RetrogeneDB ID: retro_nleu_1550

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397299.1:765873..766822(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: QRSL1
• Ensembl ID: ENSNLEG00000013383
• Aliases: None
• Description: Glutamyl-tRNA(Gln) amidotransferase subunit A, mitochondrial [Source:UniProtKB/TrEMBL;Acc:G1RSQ2]

Sequence

>retro_nleu_1550
GGTTTCAAACCAAGCTATGGCTTACTTTCCCATCATGGTCTCATTGCCCTGGTGAATTTGATGGATCTGCTAGGAATCTT
AACCAGATGTGTGGATGATGCAGCAATTGTGTTGGGTGTACTGACTGGACACGACCTCAAGGATTCTACCACAGTACAAG
ATCCTGTTAAACCATTCATACTTCCCAGTTTGACAGATGTAAACAAACTATGTATAGGAATTCCAAAAAAATATCTTGTA
CCATAATTATTAGTGAAGTACAATCTCTTTGGTCCAAAGCTGCTGATCTCTTTGAGTCTGCGAGGGCCAAAGTAATTGAA
GCATCCCTTCCTTACACCAGTTATTCAGTTGTCTGTTACCATGTATTGTGCACATTGGAAGTGGCATCAAATATGGCAAG
ATTTGATGGGCTACGATATGGTCACAGAGGTGACAATGATGTTTCCACTGAAGCCAGGTATGCTGCAACCAGACAAGGAT
TCAATGATGTGGTGAGAGGAAGAATTCTCTCAGGAAACTTTTTCTTGTTAAAAAAAACTATGAAAATTATTTCATCAAAG
CACAGAAGGTGAGATGCCTCATTGCTAATAATTTTGTGAAAGCTTTTAATTCTGGAGTACATGTCTTGCTAACTCCCACC
ACCTTGAGTGAGGCAGTACCATACCTGGAATTCATCAAAGAAGACAATACAACAAGAAGCACCCAGGATGATAGTTTCAC
ACAGGCTATAAACATGGCAGGATTGCCAGCAGCAAGTATTCCTGTTGCACTCTCAGACCAAGGGTTGCCAATAGGACTGT
AGTTTACTGAATGTGCGTTTTGTGACCAGCATCTTCTTATAGTAGCCAAATGATTTGAAAAACAAGTACGGTTTTCTGTT
ATTCAACTTCAAGAACTCATGGATGATTGTTCATCAATCCTTGAAAATGAAAAGCTAGCCTCTGTCTCT

Alignment

ORF - retro_nleu_1550 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.13 %
• Parental protein coverage: 60.65 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GFKPSYGLVSRHGLIPLVNSMDVPGILTRCVDDAAVVLGALAGPTPKDSTTVHDPINKPFMLPSLADVSK
          GFKPSYGL.S.HGLI.LVN.MD..GILTRCVDDAA.VLG.L.G...KDSTTV.DP..KPF.LPSL.DV.K
Retrocopy GFKPSYGLLSHHGLIALVNLMDLLGILTRCVDDAAIVLGVLTGHDLKDSTTVQDPV-KPFILPSLTDVNK

Parental  LCIGIPKEYLVPELS-SEVQSLWSKAADLFKSEGAKVVEVSLPHTSYSIVCYHVLCTSEVASNMARFDGL
          LCIGIPK.YLVP.L..SEVQSLWSKAADLF.S..AKV.E.SLP.TSYS.VCYHVLCT.EVASNMARFDGL
Retrocopy LCIGIPKKYLVP*LL<SEVQSLWSKAADLFESARAKVIEASLPYTSYSVVCYHVLCTLEVASNMARFDGL

Parental  QYGHRCDIDMSTEAMYAATRREGFNDVVRGRILSGNFFL-LKENYENYFVKAQKVRRLIANDFVNVFNSG
          .YGHR.D.D.STEA.YAATR..GFNDVVRGRILSGNFFL.....YENYF.KAQKVR.LIAN.FV..FNSG
Retrocopy RYGHRGDNDVSTEARYAATR-QGFNDVVRGRILSGNFFL<VXXXYENYFIKAQKVRCLIANNFVKAFNSG

Parental  VDVLLTPTTLSEAVPYLEFIKEDNRTRSAQDDIFTQPVNMAGLPAVSIPVALSNQGLPIGLQFIGRAFCD
          V.VLLTPTTLSEAVPYLEFIKEDN.TRS.QDD.FTQ..NMAGLPA.SIPVALS.QGLPIGL.F...AFCD
Retrocopy VHVLLTPTTLSEAVPYLEFIKEDNTTRSTQDDSFTQAINMAGLPAASIPVALSDQGLPIGL*FTECAFCD

Parental  QQLLTVAKWFEKQVQFPFIQLQELMDDCSAVLENEKLASVS
          Q.LL.VAK.FEKQV.F..IQLQELMDDCS..LENEKLASVS
Retrocopy QHLLIVAK*FEKQVRFSVIQLQELMDDCSSILENEKLASVS

Legend:

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

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_1550 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys 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 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,