Structure and decay of a proto-Y region in Tilapia, Oreochromis niloticus

BMC Genomics

Table 1 Putative functional mutations in the proposed inversion

Gene name	SNP location on LG1	Reference codon	SNP codon	Effect on the Y	Effect on the X	Frequency of SNP in males	Frequency of SNP in females
Ras-related protein R-Ras2 (LOC100693950)	10506882	CGA	TGA	Stop Gain	-	0.462	0
Signal peptide	10868192	TCA	TGA	-	Stop Gain	0.545	1
AMP deaminase 3 (LOC100694225)	11096201	TGA	TCA	Stop Lost	-	0.454	0
Zinc finger protein 821 (LOC100712266)	12466312	ATG	ACG	Start Lost	-	0.4	0
Zinc finger protein 821 (LOC100712266)	12466313	ATG	ATA	Start Lost	-	0.4	0
SAFB-like transcription modulator (LOC100711186)	12619332	CGA	TGA	-	Stop Gain	0.613	1
Hepatic lipase (Lipc)	12690753	TGA	CGA	Stop Lost	-	0.448	0
Ammonium transporter Rh type C 2 (LOC100706367)	13529856	ATG	ATA	-	Start Lost	0.575	1
AFG3-like protein 1 (LOC100702885)	13725056	TTA	TGA	Stop Gain	-	0.439	0
CUB and sushi domain-containing protein 1 (LOC100698036)	15189214	CAA	TAA	Stop Gain	-	0.391	0.027
CUB and sushi domain-containing protein 1 (LOC100698036)	15243948	TGC	TGA	Stop Gain	-	0.391	0
Neuromedin-K receptor (LOC100693904)	15788009	CAGG	CAGC	Splice Site Acceptor Lost	-	0.343	0
Protein FAM176A (LOC100700039)	16417062	CGA	TGA	Stop Gain	-	0.475	0
GC-rich sequence DNA-binding factor (LOC100700589)	16480688	CAGA	CAGG	Splice Site Acceptor Gain	-	0.512	0.018
BTB/POZ domain-containing protein KCTD3 (LOC100703295)	16809270	CGA	TGA	Stop Gain	-	0.52	0
Hypothetical protein (LOC100705710)	17489648	CAA	TAA	-	Stop Gain	0.452	0.97
Hypothetical protein (LOC100705710)	17507222	TAA	CAA	Stop Lost	-	0.469	0.04
Nuclear factor of activated T-cells	18194412	TGG	TGA	-	Stop Gain	0.5	0.982

Genes containing a stop codon, start codon or splice site alterations that were in intermediate frequency in males and fixed or nearly fixed in females within the proposed inversion on LG1. Bold denotes the altered SNP.

ISSN: 1471-2164