canis lupus familiaris dog - (subspecies) D	Domesticated	Association Mapping	Clark LA; Wahl JM; Rees CA ; et al. (2006) Retrotransposon insertion in SILV is responsible for merle patterning of the domestic dog.	GP00002072	Pmel Q60696	Morphology	due to a short interspersed element (SINE) insertion at the intron 10/exon 11 boundary. The SINE segregates with the merle phenotype in multiple breeds (Collie, Border Collie, Australian Shepherd, Cardigan Welsh Corgi, Dachshund, and Great Dane) and is absent from dogs representing breeds that do not have merle patterning. All examined harlequin Great Danes harbored the insertion in either a heterozygous or homozygous state.	Canis lupus familiaris dog - (subspecies)	Canis lupus familiaris dog - (subspecies) D	PMEL17	Canis lupus familiaris dog - (subspecies)	Published - Accepted by Curator
PMEL17	Coloration (coat)	Coding, Insertion	Mus musculus house mouse - (species) D	Domesticated	Linkage Mapping	Kwon BS; Halaban R; Ponnazhagan S ; et al. (1995) Mouse silver mutation is caused by a single base insertion in the putative cytoplasmic domain of Pme[...]	GP00002101	Pmel Q60696	Morphology	single nucleotide (A) insertion in the putative cytoplasmic tail of the si/si Pmel 17 cDNA clone. This insertion is predicted to alter the last 24 amino acids at the C-terminus. Also predicted is the extension of the Pmel 17 protein by 12 residues because a new termination signal is created downstream from the wild-type reading frame. The silver pmel 17 protein has a major defect at the carboxyl terminus.	Mus musculus house mouse - (species)	Mus musculus house mouse - (species) D	PMEL17	Mus musculus house mouse - (species)	Published - Accepted by Curator
PMEL17	Coloration (coat)	Cis-regulatory, Insertion	Canis lupus familiaris dog - (subspecies) D	Domesticated	Candidate Gene	Langevin M; Synkova H; Jancuskova T ; et al. (2018) Merle phenotypes in dogs - SILV SINE insertions from Mc to Mh. 1 Additional References 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, 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, 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
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
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
PVX_101445	Xenobiotic resistance (chloroquine)	Gene Amplification, Insertion	Plasmodium vivax malaria parasite P. vivax - (species) D	Intraspecific	Association Mapping	Pearson RD; Amato R; Auburn S ; et al. (2016) Genomic analysis of local variation and recent evolution in Plasmodium vivax.	GP00001483	PVX_101445 A5K913	Physiology	3 kb duplication on chromosome 14 that includes PVX_101445	Plasmodium vivax malaria parasite P. vivax - (species)	Plasmodium vivax malaria parasite P. vivax - (species) D	PVX_101445	Plasmodium vivax malaria parasite P. vivax - (species)	Published - Accepted by Curator
R-spondin-2 (RSPO2)	Hair length (moustache / eyebrows)	Cis-regulatory, Insertion	Canis lupus familiaris dog - (subspecies) D	Domesticated	Association Mapping	Cadieu E; Neff MW; Quignon P ; et al. (2009) Coat variation in the domestic dog is governed by variants in three genes.	GP00000945	Rspo2 Q8BFU0	Morphology	a 167bp insertion within the 3'UTR at position which leads to a threefold increase in transcription of RSPO2 in muzzle skin of dogs with furnishings	Canis lupus gray wolf - (species)	Canis lupus familiaris dog - (subspecies) D	R-spondin-2 (RSPO2)	Canis lupus familiaris dog - (subspecies)	Published - Accepted by Curator
