RetrogeneDB ID: retro_nleu_2224

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397335.1:3123322..3124772(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000019103
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TMEM161B
• Ensembl ID: ENSNLEG00000013645
• Aliases: None
• Description: None

Sequence

>retro_nleu_2224
GTGATAGGTATACAGCTGTTGTTACCATGGTGATGGCCAGTGTCATGCAGAAGATTATACCTCGTTATTCTCTTGCTCAA
TAGCTACTCTGTAATGGCAGTTTGAGGTGGTATCAACATTCTACAGTAGAAGAATCAAGAATTCTTGCAGGGAATCAGCA
AAAACAGAAAAGCAAAAAAGATAGGAAATATAATGGTCATATTGAAATTAAGCCATTAACCATTCCAAAGGATATTGACC
TTCGTCTAGAAACAAAGTCAGTTATAGAAGTGGATATTTTAGCATTGCATTACTTGGCAGAATACCAGTGACTGGTGGAT
TTCACAGTGGCTGCTACAGTTGTGTATCTAGTAACTGAAGTCGACTACAAGTTTATGAAGCCTACACAGGAAGTGATTAT
CAGCTTAGTGTGTTGCCTGCTTGTTTTGTCTTTTGCAATCAAAGTTCTATTTTCATTAACTACACACTATTTTAAAGTAG
AAGATGGTGGTGAAAGATCTGTTTGTGTCACCTTTGGATTTTTTTTCTTTGTCAAAGCAATGGCAGTGTTGATTGTAACA
GAAAATTATCTGGAATTTGGACTTGAAACAGGGTTTACAAATATTTCAGACAGCATGATGCAGTTTCTTGAAAAGCAGGG
TTTAGAATCTCAGAGTCCTGTTTCAAAACTTACTTTCAAATTTCTCCTGGCTATTTTCTGTTCACTCATTGGGGCTTTTT
GGACATTTCCTGGATTACGGCTGGCTCAAATGCATCTGGATGCCCTGAATTTGGCAACAGAAAAAATTACACAAACATTA
CTTCATATCAGCTTCTTGGCACATTTATTTATGGTTCTGCTCTGGGTAAAACCAGTCACCAAAGACTACATTATGAACCC
AACCTTGGGTGAAGAAAGCATCACTTTAATGACAGAAGCCACATTCGATACTCTGTGACTCTGGTTAATAATCCTGCTGT
GTGCTTTGTGGTTGGCCATGATGCATAGTTACCTGCAAGCTTATTTATATTTAGCCCAAAAATGTGTGAATCAGATGATG
AAAGAAGCAGGGTGAATAAGTACAGTTGAGCTACAGAAAATGGTGGCTTGAGTCTTTTATTATCTTTGTGTCATTGCACT
GCAGTATGTGGTGCCTCTGGTAATGCTGTTTCACACAAATCTGCTTTTGAAAACACTAGGTAATCATTCCTGGAATATTT
ATCCAGAATCTATCTCTACTTTACCAGTGGATAATAGTCTACTCTACAATTCTGTTTACTCTGAATTACCATCAGCTGAA
GAGAAGATGAAGGTTACTGTTACACAAATAACAGTGGCACTGAGCAGCTTAAAAATATTTTTACTCTTCTTTTTTGAGGA
CTTCTGTCGTTTCTGACCTGGTGGATTGCTGCTTGCCTCTTTTCTACAAGACTTTTTGGGCTTTTTTATCACCATTATCT
GACTGTGGCA

Alignment

ORF - retro_nleu_2224 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.5 %
• Parental protein coverage: 99.59 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VIGIQL-VVTMVMASVMQKIIPHYSLARWLLCNGSLRWYQHPTEEELRILAGKQQKGKTKKDRKYNGHIE
          VIGIQL.VVTMVMASVMQKIIP.YSLA..LLCNGSLRWYQH.T.EE.RILAG.QQK.K.KKDRKYNGHIE
Retrocopy VIGIQL<VVTMVMASVMQKIIPRYSLAQ*LLCNGSLRWYQHSTVEESRILAGNQQKQKSKKDRKYNGHIE

