RetrogeneDB ID: retro_nleu_215

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397261.1:39351322..39352628(-)
• Located in intron of: ENSNLEG00000016546

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAD17
• Ensembl ID: ENSNLEG00000004118
• Aliases: None
• Description: None

Sequence

>retro_nleu_215
AAGGTAACAGACTGGATTGGTCCATCATTCAATGATTTTCTAGAGTGTAGAGACATCTCTACTATTACTGCCACATCATT
AGGTGTGAATAACTGAAGTCATAGAGAAAAAATGAGTCTTCTACATTAGAAGGTAAGATGTTTCCAGCTAGAAAAATAGG
AAATCTGTCTTCCTTAGAACAGATTTATGGTTTAGAAAATTCAAAAGACTACCTGTCTGAAAATGAACCATGGGTAGATA
AATATAAACCAGAAACTTAGCATGAACTTGCTGTGCATGAAAAGAAAATCGAAGAAGTTGAAATCTGGTAAAAAGCTCAA
GTCTTAGAAAGGCAACCAAAACAGGATGAATCTATTTTATTAATAACAGGTCCTCCTGGATGTGGAAAGACAATGACCAA
AAAACACACTATCAAAGGAGCATGGTATTCAAGTACAAGAGTGGATTAATCCAGTTTTACCAGACTTCCAAAAAGATGAT
TTCAAGGAAATGTTTCATACTGAATCAAGCTTCCATATGGTTCCCTATCAGTCTCAGATAGCAGTTTTCAAAGAGTTTCT
ACTAAGAGCAACAAAGTATAACAAAGTTACAAATGCTTGGAGATCATCTGAGAACTGATAAGAAGATAATTCTGGTTGAA
GATTTACCTAACCAGTTTATCGGGATTCTCATACTTTACATGAAGTTCTACGGAAGTATGTGAAGATTGGTCAATATCCT
CTTATATTTATAATCTCTGACAGTCTCAGTGGTGATAATAATCAAAGTTTCTTGTTTCCCAAAGAAATCAGGAAGAGTGT
TCTACCTCAAATATTAGTTTCAATCCTGTGGCACCAACAATTATGATGAAATTTCTTAATCAAATAGTGACTATAGAAGC
TAACAAGAATGGAGGAAAAATTACTGTCCCTGACAAAACTTCTCTAGAGGTGCTCTGTCAAGGATGTTCTGGTGATATGA
GAAGTGCAATAAATAGCCTCCAGATTTCGTCTTCAAAAGGAGAAAACAACTTATGGCCAAGGAAAAAATGAATGTCTTTA
AAATCGAATGCCATGCTGTCAAAATCAAAACGAAGAAAAAAAACTGATAGGGTTTTTGAAAATCAAGAGGTCCAAGCTAT
TGATGGCAAAGATGTTTCTCTGTTTCTTTTCCGAGCTTTGGGGAAAATTCTATATAGTAAAAGAGCATCTTTAACAGAAT
TAGACTCACCTCGGTTGCCCTCTCATTTATCTGCATATGAACGGGATACACACTTGTTGAACCTGAGGAGGTAGTAGAAA
TGTCACACATGCCAGGAGACTAATTT

Alignment

ORF - retro_nleu_215 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.2 %
• Parental protein coverage: 65.02 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  QVTDWVDPSFDDFLECRGISTITATSLGVNNSSHR-RKNGPSTLESSRFPVRKRGKLSSLEQIYGLENSK
          .VTDW..PSF.DFLECR.ISTITATSLGVNN.SHR.RKN..STLE...FP.RK.G.LSSLEQIYGLENSK
Retrocopy KVTDWIGPSFNDFLECRDISTITATSLGVNN*SHR<RKNESSTLEGKMFPARKIGNLSSLEQIYGLENSK

Parental  EYLSENEPWVDKYKPETQHELAVHKKKIEEVETWLKAQVLERQPKQGGSILLITGPPGCGKTTTIK-ILS
          .YLSENEPWVDKYKPET.HELAVH.KKIEEVE.W.KAQVLERQPKQ..SILLITGPPGCGKT.T.K..LS
Retrocopy DYLSENEPWVDKYKPET*HELAVHEKKIEEVEIW*KAQVLERQPKQDESILLITGPPGCGKTMTKK>TLS

Parental  KEYGIQVQEWINPVLPDFQKDDFKGMFNTESSFHMFPYQSQIAVFKEFLLRATKYNK-LQMLGDDLRTDK
          KE.GIQVQEWINPVLPDFQKDDFK.MF.TESSFHM.PYQSQIAVFKEFLLRATKYNK.LQMLGD.LRTDK
Retrocopy KEHGIQVQEWINPVLPDFQKDDFKEMFHTESSFHMVPYQSQIAVFKEFLLRATKYNK>LQMLGDHLRTDK

Parental  KIILVEDLPNQF-YRDSHTLHEVLRKYVRIGRCPLIFIISDSLSGDNNQRLLF-PKEI-QECSISNISFN
          KIILVEDLPNQF.YRDSHTLHEVLRKYV.IG..PLIFIISDSLSGDNNQ..LF.PK....ECS.SNISFN
Retrocopy KIILVEDLPNQF<YRDSHTLHEVLRKYVKIGQYPLIFIISDSLSGDNNQSFLF>PKKS>EECSTSNISFN

Parental  PVAPTIMMKFLNRIVTIEANKNGGKITVPDKTSLELLCQGCSGDIRSAINSLQFSSSKGENNLWPRKKGM
          PVAPTIMMKFLN.IVTIEANKNGGKITVPDKTSLE.LCQGCSGD.RSAINSLQ.SSSKGENNLWPRKK.M
Retrocopy PVAPTIMMKFLNQIVTIEANKNGGKITVPDKTSLEVLCQGCSGDMRSAINSLQISSSKGENNLWPRKK*M

Parental  SLKSDAVLSKSKRRKKPDRVFENQEVQAIGGKDVSLFLFRALGKILYCKRASLTELDSPRLPSHLSEYER
          SLKS.A.LSKSKR....DRVFENQEVQAI.GKDVSLFLFRALGKILY.KRASLTELDSPRLPSHLS.YER
Retrocopy SLKSNAMLSKSKRXXXXDRVFENQEVQAIDGKDVSLFLFRALGKILYSKRASLTELDSPRLPSHLSAYER

Parental  DT-LLVEPEEVVEMSHMPGDLF
          DT..LVEPEEVVEMSHMPGD.F
Retrocopy DT<TLVEPEEVVEMSHMPGD*F

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_215 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000152942	1 retrocopy	retro_hsap_3821,
Macaca mulatta	ENSMMUG00000014881	1 retrocopy	retro_mmul_1630,
Nomascus leucogenys	ENSNLEG00000004118	1 retrocopy	retro_nleu_215 ,
Pan troglodytes	ENSPTRG00000016950	1 retrocopy	retro_ptro_2599,