RetrogeneDB ID: retro_nleu_3090

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397949.1:36501..38186(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: USP6NL
• Ensembl ID: ENSNLEG00000012036
• Aliases: None
• Description: None

Sequence

>retro_nleu_3090
CAACGTTCAGAGCCATTTGCAGTCATGAATTCAGACCAGGATGTAGCACTCAAACTTGCCCAGGAGCGAGCTGAAATAGT
TGCTAAATATGACAGAGGACGACAAGGTGCAGAGATTGCACCTTGGGAAGATGCTGATTACCTTGTTTACAAAGTCATGG
ATAGATTTGGCTTTTTACATGAGCTGGAGCTCCCAGATCATAATGCGGCTGTGGAACGGCAAAAGCACCTGGAAATCGAA
AGAACTACCAAATGGCTGAAAATGCTGAAAGGATGGGAAAAATACAAGAACACTGAAAAGTTTCATAGGCGAATTTACAA
ACGAATACCACTCCAGCTCAGAGGTGAAGTCTGGGCCCTCCTTCTTGAGATCCCTAAAATGAAAGAAGAAACAAGGGACC
TGTATAGTAAATTAAAACACAGAGCACGGGGCTGTTCACCTGACATCAGACAAATAGACCTGGATGTGAACCGCACATTT
CGGGACCACATTATGTTTAGAGACAGATATGGTGTTAAGCAACAGTCCTTATTCCATGTTCTTGCTGCCTATTCTATTTA
TAATACGGAAGTCGGGTATTGTCAGGGGATGAGCCAGATCACAGCTTTACTCCTCATGTATATGAACAGGAAGACGCCTT
CTGGGCCCTGGTCAAACTCTTCTCAGGCCCTAAACATGCCATGCATGGCTTTTTTGTCCAAGGTTTTCCTAAACTCTTGA
GGTTTCAAGAACATCATGAAAAAATACTGAACAAATGTCTGTCCAAGCTTAAGCAACACTTGGATTCTCAAGAAATCTAC
ACAATGAAATGGTTTTTTCAGTGTTTCCTTAATCGTACTCCCTTTACACTAAACCTCAGAATATGGGATATCTACATCTT
TGAAGGAGAACGAGTTCTTACTGCTATGTCTTACACAATCTTAAAATTACACAAGAAACATCTAATGAAATTGTCCATGG
AAGAACTTGTAGAATTTCTTCAGGAGACCCTGGCAAAGGACTTTTTCTTTGAAGATGGTTTTGTGATAGAGCAACTTCAG
ATTTCTATGGCAGAACTAAAGTGGGCAAAGTTAGACCTTCCAGAACCTGGTAAAGAGGATGAATATCCAAAGAAGCCCTT
GGGGCAGCTTCCACCTGAACTTCAGTCTTGGGGCGTCCATCACTTGAGCAACGGACAGAGGAGCGTGGGCCGGCCGAGCC
CGCGGGCCAGCGGCAGGAGGGAGAGCGGGGCGCCCCACAGGAGGCACAAGCACTCCCCGCACCCCCAGAGCAGGACCGGG
AGGCCCGAGAGAGCGCAGCCGCCAAGACGGAAATCGGTGGTGGAGGAGAGCAAAAAGCTTAAAGATGAGGCAGATGTTCA
AAGAAAACTCCCATCAGGTCCACAGGACAGTTCCAGGCAATATAATCACACAGCTGCCAACCAAAATAGCAACGCCGCTT
CAAATATCAGGAAGGAATTTGTGCCCAAATGGAATAAACCGTCAGACGTCTCAGCTATGGAGAGAACTGCCAAATACACC
ATGGAAGGCAAAGGTCGAGCAGCGCACCCCACGCTCGCACTCACCGCCCCAGGCCCTGCCGAGGTGCGGGTGTCAAAAGT
GCGGCCAAAGATGAAGGCCCTGGATGCTGAGGATGGGAAGCGGGGCTCCACTGCATCGCAGTATGACAACGGGCCGGGCC
CGGAG