Parental  SKPLTIPKDIDLHLETKSVTEVDTLALHYFPEYQWLVDFTVAATVVYLVTEVYYNFMKPTQEMNISLVWC
          .KPLTIPKDIDL.LETKSV.EVD.LALHY..EYQ.LVDFTVAATVVYLVTEV.Y.FMKPTQE..ISLV.C
Retrocopy IKPLTIPKDIDLRLETKSVIEVDILALHYLAEYQ*LVDFTVAATVVYLVTEVDYKFMKPTQEVIISLVCC

Parental  LLVLSFAIKVLFSLTTHYFKVEDGGERSVCVTFGFFFFVKAMAVLIVTENYLEFGLETGFTNFSDSAMQF
          LLVLSFAIKVLFSLTTHYFKVEDGGERSVCVTFG...FVKAMAVLIVTENYLEFGLETGFTN.SDS.MQF
Retrocopy LLVLSFAIKVLFSLTTHYFKVEDGGERSVCVTFGXXXFVKAMAVLIVTENYLEFGLETGFTNISDSMMQF

Parental  LEKQGLESQSPVSKLTFKFFLAIFCSLIGAFLTFPGLRLAQMHLDALNLATEKITQTLLHINFLAPLFMV
          LEKQGLESQSPVSKLTFKF.LAIFCSLIGAF.TFPGLRLAQMHLDALNLATEKITQTLLHI.FLA.LFMV
Retrocopy LEKQGLESQSPVSKLTFKFLLAIFCSLIGAFWTFPGLRLAQMHLDALNLATEKITQTLLHISFLAHLFMV

Parental  LLWVKPITKDYIMNPPLGKESIPLMTEATFDTLRLWLIILLCALRLAMMRSHLQAYLNLAQKCVDQMKKE
          LLWVKP.TKDYIMNP.LG.ESI.LMTEATFDTL.LWLIILLCAL.LAMM.S.LQAYL.LAQKCV.QM.KE
Retrocopy LLWVKPVTKDYIMNPTLGEESITLMTEATFDTL*LWLIILLCALWLAMMHSYLQAYLYLAQKCVNQMMKE

Parental  AGRISTVELQKMVARVFYYLCVIALQYVAPLVMLLHTTLLLKTLGNHSWGIYPESISTLPVDNNLLSNSV
          AG.ISTVELQKMVA.VFYYLCVIALQYV.PLVML.HT.LLLKTLGNHSW.IYPESISTLPVDN.LL.NSV
Retrocopy AG*ISTVELQKMVA*VFYYLCVIALQYVVPLVMLFHTNLLLKTLGNHSWNIYPESISTLPVDNSLLYNSV

Parental  YSELPSAEGKMKVTVTQITVALSS-LKNIFTPLLFRGLLSFLTWWIAACLFSTSLFGLFYHQYLTVA
          YSELPSAE.KMKVTVTQITVALSS.LKNIFT.LLF.GLLSFLTWWIAACLFST.LFGLFYH.YLTVA
Retrocopy YSELPSAEEKMKVTVTQITVALSS<LKNIFT-LLF*GLLSFLTWWIAACLFSTRLFGLFYHHYLTVA

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_2224 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010857	1 retrocopy	retro_cjac_2671,
Homo sapiens	ENSG00000164180	1 retrocopy	retro_hsap_560,
Gorilla gorilla	ENSGGOG00000005684	1 retrocopy	retro_ggor_506,
Macaca mulatta	ENSMMUG00000009319	1 retrocopy	retro_mmul_719,
Nomascus leucogenys	ENSNLEG00000013645	1 retrocopy	retro_nleu_2224 ,
Pan troglodytes	ENSPTRG00000017064	1 retrocopy	retro_ptro_419,
Rattus norvegicus	ENSRNOG00000032414	1 retrocopy	retro_rnor_1023,
Ictidomys tridecemlineatus	ENSSTOG00000011141	1 retrocopy	retro_itri_1420,
Ictidomys tridecemlineatus	ENSSTOG00000027831	2 retrocopies	retro_itri_1419, retro_itri_1787,