r1 colored1	Coloration (seeds)	Unknown, Insertion	Zea mays (species) D	Domesticated	Linkage Mapping	Hanson MA; Gaut BS; Stec AO ; et al. (1996) Evolution of anthocyanin biosynthesis in maize kernels: the role of regulatory and enzymatic loci. 1 Additional References Kong Q; Pattanaik S; Feller A (2012) Regulatory switch enforced by basic helix-loop-helix and ACT-domain mediated dimerizations of the ma[...]	GP00000947	Z138B04_Z333J11.11 Q8S483	Morphology	insertion of transposable element Ac	Zea mays (species)	Zea mays (species) D	r1 colored1	Zea mays (species)	Published - Accepted by Curator
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
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
resistance to dieldrin	Xenobiotic resistance (insecticide)	Gene Amplification, Insertion	Drosophila melanogaster fruit fly - (species)	Intraspecific	Candidate Gene	Remnant EJ; Good RT; Schmidt JM ; et al. (2013) Gene duplication in the major insecticide target site, Rdl, in Drosophila melanogaster.	GP00002452	Rdl P25123	Physiology	113-kb duplication containing one WT copy of Rdl and a second copy with two point mutations: an Ala(301) to Ser resistance mutation and Met(360) to Ile replacement. Individuals with this duplication exhibit intermediate dieldrin resistance compared with single copy Ser(301) homozygotes and reduced temperature sensitivity and altered RNA editing associated with the resistant allele. Ectopic recombination between Roo transposable elements is involved in generating this genomic rearrangement. The duplication phenotypes were confirmed by construction of a transgenic artificial duplication integrating the 55.7-kb Rdl locus with a Ser(301) change into an Ala(301) background.	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species)	resistance to dieldrin	Drosophila melanogaster fruit fly - (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
RPS2	Pathogen resistance	Coding, Insertion N	Arabidopsis thaliana thale cress - (species) D	Intraspecific	Linkage Mapping	Mindrinos M; Katagiri F; Yu GL ; et al. (1994) The A. thaliana disease resistance gene RPS2 encodes a protein containing a nucleotide-binding site [...]	GP00001011	RPS2 Q42484	Physiology	10bp insertion close to the 5' end causing a frameshift N	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species) D	RPS2	Arabidopsis thaliana thale cress - (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
RXFP2	Horns absence Somatic sex change	Gene Amplification, Insertion	Ovis aries sheep - (species)	Domesticated	Linkage Mapping	Johnston SE; Gratten J; Berenos C ; et al. (2013) Life history trade-offs at a single locus maintain sexually selected genetic variation. 1 Additional References Wiedemar N; Drögemüller C (2015) A 1.8-kb insertion in the 3'-UTR of RXFP2 is associated with polledness in sheep.	GP00001019	RXFP2 Q8WXD0	Morphology Physiology	1833-bp genomic insertion located in the 3'-UTR region of RXFP2	Ovis aries sheep - (species)	Ovis aries sheep - (species)	RXFP2	Ovis aries sheep - (species)	Published - Accepted by Curator
SCRB15	Coloration (silk; carotenoids)	Coding, Insertion N	Bombyx mori domestic silkworm - (species) D	Domesticated	Linkage Mapping	Sakudoh T; Kuwazaki S; Iizuka T ; et al. (2013) CD36 homolog divergence is responsible for the selectivity of carotenoid species migration to the si[...]	GP00001904	SCRB15 K7ZRZ1	Morphology	In the F mutant SCRB15 mRNA structure was severely disrupted due to a 1.4 kb genomic insertion in a coding exon N	Bombyx mori domestic silkworm - (species)	Bombyx mori domestic silkworm - (species) D	SCRB15	Bombyx mori domestic silkworm - (species)	Published - Accepted by Curator
Serine/threonine protein kinase RIM15	Nitrogen use (growth efficiency)	Coding, Insertion N	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.	GP00001500	RIM15 P43565	Physiology	2 bp insertion 459_460insCA shifting the reading frame to cause an early stop codon (null allele) N	Saccharomyces cerevisiae baker's yeast - (species)	Saccharomyces cerevisiae baker's yeast - (species) D	Serine/threonine protein kinase RIM15	Saccharomyces cerevisiae baker's yeast - (species)	Published - Accepted by Curator
