RetrogeneDB ID: retro_nleu_240

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397262.1:13667785..13669329(+)
• Located in intron of: ENSNLEG00000006976

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLYR1
• Ensembl ID: ENSNLEG00000009950
• Aliases: None
• Description: None

Sequence

>retro_nleu_240
CCTCATGGAAAGAAAATGTTTCTTTGTGAAATTTTTTTGGAACATAAGATCATGCCTGGATTAAAGTGAAACAGCTGAAG
CCATATCATGCTCATAAAGAGGGAATGATAAAGATTAACAAGGGTAAACTATTCCAGCAAGTGGTGGATGCCGCCAAAGA
GTTTCTCAGGAGAGCCCAAAGGGAAAGATCAGACGTCATCCCACAATTCTGCTGATGACAAGAATCGGCTTAATTCCAGT
GAGGAGAGAAGTAGGCCAAACTCAGGTGATGAGAAGTGCAAACAGCCTGTCTGAAGGGAAAGTGAAGAAGATCATGGGAG
AAGGAAAGAAGAGGGTGTCTTCGGGCTCTTCAGAGAGAGGCTCCAAATCCCCTCTGAAAAGAATCCAAGAGCAGTCCCCA
GAAGTGGGGTCAGCCCCCAAAGGATGAGAAGAATGTCACCATCCCAGAGTCCAGTACCTTGAAGTGGATGATGGCCGGAC
CAGTGGCCACATTTAAATGGCAGCCGACCAGAAGCGAGCCTGTTAAAGATGCAGATCCTCATTTCCATCATTTCCTGCTA
AGCCAAACAGAAGCCATCTCTGTCTGTTAGCAGGCAATCACAAAGAAGTTGAAAATATGTGAAGAGGAAACTGGTTCCAC
CTCCATCCGGTCAGCTGACAGCATGGCTGTGAATGGCAGCATCACAGACAAAAAGATAGGATTTGGGGGCCTTGGTCTCA
TGAGAAGTGGAATCGTCTCTAACTTGCTAAAAATGGGTCACACAGTGACTGTCTGGAGCCGCACTGCCAAGAAACGTGAT
TTGTTCATCTAGGAGGGGGCCTGCCTGGGAAGAACCCCTGCTGAAGTCCTCTCAACCTGTGACATCACTTTTGCCCATGT
TTTGGATCCCAAGGTGGCCAAGGACCTGGTGCTGGTCCCCATTGGTATGCTGCAAGGGATCCGCCCTGGGAAGTGCTACG
TGGACCTGTCAACAGTGGACGCTGACATAGTCACTGAGCTGGCCCGGGTGATTGCGTCCAGGTCGGGGGATCGCTTTCCA
GAAGCCCCCCTCTCAGGGAATCAACAGCTTTCTAATCACGGGATGTTGGTGATCTTAGCAGCTGGAGACAGGGGCCTATA
CGAGGACTGCAGCAGCTGCTTCCAGGCAATGGGGAAGACCTCCTTCCTAGGTGAAGTTGGCAACGCAGCCAAGATGATGC
TGATCGTGAATATAGTCCAAGGGAGCTTCATGGCCACGATCACCGAGGTGCTGACCCTGGCCTAGGTGACAGATAAGTCG
CAGCAGACACTCTTGGACATCCTCAATCAGGGACAGTTGGCCAGCATCTTCCTAGACCAGAAGCGCCAAAATACTCTACA
AGGAAACTTTAAGCCTGATTTCTACCTGAAATACATGCAGCAGGATCTCTGCTTAGCCATTGCACTGGGCAATGTGGTCA
ACCATCTGACTCCCATGGCAGCTGCAGCCAACGAGGTCTACAAAAGAGCCAAGGCACTGGACCAGACCGACAATATGTCC
ACCGCGTCCCGAGCCTACATACAC

Alignment

ORF - retro_nleu_240 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.82 %
• Parental protein coverage: 93.67 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PRGKK-CFFVKFF-GTEDHAWIKVEQLKPYHAHKEEMIKINKGKRFQQAVDAVEEFLRRA-KGKDQTSSH
          P.GKK.CFFVKFF.GT.DHAWIKV.QLKPYHAHKE.MIKINKGK.FQQ.VDA..EFLRRA.KGKDQTSSH
Retrocopy PHGKK>CFFVKFF>GT*DHAWIKVKQLKPYHAHKEGMIKINKGKLFQQVVDAAKEFLRRA>KGKDQTSSH

