RetrogeneDB ID: retro_ptro_902

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:34705800..34706741(+)
• Located in intron of: ENSPTRG00000006268

Retrocopy information

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

Parental gene information

• Parental gene symbol: QRSL1
• Ensembl ID: ENSPTRG00000018462
• Aliases: None
• Description: Glutamyl-tRNA(Gln) amidotransferase subunit A, mitochondrial [Source:UniProtKB/TrEMBL;Acc:H2QTH5]

Sequence

>retro_ptro_902
AATGCTATAGTAGTTCCGAAATTGTTGGATTAGGGAGCTCTACTAATGGAAAAACAAATTTAGATGAGTTTGCTATGAGA
TCTGGAAATGCAGAAGGCGTATTTGGACCAGTTAAAAACCCCCGGAGTTATTCAAAACAATATAGAGAAAAGAGGAAGCA
GAATCTCCACTTTGAGAATGAAGATTCAGACTGGCTGATAACTGGAGGAAGCTCAGGTGGGAGTGCAGTTGCCATATCGG
CATTCACATGCTATGCGGCTTTAGGATCAGATACAAGAGGTCTGACCAGAAATCCTGCTGCCTACTGTGGGCTTGTTGGT
TTCAAACCAAACTATGGCTTAGTTTCCCATCATGGTCTCATTTCCCTGGAGGATTTGATGGAAGTGCAAGGAATCTTAAC
CAGATGTGTGGATGATGCAGCAATTGTCTTGGGTGTACTGGCTGAACATGACCCTATGGATTCTACCACGGCACAGGATC
CTGTTAAACCATTCATGATTCCCAGTTTGATAAATGTGAGCAAACTATGTATAGGTATTCCAAAGGAATATCTTGTACTG
GAATTATCAAGTGAAGTACAGTCTCTTTGGTCCAAAGCTGCTGATCTCTTTGAGTCTGAGGGGGCCAAAGCAATTGAAGT
ATCTTTTTCTCACATCACTTATTCAATTGTCTGCTACCATCTATTGTGCAGATCAGAAGCAGCATCGAGTATAGCAAGAT
TTGATGGGCTACAATATGGTCACAGATGTGACACTGATGTATCTACTGAAGCCATGTGTGCTGCAACCAGACGAGAAGGG
TTCAATGATTTTGTAAGAGGAAGAATTCTCTCAGGAAATGTTTTCTTGTTAAAATAAAAATATGAAAATTATTTCATCAA
AGCACAGAAAGTGAGATGCCTCATTGCTAATGATTTTGTGAATGCTTTTAACTCTGGAGTA

Alignment

ORF - retro_ptro_902 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.59 %
• Parental protein coverage: 59.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NATVVQKLLDQGALLM-GKTNLDEFAMGSGSTDGVFGPVKNPWSYSKQYREKRKQNPHSENEDSDWLITG
          NA.VV.KLLD.GALLM.GKTNLDEFAM.SG...GVFGPVKNP.SYSKQYREKRKQN.H.ENEDSDWLITG
Retrocopy NAIVVPKLLD*GALLM<GKTNLDEFAMRSGNAEGVFGPVKNPRSYSKQYREKRKQNLHFENEDSDWLITG

Parental  GSSGGSAAAVSAFTCYAALGSDTGGSTRNPAAHCGLVGFKPSYGLVSRHGLIPLVNSMDVPGILTRCVDD
          GSSGGSA.A.SAFTCYAALGSDT.G.TRNPAA.CGLVGFKP.YGLVS.HGLI.L...M.V.GILTRCVDD
Retrocopy GSSGGSAVAISAFTCYAALGSDTRGLTRNPAAYCGLVGFKPNYGLVSHHGLISLEDLMEVQGILTRCVDD

Parental  AAIVLGALAGPDPRDSTTVHEPINKPFMLPSLADVSKLCIGIPKEYLVPELSSEVQSLWSKAADLFESEG
          AAIVLG.LA..DP.DSTT...P..KPFM.PSL..VSKLCIGIPKEYLV.ELSSEVQSLWSKAADLFESEG
Retrocopy AAIVLGVLAEHDPMDSTTAQDPV-KPFMIPSLINVSKLCIGIPKEYLVLELSSEVQSLWSKAADLFESEG

Parental  AKVIEVSLPHTSYSIVCYHVLCTSEVASNMARFDGLQYGHRCDIDVSTEAMYAATRREGFNDVVRGRILS
          AK.IEVS..H..YSIVCYH.LC.SE.AS..ARFDGLQYGHRCD.DVSTEAM.AATRREGFND.VRGRILS
Retrocopy AKAIEVSFSHITYSIVCYHLLCRSEAASSIARFDGLQYGHRCDTDVSTEAMCAATRREGFNDFVRGRILS

Parental  GNFFLLKENYENYFVKAQKVRRLIANDFVNAFNSGV
          GN.FLLK..YENYF.KAQKVR.LIANDFVNAFNSGV
Retrocopy GNVFLLK*KYENYFIKAQKVRCLIANDFVNAFNSGV

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	0.04 RPM	9.19 RPM
SRP007412_cerebellum	0.14 RPM	12.44 RPM
SRP007412_heart	0.06 RPM	17.95 RPM
SRP007412_kidney	0.03 RPM	18.62 RPM
SRP007412_liver	0.07 RPM	10.28 RPM
SRP007412_testis	0.21 RPM	25.08 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_902 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_902 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_902 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1321
Gorilla gorilla	retro_ggor_1031
Pongo abelii	retro_pabe_1100
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 ,