SGK3	Hair (hypotrichosis)	Coding, Insertion N	Canis lupus familiaris dog - (subspecies) D	Domesticated	Association Mapping	Hytönen MK; Lohi H (2019) A frameshift insertion in SGK3 leads to recessive hairlessness in Scottish Deerhounds: a candidate g[...] 1 Additional References Parker HG; Whitaker DT; Harris AC (2020) Whole Genome Analysis of a Single Scottish Deerhound Dog Family Provides Independent Corroboration T[...]	GP00002263	Sgk3 Q9ERE3	Morphology	c.137_138insT p.Glu47GlyfsTer3 N	Canis lupus familiaris dog - (subspecies)	Canis lupus familiaris dog - (subspecies) D	SGK3	Canis lupus familiaris dog - (subspecies)	Published - Accepted by Curator
Shattering1 - OsSh1	Seed shattering	Unknown, Insertion	Oryza sativa rice - (species) D	Domesticated	Association Mapping	Lin Z; Li X; Shannon LM ; et al. (2012) Parallel domestication of the Shattering1 genes in cereals. 2 Additional References He Z; Zhai W; Wen H (2011) Two evolutionary histories in the genome of rice: the roles of domestication genes. Xu X; Liu X; Ge S (2011) Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically [...]	GP00001039	YAB2 Q10FZ7	Physiology	>4kb insertion in intron (unclear)	Oryza sativa rice - (species)	Oryza sativa rice - (species) D	Shattering1 - OsSh1	Oryza sativa 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)	Coding, Insertion	Oryzias latipes Japanese medaka - (species) D	Domesticated	Linkage Mapping	Fukamachi S; Shimada A; Shima A (2001) Mutations in the gene encoding B, a novel transporter protein, reduce melanin content in medaka.	GP00002286	SLC45A2 Q9UMX9	Morphology	tandem insertion of 195 nt identical to the adjacent ORF sequence. This tandem repeat produces an insertion of 65 amino acids	Oryzias latipes Japanese medaka - (species)	Oryzias latipes Japanese medaka - (species) D	SLC45A2=MATP	Oryzias latipes Japanese medaka - (species)	Published - Accepted by Curator
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
SlMYBATV	Coloration (anthocyanin accumulation in fruits)	Coding, Insertion N	Solanum cheesmaniae (species) D	Intraspecific	Linkage Mapping	Cao X; Qiu Z; Wang X ; et al. (2017) A putative R3 MYB repressor is the candidate gene underlying atroviolacium, a locus for anthocyanin [...]	GP00001906	CPC O22059	Morphology; Physiology	SlMYBATV encodes a R3 MYB transcription factor. 4-bp insertion predicted to result in a frame-shift that would alter the protein sequence from amino-acid position 20 onwards by inducing premature termination of translation including the R3/bHLH-binding domain N	Solanum lycopersicum tomato - (species)	Solanum cheesmaniae (species) D	SlMYBATV	Solanum cheesmaniae (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
SOD1	Xenobiotic resistance (paraquat)	Coding, Insertion	Drosophila melanogaster fruit fly - (species) D	Intraspecific	Candidate Gene	Vontas JG; Tsakas SC; Loukas M ; et al. (2001) Low-activity allele of copper-zinc superoxide dismutase (CuZnSOD) in Drosophila increases paraquat g[...]	GP00001985	Sod1 P61851	Physiology	Insertion of a 0.68kb truncated P-element 47bp downstream of the transcription start site.	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species) D	SOD1	Drosophila melanogaster fruit fly - (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
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
Starch branching enzyme (SBEI) = rugosus (R)	Starch structure Seed aspect	Coding, Insertion N	Pisum sativum pea - (species) D	Domesticated	Linkage Mapping	Bhattacharyya MK; Smith AM; Ellis TH ; et al. (1990) The wrinkled-seed character of pea described by Mendel is caused by a transposon-like insertion in a[...]	GP00001078	SBEI Q41058	Physiology Morphology	800 bp TE insertion; probably disrupts the last 61 amino acids of the SBEI protein N	Pisum sativum pea - (species)	Pisum sativum pea - (species) D	Starch branching enzyme (SBEI) = rugosus (R)	Pisum sativum pea - (species)	Published - Accepted by Curator