Alignment

ORF - retro_nleu_3090 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.12 %
• Parental protein coverage: 66.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QGQADYLTKDSDQDVALKLAQERAEIVAKYDRGREGAEIEPWEDADYLVYKVTDRFGFLHEEELPDHNAA
          Q.........SDQDVALKLAQERAEIVAKYDRGR.GAEI.PWEDADYLVYKV.DRFGFLHE.ELPDHNAA
Retrocopy QRSEPFAVMNSDQDVALKLAQERAEIVAKYDRGRQGAEIAPWEDADYLVYKVMDRFGFLHELELPDHNAA

Parental  VERQKHLEIERTTKWLKMLKGWEKYKNTEKFHRRIYKGIPLQLRGEVWALLLEIPKMKEETRDLYSKLKH
          VERQKHLEIERTTKWLKMLKGWEKYKNTEKFHRRIYK.IPLQLRGEVWALLLEIPKMKEETRDLYSKLKH
Retrocopy VERQKHLEIERTTKWLKMLKGWEKYKNTEKFHRRIYKRIPLQLRGEVWALLLEIPKMKEETRDLYSKLKH

Parental  RARGCSPDIRQIDLDVNRTFRDHIMFRDRYGVKQQSLFHVLAAYSIYNTEVGYCQGMSQITALLLMYMN-
          RARGCSPDIRQIDLDVNRTFRDHIMFRDRYGVKQQSLFHVLAAYSIYNTEVGYCQGMSQITALLLMYMN.
Retrocopy RARGCSPDIRQIDLDVNRTFRDHIMFRDRYGVKQQSLFHVLAAYSIYNTEVGYCQGMSQITALLLMYMN<

Parental  EEDAFWALVKLFSGPKHAMHGFFVQGFPKLLRFQEHHEKILNKFLSKLKQHLDSQEIYTSFYTMKWFFQC
          .EDAFWALVKLFSGPKHAMHGFFVQGFPKLLRFQEHHEKILNK.LSKLKQHLDSQEI....YTMKWFFQC
Retrocopy QEDAFWALVKLFSGPKHAMHGFFVQGFPKLLRFQEHHEKILNKCLSKLKQHLDSQEI----YTMKWFFQC

Parental  FLDRTPFTLNLRIWDIYIFEGERVLTAMSYTILKLHKKHLMKLSMEELVEFFQETLAKDFFFEDDFVIEQ
          FL.RTPFTLNLRIWDIYIFEGERVLTAMSYTILKLHKKHLMKLSMEELVEF.QETLAKDFFFED.FVIEQ
Retrocopy FLNRTPFTLNLRIWDIYIFEGERVLTAMSYTILKLHKKHLMKLSMEELVEFLQETLAKDFFFEDGFVIEQ

Parental  LQISMAELKRAKLDLPEPGKEDEYPKKPLGQLPPELQSWGVHHLSNGQRSVGRPSPQASGRRESGAPHRR
          LQISMAELK.AKLDLPEPGKEDEYPKKPLGQLPPELQSWGVHHLSNGQRSVGRPSP.ASGRRESGAPHRR
Retrocopy LQISMAELKWAKLDLPEPGKEDEYPKKPLGQLPPELQSWGVHHLSNGQRSVGRPSPRASGRRESGAPHRR

Parental  HEYSPHPQSRTGMPERAQPPRQKLVEEESRKLKDEADVQRKLPSGPQDSSRQYNHAAANQNSNATSNIRK
          H..SPHPQSRTG.PERAQPPR.K.V.EES.KLKDEADVQRKLPSGPQDSSRQYNH.AANQNSNA.SNIRK
Retrocopy HKHSPHPQSRTGRPERAQPPRRKSVVEESKKLKDEADVQRKLPSGPQDSSRQYNHTAANQNSNAASNIRK

Parental  EFVPKWNKPSDVSATERTAKYTMEGKGRAAHPTLAVTAPGPAEVRVSNVRPKMKALDAEDGKRGSTASQY
          EFVPKWNKPSDVSA.ERTAKYTMEGKGRAAHPTLA.TAPGPAEVRVS.VRPKMKALDAEDGKRGSTASQY
Retrocopy EFVPKWNKPSDVSAMERTAKYTMEGKGRAAHPTLALTAPGPAEVRVSKVRPKMKALDAEDGKRGSTASQY

Parental  DNVPGPE
          DN.PGPE
Retrocopy DNGPGPE

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_3090 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000012036	1 retrocopy	retro_nleu_3090 ,