RetrogeneDB ID: retro_pabe_230

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:27350273..27351242(+)
• Located in intron of: None

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_230
GTTGGTTTCAAACCAAGCTATGGCTTACTTTCCCGTCATGGTCTCATTCCGCTGGTGAATTTGATGGATCTGCCAGGTAT
CTTAACCAGAAGTGTGGATGATACAGCAATTGTGTTGGGTGTACTGGCTGGACATGACCTCAAGGATTCTACCACAGTAC
AAGATCCTGTTAAACCATTCATACTTCCCAGTTTGGCAGATGTAAACAAACTATGTATAGGAATTCCAAAAAAAATCTTG
TACCATAATTGTCAGTGAAATACAATCTCTTTGGTCCAAAGCTGCTGACCTCTTTGAGTCTGCGAGGGCCAAAGTAATTG
AAGTATCCCTTCCTCACACCAATTATTCAGTTGTCTGCTACCATGTATTTTTATTGTGCACACTGGAAGTGGCATCAAAT
ATGGCAAGATTTGATGGGCTACGATATGGTCACAGATGTAACATTGATGTGTCCACTGAAGCCAGGTATGCTGCAACCAG
ACAAGAAGGATTCAGTGATGTGGTGAGAAGAAGAATTCTCTCAGGAAACTTTTTCTTGTTAAAAAAAACTATGAAAATTA
TTTCATCAAAGCACAGAAGGTGAGATACCTCATCAATAATTATTTTGTGAATGCTTTTAACTCTGGAGTAGATGTCTTGC
TAACTCCCACCACCTTGAGTGAGGCAGTACTATACTTGGAATTCATCAAAGAAGACAATACAACAAGAAGTGCCCAGGAT
GATAGTTTCACACAGGCTGTAAACATGGCAGGATTGCCAACAGTGAATATTCCTGTTGCACTTTCAAACCAAGGGTTGCC
AATAGGACTGTAGTTTACTGAATGTGCATTTTGTGACCAGCAGCTTCTTACAGTAGCCAAATGATTTGAAAAACAAGTAC
AGTTTTCTGTTATTCAACTTCAAGAACTCATGGATGATTGTTCATCAATCCTTGAAAATGAAAAGCTAGCCTCTGTCTCT
CTAAAACAG

Alignment

ORF - retro_pabe_230 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.71 %
• Parental protein coverage: 61.17 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VGFKPSYGLVSRHGLIPLVNSMDVPGILTRCVDDAAIVLGALAGPDPRDSTTVHDPINKPFMLPSLADVS
          VGFKPSYGL.SRHGLIPLVN.MD.PGILTR.VDD.AIVLG.LAG.D..DSTTV.DP..KPF.LPSLADV.
Retrocopy VGFKPSYGLLSRHGLIPLVNLMDLPGILTRSVDDTAIVLGVLAGHDLKDSTTVQDPV-KPFILPSLADVN

Parental  KLCIGIPKEYL-VPELS-SEVQSLWSKAADLFESEGAKVIEVSLPHTSYSIVCYHV--LCTSEVASNMAR
          KLCIGI....L.VP.LS.SE.QSLWSKAADLFES..AKVIEVSLPHT.YS.VCYHV..LCT.EVASNMAR
Retrocopy KLCIGIXXXXL<VP*LS<SEIQSLWSKAADLFESARAKVIEVSLPHTNYSVVCYHVFLLCTLEVASNMAR

Parental  FDGLQYGHRCDIDVSTEAMYAATRREGFNDVVRGRILSGNYFL-LKENYENYFVKAQKVRRLIANDFVNV
          FDGL.YGHRC.IDVSTEA.YAATR.EGF.DVVR.RILSGN.FL.....YENYF.KAQKVR.LI.N.FVN.
Retrocopy FDGLRYGHRCNIDVSTEARYAATRQEGFSDVVRRRILSGNFFL<VXXXYENYFIKAQKVRYLINNYFVNA

Parental  FNSGVDVLLTPTTLSEAVPYLEFIKEDNRTRSAQDDIFTQAVNMAGLPAVSIPVALSNQGLPIGLQFIGR
          FNSGVDVLLTPTTLSEAV.YLEFIKEDN.TRSAQDD.FTQAVNMAGLP.V.IPVALSNQGLPIGL.F...
Retrocopy FNSGVDVLLTPTTLSEAVLYLEFIKEDNTTRSAQDDSFTQAVNMAGLPTVNIPVALSNQGLPIGL*FTEC

Parental  AFCDQQLLTVAKWFEKQVEFPVIQLQELMDDCSAVLENEKLASVSLKQ
          AFCDQQLLTVAK.FEKQV.F.VIQLQELMDDCS..LENEKLASVSLKQ
Retrocopy AFCDQQLLTVAK*FEKQVQFSVIQLQELMDDCSSILENEKLASVSLKQ

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	3.76 RPM
SRP007412_cerebellum	0.00 RPM	7.42 RPM
SRP007412_heart	0.00 RPM	10.54 RPM
SRP007412_kidney	0.00 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_230 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_230 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_230 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_514
Gorilla gorilla	retro_ggor_474
Macaca mulatta	retro_mmul_429

---

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,