RetrogeneDB ID: retro_nleu_391

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397264.1:18216868..18218308(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DOK1
• Ensembl ID: ENSNLEG00000001010
• Aliases: None
• Description: None

Sequence

>retro_nleu_391
ATGGACAGAGCTGTGATGGAAGGGCCACTCTTTTCGCAGAGTCAGCACTTTGGGACCAAGAGGTGGAGGAAGACCTGGGC
TGTGCTCTACCCGGCCAGTCCCCATGGTGTAGCGCGGCTCGAGTTCTTTGACCATGAGGGGTCGAGCTCTGGGAGTGGCC
GAGGGAGCTCGTGCCGTCTGGACTGCAAGGTGATCCATCTGGCGAAGTGTATGAGTTTGGCCCCCGTGGCCGTGGAGAGC
CTCCCTGAGCCCAGCACCACTGCCTTCCACCTGGACACTGCACAGCACTAGCACCTGCTGGCTGTTGATGTGCCGTCCAG
TGCAGCCTGGTTGCAGACGCTGTGCCAAAACCCCTTTCGGAAAGGCAGCTGGACTCTGGAACCTACCAATAACCCACCTG
AGCTTTCTGCCCTAGAGATGCTGGAGAACTCCTTGTGCAGCCCCACCTGGGAAGGACCCCAGTTCTGGGTAACGGTGCAG
AGGACTGAGGCAGTCGAGCACTGTGGCCTGCATGCTTCCTATGTGCTGAGGGTGGAGGCTGAAAGGCTGACTCTCCTGAC
CATGGGAGCCCAGACTCAGGTACTGGAGCTGCTCCTGTCCTGGCCCTACACTCTGTTGCATCGCTATGGCCGGGACAAGG
TCATGTCCTCTTTTGAGGCCAGCGCCGTTGCCTCTTGGGCCCTGGAACCTTCACTTTCCAGACGGCACAGGGAAATGACA
TCTTCCAGGCAGGTGAGACTGCCATCCACCGGCAGAAGGCCCAGGGAAAGGCCAGACAGGGGCACAATGTTCTCAGAGCT
GATTCCTCTGAAAGGAAGGTGGCAGAGGGGAAGCTATCTTCCCCACCTGGCCCCAAGAGCTCCTTGACAGCCCCCCAGCC
CTGTATGCTGAGCCCTTAGGCTCCCTGCACATTGCTTCAGGCCCATCCCAGGGCTCCCTATACTCAGACCTCTTGGACAG
CACCCTTTCTCGGGCAGGAAAGGGAGTACAATGGAAGAAACCTCTCTGTTGGGACTTGTATGAGCATGAGCAGCAGCAGT
TGCTGAAGGCTAAGCTGACGGACCCCAAAAAGGATCCCATCTATGATGAACCCGAGGCCCTGGCCCCAGCCCTTCCCCAG
GGCCTTTATGATCTGCCTTAGGAGCCCAAAGATGCGTGGGATGTCAAGCTCAGGTAAAGTAGGAGGGCTACAAGCTCCCC
TACAACCCTGCCACTGATGACTATGCTGTGCCACCTACCCAGAGAACAAAGACCCTCCCTGCTTCCAAGTCCCAGGGCCC
AGCCTTCCCTGAACCTAGTACTGCAACTGGCAGGAGCAGCAAAAGCCACAACTCAGCCCTGTACAGCCAGGTCCAGAAAA
GTGGGGCCTCAGGGAGCTGGGACTGTGTGCTTTCTACAGCAGGGACTGACAGGACTGGGGTCAAGTCAAAGGTCTCTACC

Alignment

ORF - retro_nleu_391 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.96 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MDGAVMEGPLFLQSQRFGTKRWRKTWAVLYPASPHGVARLEFFDHKGSSSGGGRGSSRRLDCKVIRLAEC
          MD.AVMEGPLF.QSQ.FGTKRWRKTWAVLYPASPHGVARLEFFDH.GSSSG.GRGSS.RLDCKVI.LA.C
Retrocopy MDRAVMEGPLFSQSQHFGTKRWRKTWAVLYPASPHGVARLEFFDHEGSSSGSGRGSSCRLDCKVIHLAKC