StCDF1	Latitudinal adaptation	Coding, Insertion N	Solanum tuberosum potato - (species) D	Domesticated	Linkage Mapping	Kloosterman B; Abelenda JA; Gomez Mdel M ; et al. (2013) Naturally occurring allele diversity allows potato cultivation in northern latitudes.	GP00001079	CDF1 Q8W1E3	Physiology	+7bp insertion resulting in frameshift and truncated protein N	Solanum tuberosum potato - (species)	Solanum tuberosum potato - (species) D	StCDF1	Solanum tuberosum potato - (species)	Published - Accepted by Curator
StCDF1	Latitudinal adaptation	Coding, Insertion	Solanum tuberosum potato - (species) D	Domesticated	Linkage Mapping	Kloosterman B; Abelenda JA; Gomez Mdel M ; et al. (2013) Naturally occurring allele diversity allows potato cultivation in northern latitudes.	GP00001080	CDF1 Q8W1E3	Physiology	865bp insertion leading to a fusion protein	Solanum tuberosum potato - (species)	Solanum tuberosum potato - (species) D	StCDF1	Solanum tuberosum potato - (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
Taqpep	Coloration (coat)	Coding, Insertion N	Acinonyx jubatus cheetah - (species) D	Intraspecific	Candidate Gene	Kaelin CB; Xu X; Hong LZ ; et al. (2012) Specifying and sustaining pigmentation patterns in domestic and wild cats.	GP00001105	Lvrn Q2KHK3	Morphology	1bp insertion resulting in frameshift p.N977Kfs110 N	Acinonyx jubatus cheetah - (species)	Acinonyx jubatus cheetah - (species) D	Taqpep	Acinonyx jubatus cheetah - (species)	Published - Accepted by Curator
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
timeless (tim)	Diapause Locomotor activity	Coding, Insertion N	Drosophila melanogaster fruit fly - (species) D	Intraspecific	Candidate Gene	Tauber E; Zordan M; Sandrelli F ; et al. (2007) Natural selection favors a newly derived timeless allele in Drosophila melanogaster. 1 Additional References Sandrelli F; Tauber E; Pegoraro M (2007) A molecular basis for natural selection at the timeless locus in Drosophila melanogaster.	GP00001129	TIMELESS Q9UNS1	Physiology Behavior; Physiology	1bp insertion; allows production of longer protein from upstream start codon N	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species) D	timeless (tim)	Drosophila melanogaster fruit fly - (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
TRIM5alpha-CypA chimeric gene	Pathogen resistance (retroviruses)	Other, Insertion	Aotus night monkeys - (genus)	Intergeneric or Higher	Candidate Gene	Sayah DM; Sokolskaja E; Berthoux L ; et al. (2004) Cyclophilin A retrotransposition into TRIM5 explains owl monkey resistance to HIV-1. 1 Additional References Nisole S; Lynch C; Stoye JP (2004) A Trim5-cyclophilin A fusion protein found in owl monkey kidney cells can restrict HIV-1.	GP00001136	TRIM5 Q9C035	Physiology	LINE-mediated retrotransposition of the CyclophilinA gene between exons 7 and 8 of TRIM5alpha	Platyrrhini New World monkeys - (parvorder)	Aotus night monkeys - (genus)	TRIM5alpha-CypA chimeric gene	Aotus night monkeys - (genus)	Published - Accepted by Curator
TRIM5alpha-CypA chimeric gene	Pathogen resistance (retroviruses)	Other, Insertion	Macaca macaques - (genus)	Intergeneric or Higher	Candidate Gene	Stoye JP; Yap MW (2008) Chance favors a prepared genome.	GP00001137	TRIM5 Q9C035	Physiology	LINE-mediated retrotransposition of the CyclophilinA gene into 3'UTR (exon 8) of TRIM5alpha	Cercopithecidae Old World monkeys - (family)	Macaca macaques - (genus)	TRIM5alpha-CypA chimeric gene	Macaca macaques - (genus)	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
