RetrogeneDB ID: retro_nleu_378

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397264.1:6127003..6127988(+)
• Located in intron of: ENSNLEG00000016423

Retrocopy information

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

Parental gene information

• Parental gene symbol: LDHAL6A
• Ensembl ID: ENSNLEG00000017780
• Aliases: None
• Description: None

Sequence

>retro_nleu_378
ATGGTAACTATCCAGAATGAATTTATTGAGAATTTTGCTTCAGAGGAGGTTATTCACCACAGTAAGGTCTCCATTATAAG
AACTGGATCAGTTAACATGGCCCGTGCAATCACCATGTTATAAAAGACTTGAGGGATGAAGTTGCCTTTGTAGCTGTTGA
TAATGGTGAATTGAAGGGTGTGAGACAATGGATCTTAAACATGGCAGTCTTTTCCTAAAACTGCCAAATAGTGCTTCCAG
CGAAGATTATCTCATCTCTGTAAACTCCAACCTAGTGATTATCACATCAGGTGCCTGCCAGGAAAAAGGTGAAACACTTT
AATGTAGTCAGTCTAAATGTGGCCATCGTTAAATTAATGATGTCAAATATTACTCAATATAGTCCTGCTGCAAACTGATA
GTTTCCAGTCCAATGGATATCTTAATTTATGTAGCTCGGAAGTTGAGTACATTTTTCGAAACCCATATTATTGGAAATGG
CTGTAATCTGGACACTGCCCATTTCCATTTCTTGACTGTGCAAATGTTGGAATCCACTCTGGAAGCTGCCATGGGTGGAT
CTTTGGAGAGTGTGGGGACTCAAGTGTTCCTGTGTGGAGTGGAGTGAACATTGCTGGTGTCCCTCTGAAGGATCTGAACT
CAGATAAAGGAATTGATCAAGATCTAGAGCAAGGGGGAAAATGTCCACAAAGAAGTGATTGCCAGTGCTTATGAAATTAT
GAAAATGAAAGGTTATACTTCTTGGACCATTGGCCCATCTGTAACTGATTGAACAGAAAGTATTTTAGAGGATCCTAGGA
GAGTGCATTCAGTTTCCACATAATTAAGGGCCTCTATGGAATGAATGAAGTATTCCTCAGTGTTCCTCGTATCTGAGAGA
GAATGGTCTTGCAGACCTTACACAGGTAAAGCTGACCCTTGAATAGGCAGCCCATTTGTAAAGGAGCACAGAAACACTTT
GGGAATTCAGAAGAAGCTCAAGCTT

Alignment

ORF - retro_nleu_378 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.57 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  MATVKSELTKNFAEEEAIHHNKISIVGTGSVGVACAISIL-LKGLSDELVLVDVDEGK-LKG-ETMDLQH
          M.T...E...NFA.EE.IHH.K.SI..TGSV..A.AI..L..K.L.DE...V.VD.G....G.ETMDL.H
Retrocopy MVTIQNEFIENFASEEVIHHSKVSIIRTGSVNMARAITML<IKDLRDEVAFVAVDNGE<IEGCETMDLKH

Parental  GSPFMKMPNIVSSKDYLVTANSNLVIITAGARQ-KKGETRLDLVQRNVSIFKLMIPNITQYSPH-CKLLI
          GS.F.K.PN..SS.DYL...NSNLVIIT.GA.Q.KK.......V..NV.I.KLM..NITQYSP..CKL.I
Retrocopy GSLFLKLPNSASSEDYLISVNSNLVIITSGACQ>KKVK-HFNVVSLNVAIVKLMMSNITQYSPA<CKL-I

Parental  VTNPVDILTYVAWKLSAFPKNRVIGSGCNLDSARFRYFIGQRL-GIHSESCHGLILGEHGDSSVPVWSGV
          V..P.DIL.YVA.KLS.F.....IG.GCNLD.A.F.....Q.L.GIHS.SCHG.I.GE.GDSSVPVWSGV
Retrocopy VSSPMDILIYVARKLSTFFETHIIGNGCNLDTAHFHFLTVQML<GIHSGSCHGWIFGECGDSSVPVWSGV

Parental  NIAGVPLKDLNPDIGTDKDPEQ-WENVHKKVISSGYEMVKMKGYTSWGISLSVADLTESILKNLRRVHPV
          NIAGVPLKDLN.D.G.D.D.EQ..ENVHK.VI.S.YE..KMKGYTSW.I..SV.D.TESIL...RRVH.V
Retrocopy NIAGVPLKDLNSDKGIDQDLEQ>GENVHKEVIASAYEIMKMKGYTSWTIGPSVTD*TESILEDPRRVHSV

Parental  ST-LSKGLYGINEEIFLSVPCI-LGENGITDLIKVKLTLEEEACLQKSAETLWE-IQKELKL
          ST...KGLYG.N.E.FLSVP.I.L.ENG..DL..VKLTLE..A.L..S.ETLWE.IQK.LKL
Retrocopy ST<IIKGLYGMN-EVFLSVPRI<LRENGLADLTQVKLTLE*AAHL*RSTETLWE<IQKKLKL

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_378 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 9 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007067	2 retrocopies	retro_cjac_164, retro_cjac_2180,
Homo sapiens	ENSG00000166800	2 retrocopies	retro_hsap_42, retro_hsap_905,
Macaca mulatta	ENSMMUG00000014614	2 retrocopies	retro_mmul_1111, retro_mmul_261,
Nomascus leucogenys	ENSNLEG00000017767	4 retrocopies	retro_nleu_1037, retro_nleu_1303, retro_nleu_1766, retro_nleu_820,
Nomascus leucogenys	ENSNLEG00000017780	2 retrocopies	retro_nleu_29, retro_nleu_378 ,
Otolemur garnettii	ENSOGAG00000009261	1 retrocopy	retro_ogar_2662,
Pongo abelii	ENSPPYG00000003435	2 retrocopies	retro_pabe_203, retro_pabe_779,
Pan troglodytes	ENSPTRG00000003423	1 retrocopy	retro_ptro_62,
Tarsius syrichta	ENSTSYG00000008062	4 retrocopies	retro_tsyr_1811, retro_tsyr_2064, retro_tsyr_2071, retro_tsyr_731,