Phylogenetic patterns of emergence of new genes support a model of frequent de novoevolution

BMC Genomics

Table 1 List of overprinted genes detected via a phylostratigraphic approach based on annotated ORFs in Ensembl

ENSMUS IDs				Phylostratum		Comment
Gene	Newer protein	Older protein	Gene name	Overprint	Original
G00000029642	P00000106186	P00000058355	Polr1d	5	2	Same start as main gene, but acquired additional exons
G00000030970	P00000127123	P00000033269	Ctbp2	12	1	Same start as main gene, but acquired an additional internal exon
G00000035504	P00000100994	P00000100995	Reep6	17	2	New initiation codon creates second reading frame
G00000089756	P00000104646	P00000104577	Gm8898	18	2	Same start, but new splice variant; paralog of Gm4723
G00000078898	P00000104676	P00000104675	Gm4723	18	2	Same start, but new splice variant; paralog of Gm8898
G00000038227	P00000133896	P00000046939	Hoxa9	18	2	New starting exon initiates a separate reading frame
G00000067786	P00000134415	P00000085836	Nnat	18	16	Same start, alternative splicing leads to new reading frames
G00000044405	P00000105110	P00000051732	Adig	20	16	Same start as main gene, but acquired an additional internal exon
G00000025144	P00000101761	P00000026137	Stra13	20	2	Gain of alternative second exon induces a shift from the older frame
G00000033720	P00000109417	P00000041872	Sfxn5	20	2	Alternative first exon and last exons, common second exon
G00000063235	P00000107087	P00000077036	Ptpmt1	20	1	Alternative transcription start site and start codon
G00000044303	P00000030237	P00000061847	Cdkn2a^a	16	1	New starting exon initiates a separate reading frame. Also known as Arf, Pctr1, MTS1, Ink4a
G00000027523	P00000104716	P00000085184	Gnas^b	18	2	New initiation codon creates second reading frame. Also known as Nesp, GPSA

ISSN: 1471-2164