tryptophan phenylalanine hydroxylase	Enzymatic activity	Coding, Insertion	Drosophila melanogaster fruit fly - (species) D	Intraspecific	Candidate Gene	Ruiz-Vázquez P; Silva FJ (1999) Aberrant splicing of the Drosophila melanogaster phenylalanine hydroxylase pre-mRNA caused by the in[...]	GP00002003	Hn P17276	Physiology	insertion of the transposable element B104/roo in the exon 3 of the Phenylalanine hydroxylase gene. Its presence alters the Phenylalanine hydroxylase splicing pattern; producing at least two aberrant mRNAs which contain part of the B104 sequence interrupting the coding region. This aberrant splicing is provoked by the use of a cryptic donor site encoded by the B104 3' long terminal repeat in combination with either the gene intron 3 acceptor site or a novel acceptor site generated by the target duplication caused by transposition. One of them; referred as mRNA type 1; encodes a truncated protein that could be predictably non-functional. In mRNA type 2; in spite of a 42 nt insertion; the Phenylalanine hydroxylase reading frame is not altered and it would encode for a protein with 14 extra amino acids which would be able to account for the low enzyme activity detected in this mutant.	Drosophila melanogaster fruit fly - (species)	Drosophila melanogaster fruit fly - (species) D	tryptophan phenylalanine hydroxylase	Drosophila melanogaster fruit fly - (species)	Published - Accepted by Curator
TT8	Coloration (seed)	Coding, Insertion N	Brassica rapa field mustard - (species) D	Domesticated	Linkage Mapping	Li X; Chen L; Hong M ; et al. (2012) A large insertion in bHLH transcription factor BrTT8 resulting in yellow seed coat in Brassica rapa.	GP00002077	TT8 Q9FT81	Morphology	insertion of a Helitron transposon of 4320 bp in intron 2 starting with 5' TC and ending with 3'CTAG containing a 17 bp palindromic region forming a hairpin - prevents transcription N	Brassica rapa field mustard - (species)	Brassica rapa field mustard - (species) D	TT8	Brassica rapa field mustard - (species)	Published - Accepted by Curator
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
Twist1	Horn shape (scurs)	Coding, Insertion N	Bos taurus cattle - (species) D	Domesticated	Linkage Mapping	Capitan A; Grohs C; Weiss B ; et al. (2011) A newly described bovine type 2 scurs syndrome segregates with a frame-shift mutation in TWIST1.	GP00002034	Twist1 P26687	Morphology; Physiology	small duplication (c.148_157dup (p.A56RfsX87)) that causes a frameshift and inactivates the gene. N	Bos taurus cattle - (species)	Bos taurus cattle - (species) D	Twist1	Bos taurus cattle - (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 (TYR)	Coloration (feathers)	Coding, Insertion	Gallus gallus chicken - (species) D	Domesticated	Candidate Gene	Chang CM; Coville JL; Coquerelle G ; et al. (2006) Complete association between a retroviral insertion in the tyrosinase gene and the recessive white m[...]	GP00002309	Tyr P11344	Morphology	insertion of a complete avian retroviral sequence in intron 4 causes aberrant transcripts lacking exon 5	Gallus gallus chicken - (species)	Gallus gallus chicken - (species) D	tyrosinase (TYR)	Gallus gallus chicken - (species)	Published - Accepted by Curator
tyrosinase (TYR)	Coloration (coat)	Coding, Insertion N	Bos taurus cattle - (species) D	Domesticated	Candidate Gene	Schmutz SM; Berryere TG; Ciobanu DC ; et al. (2004) A form of albinism in cattle is caused by a tyrosinase frameshift mutation.	GP00002315	Tyr P11344	Morphology	c.925_926insC N	Bos taurus cattle - (species)	Bos taurus cattle - (species) D	tyrosinase (TYR)	Bos taurus cattle - (species)	Published - Accepted by Curator