Parental  VSVAPVTVETPPEPGATAFRLDTAQRSHLLAADAPSSAAWVQTLCRNAFPKGSWTLAPTDNPPKLSALEM
          .S.APV.VE..PEP..TAF.LDTAQ..HLLA.D.PSSAAW.QTLC.N.F.KGSWTL.PT.NPP.LSALEM
Retrocopy MSLAPVAVESLPEPSTTAFHLDTAQH*HLLAVDVPSSAAWLQTLCQNPFRKGSWTLEPTNNPPELSALEM

Parental  LENSLYSPTWEGSQFWVTMQRTEAAERCGLHGSYVLRVEAERLTLLTVGAQSQILEPLLTWPYTLLRRYG
          LENSL.SPTWEG.QFWVT.QRTEA.E.CGLH.SYVLRVEAERLTLLT.GAQ.Q.LE.LL.WPYTLL.RYG
Retrocopy LENSLCSPTWEGPQFWVTVQRTEAVEHCGLHASYVLRVEAERLTLLTMGAQTQVLELLLSWPYTLLHRYG

Parental  RDKVMFSFEAG-RRCPSGPGTFTFQTAQGNDIFQAVETAIHRQKAQGKAGQGHDVLRADSHEGEVAEGKL
          RDKVM.SFEA..RRC..GPGTFTFQTAQGNDIFQA.ETAIHRQKAQGKA.QGH.VLRADS.E..VAEGKL
Retrocopy RDKVMSSFEAS<RRCLLGPGTFTFQTAQGNDIFQAGETAIHRQKAQGKARQGHNVLRADSSERKVAEGKL

Parental  PSLPG-PQELLDSPPALYAEPLDSLRIAPCPFQDSLYSDPLDSTPARAGEGVQRQKPLYWDLYEHAQQQL
          .S.PG.PQELLDSPPALYAEPL.SL.IA..P.Q.SLYSD.LDST..RAG.GVQ..KPL.WDLYEH.QQQL
Retrocopy SSPPG<PQELLDSPPALYAEPLGSLHIASGPSQGSLYSDLLDSTLSRAGKGVQWKKPLCWDLYEHEQQQL

Parental  LKAKLTDPKEDPVYDEPEGLAPVPPQGLYDLPREPKDAW-WCQARVKEEGYELPYNPATDDYAVPPPRST
          LKAKLTDPK.DP.YDEPE.LAP..PQGLYDLP.EPKDAW..CQA.VK.EGY.LPYNPATDDYAVPP...T
Retrocopy LKAKLTDPKKDPIYDEPEALAPALPQGLYDLP*EPKDAW<GCQAQVK*EGYKLPYNPATDDYAVPPTQRT

Parental  KPLPAPKPQGPAFPEPGTATGSGIKSHNSALYSQVQKSGTSGSWDCGLSRVGTDKTRGKSEGST
          K.LPA.K.QGPAFPEP.TATG...KSHNSALYSQVQKSG.SGSWDC.LS..GTD.T..KS..ST
Retrocopy KTLPASKSQGPAFPEPSTATGRSSKSHNSALYSQVQKSGASGSWDCVLSTAGTDRTGVKSKVST

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_391 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000115325	1 retrocopy	retro_hsap_891,
Macaca mulatta	ENSMMUG00000002139	1 retrocopy	retro_mmul_1103,
Nomascus leucogenys	ENSNLEG00000001010	1 retrocopy	retro_nleu_391 ,
Pongo abelii	ENSPPYG00000012264	1 retrocopy	retro_pabe_767,
Pan troglodytes	ENSPTRG00000012100	1 retrocopy	retro_ptro_615,