RetrogeneDB ID: retro_pabe_403

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:79713460..79713899(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: GM2A
• Ensembl ID: ENSPPYG00000015962
• Aliases: None
• Description: GM2 ganglioside activator [Source:HGNC Symbol;Acc:4367]

Sequence

>retro_pabe_403
GTGCAATCCCTGATGGAGGCTCCATTCCTGATTGTCCTGGGCTTGCTTCTTGCAGGCCTAGCAGCCCCTGCCCACGTCCA
CCTGAACCAGATCAGTAGCTTTCCCTGGGATAACTGGGACAAAGGGAAGGACTCTGTGGTGATCAAAAGCCTGTCTCTGG
AAGCTGACCCCAACGTCGTTCCTGGGAACGTGATCATCAGTGCTGAGGACAAGAACCAGTGTCCCCCTCAAATCTCCTCT
GAAGCTGGAATTAACTGTAGAGAAGGAAGTGTCTGGCTTCTGGGTCAAGATCTCATGCATGGAACAGATTGGTAGCTGTG
CCTATGAAGACTTCTGTGATGTGCTTGATACTTTCATTCATCCTGGGGAGCTCTGCCCAGAGCCCCTGCATATCTATGGG
CTTCTTTGCCACTGTCCCTTCAAAGTAGGCACCTACTCA

Alignment

ORF - retro_pabe_403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.27 %
• Parental protein coverage: 75.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQSVMQAPLLIALGLL---LAAPAQAHLKKLSSFSWDNCDEGKDPAVIRSLTLEPDPIIVPGNVTLSVMG
          .QS.M.AP.LI.LGLL...LAAPA..HL...SSF.WDN.D.GKD..VI.SL.LE.DP..VPGNV..S...
Retrocopy VQSLMEAPFLIVLGLLLAGLAAPAHVHLNQISSFPWDNWDKGKDSVVIKSLSLEADPNVVPGNVIISAED

Parental  S-TSVPLSSPLKVDLVLEKEVAGLWIKIPCTDYIGSCTFEQFCDVLDMLIPTGEPCPEPLRTYGLPCHCP
          ..TSVPL.SPLK..L..EKEV.G.W.KI.C...IGSC..E.FCDVLD..I..GE.CPEPL..YGL.CHCP
Retrocopy K>TSVPLKSPLKLELTVEKEVSGFWVKISCMEQIGSCAYEDFCDVLDTFIHPGELCPEPLHIYGLLCHCP

Parental  FKEGTYS
          FK.GTYS
Retrocopy FKVGTYS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	24.16 RPM
SRP007412_cerebellum	0.00 RPM	36.12 RPM
SRP007412_heart	0.00 RPM	12.94 RPM
SRP007412_kidney	0.00 RPM	34.70 RPM
SRP007412_liver	0.00 RPM	20.53 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_403 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_403 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_403 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_221

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000020587	1 retrocopy	retro_ecab_510,
Homo sapiens	ENSG00000196743	2 retrocopies	retro_hsap_264, retro_hsap_2715,
Gorilla gorilla	ENSGGOG00000015302	2 retrocopies	retro_ggor_1891, retro_ggor_313,
Macropus eugenii	ENSMEUG00000010421	1 retrocopy	retro_meug_1818,
Microcebus murinus	ENSMICG00000000690	1 retrocopy	retro_mmur_518,
Myotis lucifugus	ENSMLUG00000003215	1 retrocopy	retro_mluc_920,
Macaca mulatta	ENSMMUG00000022869	1 retrocopy	retro_mmul_454,
Nomascus leucogenys	ENSNLEG00000010966	1 retrocopy	retro_nleu_866,
Oryctolagus cuniculus	ENSOCUG00000015837	1 retrocopy	retro_ocun_704,
Ochotona princeps	ENSOPRG00000006171	1 retrocopy	retro_opri_1169,
Pongo abelii	ENSPPYG00000015962	1 retrocopy	retro_pabe_403 ,
Pan troglodytes	ENSPTRG00000017431	2 retrocopies	retro_ptro_1834, retro_ptro_221,
Ictidomys tridecemlineatus	ENSSTOG00000028500	1 retrocopy	retro_itri_759,
Tursiops truncatus	ENSTTRG00000000503	1 retrocopy	retro_ttru_488,