Parental  NSSDDKNRRNSSEERSRPNSGDEKR-KLSLSEGKVKKNMGEGKKRVSSGSS-ERGSKSPLKRAQEQSPRK
          NS..D...R..S.E..............SLSEGKVKK.MGEGKKRV.S..S..R....PL......SP.K
Retrocopy NSA-DDKNRLNSSEERSRPNSGDEK>ANSLSEGKVKKIMGEGKKRV-SSGS>QREAPNPL*KESKSSPQK

Parental  RGRPPKDEKDLTIPESSTVKGMMAGPMAAFKWQPTASEPVKDADPHFHHFLLSQTEKPAVCYQAITKKLK
          .G.PPKDEK..TIPESST.K.MMAGP.A.FKWQPT.SEPVKDADPHFHHFLLSQTE...VC.QAITKKLK
Retrocopy WGQPPKDEKNVTIPESSTLKWMMAGPVATFKWQPTRSEPVKDADPHFHHFLLSQTEAISVC*QAITKKLK

Parental  ICEEETGSTSIQAADSTAVNGSITPTDKKIGFLGLGLMGSGIVSNLLKMGHTVTVWNRTAEKCDLFIQEG
          ICEEETGSTSI..ADS.AVNGSIT..DKKIGF.GLGLM.SGIVSNLLKMGHTVTVW.RTA.K.DLFI.EG
Retrocopy ICEEETGSTSIRSADSMAVNGSIT--DKKIGFGGLGLMRSGIVSNLLKMGHTVTVWSRTAKKRDLFI*EG

Parental  ARLGRTPAEVVSTCDITFACVSDPKAAKDLVLGPSGVLQGIRPGKCYVDMSTVDADTVTELAQVIVSRGG
          A.LGRTPAEV.STCDITFA.V.DPK.AKDLVL.P.G.LQGIRPGKCYVD.STVDAD.VTELA.VI.SR.G
Retrocopy ACLGRTPAEVLSTCDITFAHVLDPKVAKDLVLVPIGMLQGIRPGKCYVDLSTVDADIVTELARVIASRSG

Parental  -RFLEAPVSGNQQLSNDGMLVILAAGDRGLYEDCSSCFQAMGKTSFFLGEVGNAAKMMLIVNMVQGSFMA
          .RF.EAP.SGNQQLSN.GMLVILAAGDRGLYEDCSSCFQAMGKTS.FLGEVGNAAKMMLIVN.VQGSFMA
Retrocopy DRFPEAPLSGNQQLSNHGMLVILAAGDRGLYEDCSSCFQAMGKTS-FLGEVGNAAKMMLIVNIVQGSFMA

Parental  TIAEGLTLAQVTGQSQQTLLDILNQGQLASIFLDQKCQNILQGNFKPDFYLKYIQKDLRLAIALGDAVNH
          TI.E.LTLA.VT..SQQTLLDILNQGQLASIFLDQK.QN.LQGNFKPDFYLKY.Q.DL.LAIALG..VNH
Retrocopy TITEVLTLA*VTDKSQQTLLDILNQGQLASIFLDQKRQNTLQGNFKPDFYLKYMQQDLCLAIALGNVVNH

Parental  PTPMAAAANEVYKRAKALDQSDNDMSAVYRAYIH
          .TPMAAAANEVYKRAKALDQ.DN.MS...RAYIH
Retrocopy LTPMAAAANEVYKRAKALDQTDN-MSTASRAYIH

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_240 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019912	1 retrocopy	retro_cjac_2514,
Erinaceus europaeus	ENSEEUG00000011783	1 retrocopy	retro_eeur_477,
Homo sapiens	ENSG00000140632	1 retrocopy	retro_hsap_2432,
Gorilla gorilla	ENSGGOG00000016258	1 retrocopy	retro_ggor_1512,
Macaca mulatta	ENSMMUG00000009567	1 retrocopy	retro_mmul_621,
Nomascus leucogenys	ENSNLEG00000009950	1 retrocopy	retro_nleu_240 ,
Oryctolagus cuniculus	ENSOCUG00000010486	1 retrocopy	retro_ocun_680,
Pongo abelii	ENSPPYG00000007072	1 retrocopy	retro_pabe_1791,
Pan troglodytes	ENSPTRG00000007730	1 retrocopy	retro_ptro_1404,