RetrogeneDB ID: retro_ogar_3517

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL874228.1:9321..10315(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000031504
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GAPDHS
• Ensembl ID: ENSOGAG00000009491
• Aliases: None
• Description: glyceraldehyde-3-phosphate dehydrogenase, spermatogenic [Source:HGNC Symbol;Acc:24864]

Sequence

>retro_ogar_3517
AAACTGAAGGTCGGAATAAACGGCTTTGGTTGGATTGGGCACCTGGTCTGCAGGGCTGCTTTTTACTCTGCCAAAGTGGA
TATTGTCACCACCAATGACCCCTTCATTGACCTCAACTACATGGTCTACATGTTCCAGTATGATTCCACCCATGGCAAAT
TCCATGGCACAGTCAAGGCTGAGAACGGGAAGCTTGTCATCAATGGAAATCCCATAACCATCTTCCAGGAGCGAGATCCC
ACCAAAATCAAATGGGGTGAGGCAGGTGCTGAGTATGTTGTGGAGTCCACTGGCATCTTCACCACCATGGAGAAAGCTGG
GGCTGACCTCTAGAGGGTGCCAAAAGGGTCATCATCTCTGCCCTTTCTGCTGATGCTCCCGTGTTCATGATGGGTGTGAA
CCATAAGTACAAAAACAGCCTCAGCATTGTCAGCAATGCCTCCTGCACCACCAACTGCTTAGCCCCCTTAGCTAAGGTCA
TCCATAACAACTTTGGCATTGTGGAGGGACTCATGACCACAGTCCATCCCATCACTGCCACCCAGAAGACTGTGGATGGC
CCCTCTGGGAAGTTGTGGCATGATGGTCACGGGGCTCTCCAGAACATCATCCCTGCCTCAACTGGTGCAGCCAAGGCTGT
GGGCAAGGTCATCCCTAAGCTGAATGGGAAGCTTACTGGCGTGGCTTCCGTGTCCCCACTGCCAACATGTTGGTCATGGA
TCTCACCTGCCATCTGGAGAAGGCTGCCAAATACAATGATATCAAGAAGGTGGTGAAGCAGGCATCAGAGGGCCCCCTCA
AGGGCATCCTGAGTTACACTGAGCACCAGGTCGTCACCTCTGACTTCAACAGTGACAGCCATTCTTCCACCTTTGATGCT
GGGGCTGGCATTGCCCTCAATGACCACTTTGTCAAACTCATTGCCTGGTATGATAATGAATTTCACTACAGCAACAGGGT
GGTGGATCTTATGGCCCACATGGCCTCCAAGGAG

Alignment

ORF - retro_ogar_3517 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.2 %
• Parental protein coverage: 77.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ELTVGINGFGRIGRLVLRACMEKG-VKVVAVNDPFIDPEYMVYMFKYDSTHGRYKGNVDYKNGQLVVDNQ
          .L.VGINGFG.IG.LV.RA......V..V..NDPFID..YMVYMF.YDSTHG...G.V...NG.LV....
Retrocopy KLKVGINGFGWIGHLVCRAAFYSAKVDIVTTNDPFIDLNYMVYMFQYDSTHGKFHGTVKAENGKLVINGN

Parental  EITVYQCKAPKEIPWRNVGSPYVVESTGVYLSLEATSDHI-SAGAQRVVICAPSPDAPMFVMGVNENDYN
          .IT..Q...P..I.W...G..YVVESTG.....E.........GA.RV.I.A.S.DAP.F.MGVN.....
Retrocopy PITIFQERDPTKIKWGEAGAEYVVESTGIFTTMEKAGADL<LEGAKRVIISALSADAPVFMMGVNHK--Y

Parental  PNSMNIVSNASCTTNCLAPLAKVIHEQFGIVEGLMTTVHSYTATQKTVDGPSRKAWRDGRGAHQNIIPAS
          .NS..IVSNASCTTNCLAPLAKVIH..FGIVEGLMTTVH..TATQKTVDGPS.K.W.DG.GA.QNIIPAS
Retrocopy KNSLSIVSNASCTTNCLAPLAKVIHNNFGIVEGLMTTVHPITATQKTVDGPSGKLWHDGHGALQNIIPAS

Parental  TGAAKAVGSVIPALKGKLTGMA-FRVPTPDVSVVDLTCRLARPTPYSAIKEAMKTAAKGPMAGILAYTED
          TGAAKAVG.VIP.L.GKLTG.A.FRVPT....V.DLTC.L.....Y..IK...K.A..GP..GIL.YTE.
Retrocopy TGAAKAVGKVIPKLNGKLTGVA<FRVPTANMLVMDLTCHLEKAAKYNDIKKVVKQASEGPLKGILSYTEH

Parental  EVVSTDFTGDTHSSIFDAKAGIALNDTFVKLISWYDNEYGYSNRVVDLLRYMFSRE
          .VV..DF..D.HSS.FDA.AGIALND.FVKLI.WYDNE..YSNRVVDL...M.S.E
Retrocopy QVVTSDFNSDSHSSTFDAGAGIALNDHFVKLIAWYDNEFHYSNRVVDLMAHMASKE

Legend:

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

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_3517 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000061099	2 retrocopies	retro_mmus_3024, retro_mmus_528,
Otolemur garnettii	ENSOGAG00000009491	25 retrocopies	retro_ogar_1269, retro_ogar_1332, retro_ogar_1460, retro_ogar_1472, retro_ogar_1798, retro_ogar_1968, retro_ogar_2074, retro_ogar_2266, retro_ogar_2376, retro_ogar_2446, retro_ogar_2469, retro_ogar_2631, retro_ogar_2647, retro_ogar_2884, retro_ogar_2957, retro_ogar_315, retro_ogar_3197, retro_ogar_3262, retro_ogar_3517 , retro_ogar_355, retro_ogar_468, retro_ogar_582, retro_ogar_632, retro_ogar_658, retro_ogar_785,
Petromyzon marinus	ENSPMAG00000009321	1 retrocopy	retro_pmar_9,
Pan troglodytes	ENSPTRG00000010848	1 retrocopy	retro_ptro_2211,
Tupaia belangeri	ENSTBEG00000008617	16 retrocopies	retro_tbel_1017, retro_tbel_1193, retro_tbel_124, retro_tbel_1650, retro_tbel_1685, retro_tbel_2010, retro_tbel_2486, retro_tbel_249, retro_tbel_2793, retro_tbel_2832, retro_tbel_2873, retro_tbel_2929, retro_tbel_3117, retro_tbel_425, retro_tbel_4292, retro_tbel_4346,