RetrogeneDB ID: retro_nleu_1608

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397301.1:749236..749690(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VDAC2
• Ensembl ID: ENSNLEG00000016857
• Aliases: None
• Description: voltage-dependent anion channel 2 [Source:HGNC Symbol;Acc:12672]

Sequence

>retro_nleu_1608
GACCAGCTTTGTCAAGGTTTGAAACTAATATTTGATACTACCTTCTTACCAATCACAGGAAACAAAAGTGGTAAAATCAA
GTCTTCTTGCAAGAGGGAGTGCATAAACCTTGCCTGTGATGTTAATTTTGATTTTGCTGGACCAGCAATCTATGCTTCAG
CTGTCTTTGGTTACGAGGGCTGGCTTGCTGGGTACCAGATGACCACTGGTAGTGCCACCTCAAAGCTGACAAGGAATAAC
TCTGCAGTGGGCTACCAGATGGGGGACTTCCAGCTACACACTAATAACAATAATGGGGCAGAATTTGGAGGCTCAGTTTA
TCAGAAGGTATGTGACAATCTTGACACTTCAGTAAACTTTGCTTGGACATCAAGTACCAACTGCACTCATTTTGTCTTGC
CGCTAAACATCGGCTGCATTTCACTGCTTCTGTTTTTGCAAAAGTCAACAACTC

Alignment

ORF - retro_nleu_1608 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.92 %
• Parental protein coverage: 60.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DQICQGLKLTFDTTFSPNTGKKSGKIKSSYKRECINLGCDVDFDFAGPAIHGSAVFGYEGWLAGYQMTFD
          DQ.CQGLKL.FDTTF.P.TG.KSGKIKSS.KRECINL.CDV.FDFAGPAI..SAVFGYEGWLAGYQMT..
Retrocopy DQLCQGLKLIFDTTFLPITGNKSGKIKSSCKRECINLACDVNFDFAGPAIYASAVFGYEGWLAGYQMTTG

Parental  SAKSKLTRNNFAVGYRTGDFQLHTNVNDGTEFGGSIYQKVCEDLDTSVNLAWTSGTNCTR-FGIAAKYQL
          SA.SKLTRNN.AVGY..GDFQLHTN.N.G.EFGGS.YQKVC..LDTSVN.AWTS.TNCT..F..AAK..L
Retrocopy SATSKLTRNNSAVGYQMGDFQLHTNNNNGAEFGGSVYQKVCDNLDTSVNFAWTSSTNCTH<FCLAAKHRL

Parental  DPTAS-HFCKSQQL
          ..TAS..FCKSQQL
Retrocopy HFTAS<CFCKSQQL

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_1608 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 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000008623	2 retrocopies	retro_eeur_192, retro_eeur_343,
Nomascus leucogenys	ENSNLEG00000008023	11 retrocopies	retro_nleu_1044, retro_nleu_1318, retro_nleu_1561, retro_nleu_189, retro_nleu_1991, retro_nleu_2707, retro_nleu_3019, retro_nleu_433, retro_nleu_492, retro_nleu_873, retro_nleu_880,
Nomascus leucogenys	ENSNLEG00000012890	1 retrocopy	retro_nleu_2593,
Nomascus leucogenys	ENSNLEG00000016857	1 retrocopy	retro_nleu_1608 ,
Rattus norvegicus	ENSRNOG00000013505	1 retrocopy	retro_rnor_2652,
Tupaia belangeri	ENSTBEG00000001946	4 retrocopies	retro_tbel_1504, retro_tbel_1541, retro_tbel_1885, retro_tbel_4597,
Vicugna pacos	ENSVPAG00000008068	1 retrocopy	retro_vpac_156,