tyrosinase (TYR)	Coloration (amelanism)	Coding, Insertion N	Oryzias latipes Japanese medaka - (species) D	Domesticated	Candidate Gene	Koga A; Hori H (1997) Albinism due to transposable element insertion in fish.	GP00002372	Tyr P11344	Morphology	"i4 allele was found to contain a 4.7- kb transposable element in the 5th exon" "Tyr-i4 contains a 4.7-kb insertion in exon 5 (Fig. 3). If the inserted fragment was transcribed, the amino acid sequence would be altered after the 469th residue, with a termination codon (UAG) at amino acid position 471. The i4/i4 genotype exhibits a quasi-albino phenotype. This may be explained by generation of a tyrosinase protein that only lacks its C-terminus region. The wild-type tyrosinase has a highly hydrophobic amino acid block at its C terminus (aa 480 - aa 500) which is thought to be part of a membrane spanning domain (Inagaki et al., 1994). A possible explanation is that the mutant tyrosinase encoded by Tyr- i4 lacks this region, so that it cannot be positioned properly on the membrane" N	Oryzias latipes Japanese medaka - (species)	Oryzias latipes Japanese medaka - (species) D	tyrosinase (TYR)	Oryzias latipes Japanese medaka - (species)	Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)	Coloration (coat)	Cis-regulatory, Insertion N	Neovison vison American mink - (species) D	Domesticated	Candidate Gene	Cirera S; Markakis MN; Kristiansen T ; et al. (2016) A large insertion in intron 2 of the TYRP1 gene associated with American Palomino phenotype in Ameri[...]	GP00002241	Tyrp1 P07147	Morphology	Large insertion in intron 2 resulting in aberrant transcript N	Neovison vison American mink - (species)	Neovison vison American mink - (species) D	tyrosinase-related protein 1 (TYRP1)	Neovison vison American mink - (species)	Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)	Coloration (feathers)	Coding, Insertion N	Falco cherrug Saker falcon - (species) D	Intraspecific	Candidate Gene	Cortimiglia C; Castiglioni B; Pizzi F ; et al. (2017) Involvement of tyrosinase-related protein 1 gene in the light brown plumage phenotype of Falco cherr[...]	GP00002285	Tyrp1 P07147	Morphology	c.79_80insT in exon 1 resulting in a frameshift change and a premature stop codon at position 81 of the deduced protein sequence ; which in the wild-type form contains 536 amino acids N	Falco cherrug Saker falcon - (species)	Falco cherrug Saker falcon - (species) D	tyrosinase-related protein 1 (TYRP1)	Falco cherrug Saker falcon - (species)	Published - Accepted by Curator
TZP	Plant growth (hypocotyl growth - light and temperature dependant)	Coding, Insertion N	Arabidopsis thaliana thale cress - (species)	Intraspecific	Linkage Mapping	Loudet O; Michael TP; Burger BT ; et al. (2008) A zinc knuckle protein that negatively controls morning-specific growth in Arabidopsis thaliana.	GP00001269	TZP Q9FIX7	Morphology	8bp insertion causing premature stop N	Arabidopsis thaliana thale cress - (species)	Arabidopsis thaliana thale cress - (species)	TZP	Arabidopsis thaliana thale cress - (species)	Published - Accepted by Curator
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
VRS1 = SIX-ROWED SPIKE 1	Plant architecture Inflorescence architecture	Coding, Insertion N	Hordeum vulgare (species) D	Domesticated	Linkage Mapping	Komatsuda T; Pourkheirandish M; He C ; et al. (2007) Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene. 1 Additional References Ramsay L; Comadran J; Druka A (2011) INTERMEDIUM-C, a modifier of lateral spikelet fertility in barley, is an ortholog of the maize domes[...]	GP00001190	Vrs1 A1IHK8	Morphology Morphology	1bp insertion resulting in frameshift N	Hordeum vulgare (species)	Hordeum vulgare (species) D	VRS1 = SIX-ROWED SPIKE 1	Hordeum vulgare (species)	Published - Accepted by Curator
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, 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
