RetrogeneDB ID: retro_nleu_545

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397267.1:17540538..17541465(+)
• Located in intron of: ENSNLEG00000003836

Retrocopy information

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

Parental gene information

• Parental gene symbol: TARBP2
• Ensembl ID: ENSNLEG00000017690
• Aliases: None
• Description: None

Sequence

>retro_nleu_545
AGGGCCCACCGGCCTAATTTCATCTTCTGGGTCACTGTTGGCAACACCAGCTGCACTGGTCAGAGCCCCAGGAAGAAGGT
AGTCAAGCACAAGGCAGCTGAGGTGGCCCTCAAACACCTCAAAGTGGGGAGCATGTTGGAGCCGGCCCCGGAGGACAGCA
GTTCTTTTTCTCCCCTAGACTCTTCACTGCCTGAGGACTTTCCGGTTTTTACTGCCGCAGCAGCTGCTACCCCAGTTTCA
TCTGTTTTCCTAACCAGGAGCACCCCCATGGAAAAGCAGCCCCCGCTCCTCCCTTCAGCAGTCTGAGTGCATCCCTGTTG
GTGCTCTTCAGAAACTGGTGGTGCAGAAAGGCTGGTGGTTGCCAGAGTACACAGTGACCTAGGAGTCCAGGCCAGATCAC
CACGAAGAATTGACCTGACGAGTGGAGCGTTTCATTGAGATTGGCAGTGGCACTTCCAAAAAATCAACAAGTTGTAATAC
GGTGACCAAAATGCTGCTTCGAGTGCACATGGTGTCTCTGGATGCCTGAGATGGCAATGAGGCAGAGCCTCGTGATGACT
ACTTCTCCATTGATGTGGGCTCCCGCCTGGATGGTCTTCAGAACCAGGGCCCAGGCTGCACCTGAGATTTTCTACCAAAT
TCACTGGAGAGAAGATCCTGTCCTTCTGCAATTGTTCCCTGGGCTCCCTAGGTGCCCTGGGCCCTGCCTGCTGCCGTGTC
CTCAGTGAGCTCTCTGAGAAGCAGGCCTTCCATGTCAGTTACCTGGATGTTGAGGAGCTGAGCCTGAGTAGACTCTGCCA
GTGTCTGGTGGAACTGTCCCTCCAGCCGGCCACTGCGTATCATGGCTCTGCAACCACCAGGGAGGCAGTCCGTGGTGAGG
CTGCTTACTGTACCCTGCAGTACCACAAGATCATGATGGGCAGCAAG

Alignment

ORF - retro_nleu_545 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.59 %
• Parental protein coverage: 84.97 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QAHQPNFTFRVTVGDTSCTGQGPSKKAAKHKAAEVALKHLKGGSMLEPALEDSSSFSPLDSSLPEDIPVF
          .AH.PNF.F.VTVG.TSCTGQ.P.KK..KHKAAEVALKHLK.GSMLEPA.EDSSSFSPLDSSLPED.PVF
Retrocopy RAHRPNFIFWVTVGNTSCTGQSPRKKVVKHKAAEVALKHLKVGSMLEPAPEDSSSFSPLDSSLPEDFPVF

Parental  TAAAAATPVPSVVLTRSPPMELQPPVSP-QQSECNPVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTM
          TAAAAATPV.SV.LTRS.PME.QPP..P.QQSEC.PVGALQ.LVVQKGW.LPEYTVT.ES.P.H..E...
Retrocopy TAAAAATPVSSVFLTRSTPMEKQPPLLP>QQSECIPVGALQKLVVQKGWWLPEYTVT*ESRPDHHEE--L

Parental  TCRVERFIEIGSGTSKKLAKRNAAAKMLLRVHTVPLDARDGNEVEPDDDHFSIGVGSRLDGLRNRGPGCT
          T.RVERFIEIGSGTSKK....N...KMLLRVH.V.LDA.DGNE.EP.DD.FSI.VGSRLDGL.N.GPGCT
Retrocopy T*RVERFIEIGSGTSKKSTSCNTVTKMLLRVHMVSLDA*DGNEAEPRDDYFSIDVGSRLDGLQNQGPGCT

Parental  WDSLRNSV-GEKILSLRSCSLGSLGALGPACCRVLSELSEEQAFHVSYLDIEELSLSGLCQCLVELSTQP
          .D.L.NS..GEKILS...CSLGSLGALGPACCRVLSELSE.QAFHVSYLD.EELSLS.LCQCLVELS.QP
Retrocopy *DFLPNSL<GEKILSFCNCSLGSLGALGPACCRVLSELSEKQAFHVSYLDVEELSLSRLCQCLVELSLQP

Parental  ATVCHGSATTREAARGEAARRALQYLKIMAGSK
          AT..HGSATTREA.RGEAA...LQY.KIM.GSK
Retrocopy ATAYHGSATTREAVRGEAAYCTLQYHKIMMGSK

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_545 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018668	1 retrocopy	retro_cjac_1526,
Homo sapiens	ENSG00000139546	1 retrocopy	retro_hsap_3995,
Gorilla gorilla	ENSGGOG00000012637	1 retrocopy	retro_ggor_2682,
Mus musculus	ENSMUSG00000023051	1 retrocopy	retro_mmus_2820,
Nomascus leucogenys	ENSNLEG00000017690	1 retrocopy	retro_nleu_545 ,
Pongo abelii	ENSPPYG00000004583	1 retrocopy	retro_pabe_3281,
Pan troglodytes	ENSPTRG00000005020	1 retrocopy	retro_ptro_2712,