RetrogeneDB ID: retro_nleu_1251

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397286.1:23752839..23753696(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RUVBL2
• Ensembl ID: ENSNLEG00000004769
• Aliases: None
• Description: None

Sequence

>retro_nleu_1251
ATGGCAACTGTGATGACCGTGACCAATGTCCCAGAGATCTATGATGTAAAGAGGATTGAGCATAGAGGTGTTCACTCCCA
CATCTGAGGACTGGGGCTGGATGATGCTTTGGAGGCTCAACAGGCTTCCCAGGGCATGGTGGGTCAGCTTTGCTGCACAG
CGGGCAGCTGGTGTGGGGCTGGAGATGATCCATAAAGGGAAGATTGTCAAGTGGGCAGTCCTCATTGCTGGTCAGCTGGG
CAGAGGGAAGACAGCCATCGCCCTAGGCATGGCATAGGCCCTGGGACCTGACACCTTGTTCATAGCCATCACCAGAAGTG
AGATCTCCCTGAAGATGAGCAAGACCCAGGCACTGACACAAGCTTTCTGGCCATCTTTTGGCATTCACTTCAAGGAGGAG
ATGGAGATCATCAAAGGGGAAGTGGTCGAGACCCACATTGATAGACCAGTGACAGGAATGGGCTCCAAGGTGGGCAAACT
GACCATCGAAACCAAGAAGATGGAGACCATCTATGACCTGGGCATGAAGATAATTGAGTCCCTGACCAAAGACAAGATCC
ACGCTGGTGACATGATCACTATTGACAAAGCAATGGGCAAGATCTCTAAGTTGGGCCACTCCTTTACATGATCCGGTGAC
TGCAACCCCATGGACTCCCAGACCAAATTCGGGCAGCCCCCATATGGGAAGCTCCAGAAATGCAAGGTGCACACTGTGTC
CCTTGCACAAGATCGACATCATCAACTCCCACACCCATGGCTTCCTGGCTCTCTTCTCATGCGACACAAGAGAGATCAAG
TCAGAAGTTGCCAAGCAGATCAATGTCAAAGTGGCCGAGTGGATGGAACAAAATAGA

Alignment

ORF - retro_nleu_1251 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.72 %
• Parental protein coverage: 62.2 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MATVTATTKVPEIRDVTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQL-AARRAAGVVLEMIREGKIA
          MATV...T.VPEI.DV.RIE..G.HSHI.GLGLDDALE..QASQGMVGQL.AA.RAAGV.LEMI..GKI.
Retrocopy MATVMTVTNVPEIYDVKRIEHRGVHSHI*GLGLDDALEAQQASQGMVGQL>AAQRAAGVGLEMIHKGKIV

Parental  GRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKEETEIIE
          ..AVLIAGQ.G.GKTAIA.GMA.ALGPDT.F.AI..SEI.SL.MSKT.ALTQAF..S.G...KEE.EII.
Retrocopy KWAVLIAGQLGRGKTAIALGMA*ALGPDTLFIAITRSEI-SLKMSKTQALTQAFWPSFGIHFKEEMEIIK

Parental  GEVVEIQIDRPATGTGSKVGKLTLKTTEMETIYDLGTKMIESLTKDKVQAGDVITIDKATGKISKLGRSF
          GEVVE..IDRP.TG.GSKVGKLT..T..METIYDLG.K.IESLTKDK..AGD.ITIDKA.GKISKLG.SF
Retrocopy GEVVETHIDRPVTGMGSKVGKLTIETKKMETIYDLGMKIIESLTKDKIHAGDMITIDKAMGKISKLGHSF

Parental  TRARDYDAMGSQTKFVQCPDGELQKRKEVVHTVS-LHEIDVINSRTQGFLALFSGDTGEIKSEVREQINA
          T...D...M.SQTKF.Q.P.G.LQK.K..VHTVS.LH.ID.INS.T.GFLALFS.DT.EIKSEV..QIN.
Retrocopy T*SGDCNPMDSQTKFGQPPYGKLQKCK--VHTVS>LHKIDIINSHTHGFLALFSCDTREIKSEVAKQINV

Parental  KVAEWREEGK
          KVAEW.E...
Retrocopy KVAEWMEQNR

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_1251 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000222	2 retrocopies	retro_cjac_329, retro_cjac_4119,
Homo sapiens	ENSG00000183207	1 retrocopy	retro_hsap_4755,
Gorilla gorilla	ENSGGOG00000009245	1 retrocopy	retro_ggor_2961,
Macropus eugenii	ENSMEUG00000000069	1 retrocopy	retro_meug_2099,
Macaca mulatta	ENSMMUG00000003915	1 retrocopy	retro_mmul_2536,
Nomascus leucogenys	ENSNLEG00000004769	1 retrocopy	retro_nleu_1251 ,
Otolemur garnettii	ENSOGAG00000007519	2 retrocopies	retro_ogar_2473, retro_ogar_3246,
Pongo abelii	ENSPPYG00000010225	1 retrocopy	retro_pabe_3701,
Pan troglodytes	ENSPTRG00000011270	1 retrocopy	retro_ptro_3168,