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	Coding, Insertion N	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[...]	GP00001201	waxy Q8L699	Physiology	Transposon insertion TS1-7 (Exon 3) N	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	Coding, Insertion N	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[...]	GP00001202	waxy Q8L699	Physiology	Transposon insertion TS1-9 (Exon 10) N	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 (glutinous rice)	Coding, Insertion N	Oryza sativa rice - (species) D	Domesticated	Candidate Gene	Hori Y; Fujimoto R; Sato Y ; et al. (2007) A novel wx mutation caused by insertion of a retrotransposon-like sequence in a glutinous cultivar o[...]	GP00002069	waxy Q8L699	Physiology	23-bp duplication in the second exon which causes loss of the function of granule-bound starch synthase (GBSS) encoded by the Wx gene N	Oryza sativa rice - (species)	Oryza sativa rice - (species) D	Waxy /GBSS	Oryza sativa rice - (species)	Published - Accepted by Curator
Waxy /GBSS	Amylose content (glutinous rice)	Coding, Insertion N	Oryza sativa rice - (species) D	Domesticated	Candidate Gene	Hori Y; Fujimoto R; Sato Y ; et al. (2007) A novel wx mutation caused by insertion of a retrotransposon-like sequence in a glutinous cultivar o[...]	GP00002070	waxy Q8L699	Physiology	insertion of 7764 bp in the ninth exon of the wx gene. Transcripts of the 'Oragamochi' wx allele are about 1-kb shorter and the deduced amino acid sequence of the transcript lacks a motif important for GBSS. The 7,764-bp insertion is a retrotransposon-like sequence with long terminal repeats; a primer binding site and a polypurine tract N	Oryza sativa rice - (species)	Oryza sativa rice - (species) D	Waxy /GBSS	Oryza sativa rice - (species)	Published - Accepted by Curator
WDR1	Coloration (flowers)	Coding, Insertion N	Petunia axillaris (species) D	Domesticated	Candidate Gene	de Vetten N; Quattrocchio F; Mol J ; et al. (1997) The an11 locus controlling flower pigmentation in petunia encodes a novel WD-repeat protein conserve[...]	GP00002093	InWDR1 Q1JUZ7	Morphology	insertion of a 300-bp dTph1 transposon in the WDR gene in the first WD-repeat (321-bp downstream of the transcription start site) N	Petunia axillaris (species)	Petunia axillaris (species) D	WDR1	Petunia axillaris (species)	Published - Accepted by Curator
Y	Coloration (fruit)	Coding, Insertion	Sorghum bicolor sorghum - (species) D	Domesticated	Candidate Gene	Chopra S; Brendel V; Zhang J ; et al. (1999) Molecular characterization of a mutable pigmentation phenotype and isolation of the first active tra[...]	GP00002068	P1 O24579	Morphology	insertion of a transposable element named Candystripe1 (Cs1) in the second intron of the Y gene - Cs1 is 23,018 bp in size and is bordered by 20-bp terminal inverted repeat sequences. It generated a 3-bp target site duplication upon insertion within the Y gene. Cs1 shares features of the CACTA superfamily of transposons.	Sorghum bicolor sorghum - (species)	Sorghum bicolor sorghum - (species) D	Y	Sorghum bicolor sorghum - (species)	Published - Accepted by Curator
yellow	Coloration (body; wing)	Coding, Insertion N	Musca domestica house fly - (species) D	Intraspecific	Candidate Gene	Heinze SD; Kohlbrenner T; Ippolito D ; et al. (2017) CRISPR-Cas9 targeted disruption of the yellow ortholog in the housefly identifies the brown body loc[...]	GP00002623	y P09957	Morphology	a 4 bp insertion at amino acid position 67 that causes a frameshift and a premature stop codon N	Musca domestica house fly - (species)	Musca domestica house fly - (species) D	yellow	Musca domestica house fly - (species)	Published - Accepted by Curator
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
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