RetrogeneDB ID: retro_pabe_1100

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:35530664..35531605(+)
• Located in intron of: ENSPPYG00000005746

Retrocopy information

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

Parental gene information

• Parental gene symbol: QRSL1
• Ensembl ID: ENSPPYG00000016883
• Aliases: None
• Description: glutaminyl-tRNA synthase (glutamine-hydrolyzing)-like 1 [Source:HGNC Symbol;Acc:21020]

Sequence

>retro_pabe_1100
AATGCTATAGTAGTTCCGAAGTTGTTGGATTAGGGAGCTCTACTAATGGAAAAACAAATTTAGATGAGTTTGCTATGAGA
TCCGGAAACGCAGAAGGCGTATTTGGACCAGTTAAAAACCCCTGGAGTTATTCAAAACAATATAGAGAAAAGAGGAAGCA
GAATCTCCACTTTGAGAATGAAGATTCAGACTGGCTGATAACTGGAGGAAGCTCAGGTGGGAGTGCAGTTGCCGTATCGG
CATTCACATGCTATGAGGCTTTAGGATCAGATACAGGAGGGCTGACCAGAAATCCTGCTGCCTACTGTGGGCTTGTTGGT
TTCAAACCAAGCTATGGCTTAATTTCCCATCATGGTCTCATTTCCCCGGAGAATTCGATGGATGTGCAAGGAATCTTAAC
CATATGTGTGGATGATGCAGCAATTGTCTTGGGTGTACTGGCTGAACATGATCCTAAGGATTCTATCACAGTACAGGATC
CTGTTAAACCATTCATGCTTCCCAGTTTGACAAATGTGAGCAAACTATGTATAGGTATTCCAAAGGTATATCTTGTACTG
GAATTATCAAGTGAAGTACGGTCTCTTTGGTCCAAAGCTGCTGACCTCTTTGAGTCTGAGGGGGCCAAAGTAATTGAAGT
ATCCTTTTCTCACATCACTTATTCAATTGTCTGCTACCATCTGTTGTGTACATCAGAAGCAGCATCGAGTATAGCAAGAT
TTGATGGGCTACAATATGGTTACAGATGTGACACTAATGTGTCTACTGAAGCCATGTATGCTGCAACCAGACGAGAAGGA
TTCAGTGATTTTGTAAGAGGAAGAATTCTCTCAGGAAATGTTTTCTTGTTAAAATAAAAGTATGAAAATTATTTCATCAA
AGCACAGAAAGTGAGATGCCTCATTGCTAATGATTTTGTGAATGGTTTTAACTCTGGAGTA

Alignment

ORF - retro_pabe_1100 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.91 %
• Parental protein coverage: 59.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NATVVQKLLDQGALLM-GKTNLDEFAMGSGSTDGVFGPVKNPWSYSKQYREKRKQNPHSKNEDSDWLITG
          NA.VV.KLLD.GALLM.GKTNLDEFAM.SG...GVFGPVKNPWSYSKQYREKRKQN.H..NEDSDWLITG
Retrocopy NAIVVPKLLD*GALLM<GKTNLDEFAMRSGNAEGVFGPVKNPWSYSKQYREKRKQNLHFENEDSDWLITG

Parental  GSSGGSAAAVSAFTCYAALGSDTGGSTRNPAAHCGLVGFKPSYGLVSRHGLIPLVNSMDVPGILTRCVDD
          GSSGGSA.AVSAFTCY.ALGSDTGG.TRNPAA.CGLVGFKPSYGL.S.HGLI...NSMDV.GILT.CVDD
Retrocopy GSSGGSAVAVSAFTCYEALGSDTGGLTRNPAAYCGLVGFKPSYGLISHHGLISPENSMDVQGILTICVDD

Parental  AAIVLGALAGPDPRDSTTVHDPINKPFMLPSLADVSKLCIGIPKEYLVPELSSEVQSLWSKAADLFESEG
          AAIVLG.LA..DP.DS.TV.DP..KPFMLPSL..VSKLCIGIPK.YLV.ELSSEV.SLWSKAADLFESEG
Retrocopy AAIVLGVLAEHDPKDSITVQDPV-KPFMLPSLTNVSKLCIGIPKVYLVLELSSEVRSLWSKAADLFESEG

Parental  AKVIEVSLPHTSYSIVCYHVLCTSEVASNMARFDGLQYGHRCDIDVSTEAMYAATRREGFNDVVRGRILS
          AKVIEVS..H..YSIVCYH.LCTSE.AS..ARFDGLQYG.RCD..VSTEAMYAATRREGF.D.VRGRILS
Retrocopy AKVIEVSFSHITYSIVCYHLLCTSEAASSIARFDGLQYGYRCDTNVSTEAMYAATRREGFSDFVRGRILS

Parental  GNYFLLKENYENYFVKAQKVRRLIANDFVNVFNSGV
          GN.FLLK..YENYF.KAQKVR.LIANDFVN.FNSGV
Retrocopy GNVFLLK*KYENYFIKAQKVRCLIANDFVNGFNSGV

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	0.06 RPM	3.76 RPM
SRP007412_cerebellum	0.12 RPM	7.42 RPM
SRP007412_heart	0.12 RPM	10.54 RPM
SRP007412_kidney	0.20 RPM	12.16 RPM
SRP007412_liver	0.00 RPM	7.34 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1100 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1100 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1100 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1321
Pan troglodytes	retro_ptro_902
Gorilla gorilla	retro_ggor_1031
Callithrix jacchus	retro_cjac_692

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017557	3 retrocopies	retro_btau_476, retro_btau_493, retro_btau_616,
Choloepus hoffmanni	ENSCHOG00000001036	1 retrocopy	retro_chof_2382,
Callithrix jacchus	ENSCJAG00000006200	4 retrocopies	retro_cjac_1421, retro_cjac_3781, retro_cjac_3919, retro_cjac_692,
Cavia porcellus	ENSCPOG00000021670	1 retrocopy	retro_cpor_179,
Homo sapiens	ENSG00000130348	3 retrocopies	retro_hsap_1321, retro_hsap_466, retro_hsap_514,
Gorilla gorilla	ENSGGOG00000008261	3 retrocopies	retro_ggor_1031, retro_ggor_445, retro_ggor_474,
Macaca mulatta	ENSMMUG00000008330	2 retrocopies	retro_mmul_429, retro_mmul_675,
Nomascus leucogenys	ENSNLEG00000013383	2 retrocopies	retro_nleu_1403, retro_nleu_1550,
Pongo abelii	ENSPPYG00000016883	3 retrocopies	retro_pabe_1100 , retro_pabe_230, retro_pabe_268,
Pan troglodytes	ENSPTRG00000018462	2 retrocopies	retro_ptro_351, retro_ptro_902,