RetrogeneDB ID: retro_nleu_1403

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397292.1:12288610..12289552(+)
• Located in intron of: ENSNLEG00000003739

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_1403
AATGCTATAGTAGTTCCGAAGATGTTGGATTAGGGAGCTCTACTGATGGAAAAACAAATTTAGATGAGTTTGCTATGAGA
TCTGGAAATGCAGAAGGCATATTTGGACCAGTTAAAAACCCCTGGAGTTATTCAAAACGATATAGAGAAAAGAGGAAGCA
GAATCTCCACTTTGAGAATGAAGATTCAGACTGGCTGATAACTGGAGGACGCTCAGGTGGGAGTGCAGTTGCCGTATCAG
CATTCACATGCTATGCGGCTTTAGGATCAGATACAGGAGGGCTGACCAGAAATCCTGCTGCCTACTGTGGGCTTGTTGGT
TTCAAACCAAGCTATGGCTTAGTTTCCAATCATGGTCTCATTTCCCTGGAGAATTTGATGGATGTGCAAGGAATCTTAAC
CAGATGTGTGGATGATGCAGCAATTGTCTTGGGTGTACTGACTGAACATGACCCTAAGGATTCTACCACAGTACAGGATC
CTGTTAAACCATTCATGCTTCCCAGTTTGACAAATGTGAGCAAACTACGTATAGGTGTTCCAAAGGAATATCTTGTACTG
GAATTATCAAGTGAAGTACAGTCTCTTTGGTCCAAAGCTGCTGACCTCTTTGAGTCTGAGGGGGCCAAAGTAATTGAAGT
ATCGTTTTCTCACATCACTTATTCAATTGTCTGCTACCATTTATTGTGCACATCAGAAGCAGCATCGAGTATAGCAAGAT
TTGATGGGCTACAATGTGGTCACAGATGTGACACTGATGTGTCTACTGAAGCCATGTATGCTGCAACCAGACGAGAAGGG
TTCAATGGTTTTGTAAGAGGAAGAATTCTCTCAGGAAATGTTTTCTTGTTAAAATAAAAATATGAAAATTATTTCATCAA
AGCACAGAAAGTGAGATGCCTCATTGCTAATGATTTTTGTGAATGCTTTTAACTTTGGAGTA

Alignment

ORF - retro_nleu_1403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.49 %
• Parental protein coverage: 59.51 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  NATVVQKLLDQGALLM-GKTNLDEFAMGSGSTDGVFGPVKNPWSYSKQYREKRKQNPHSENEDSDWLITG
          NA.VV.K.LD.GALLM.GKTNLDEFAM.SG...G.FGPVKNPWSYSK.YREKRKQN.H.ENEDSDWLITG
Retrocopy NAIVVPKMLD*GALLM<GKTNLDEFAMRSGNAEGIFGPVKNPWSYSKRYREKRKQNLHFENEDSDWLITG

Parental  G-SSGGSAAA-VSAFTCYAGLIRYRRS-TRNPAAHCG-VGFKPSYGLVSRHGLIPLVNSMDVPGILTRCV
          G.S.G...A...S........IRYRR..TRNPAA.CG.VGFKPSYGLVS.HGLI.L.N.MDV.GILTRCV
Retrocopy GRSGGSAVAV<ISIHMLCGFRIRYRRA>TRNPAAYCGLVGFKPSYGLVSNHGLISLENLMDVQGILTRCV

Parental  DDAAVVLGALAGPTPKDSTTVHDPINKPFMLPSLADVSKLCIGIPKEYLVPELSSEVQSLWSKAADLFKS
          DDAA.VLG.L....PKDSTTV.DP..KPFMLPSL..VSKL.IG.PKEYLV.ELSSEVQSLWSKAADLF.S
Retrocopy DDAAIVLGVLTEHDPKDSTTVQDPV-KPFMLPSLTNVSKLRIGVPKEYLVLELSSEVQSLWSKAADLFES

Parental  EGAKVVEVSLPHTSYSIVCYHVLCTSEVASNMARFDGLQYGHRCDIDMSTEAMYAATRREGFNDVVRGRI
          EGAKV.EVS..H..YSIVCYH.LCTSE.AS..ARFDGLQ.GHRCD.D.STEAMYAATRREGFN..VRGRI
Retrocopy EGAKVIEVSFSHITYSIVCYHLLCTSEAASSIARFDGLQCGHRCDTDVSTEAMYAATRREGFNGFVRGRI

Parental  LSGNFFLLKENYENYFVKAQKVRRLIAND-FVNVFNSGV
          LSGN.FLLK..YENYF.KAQKVR.LIAND.FVN.FN.GV
Retrocopy LSGNVFLLK*KYENYFIKAQKVRCLIAND>FVNAFNFGV

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_1403 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.

---

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,