RetrogeneDB ID: retro_nleu_2472

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397359.1:6008212..6009566(+)
• Located in intron of: ENSNLEG00000008897

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCF3
• Ensembl ID: ENSNLEG00000001742
• Aliases: None
• Description: None

Sequence

>retro_nleu_2472
GGGGCCTATTCCTCCTTTGGTAGAGACGCAGGCGTGCGCGGCCTGACTCAGGCTGGCTTCCTGCCGGGCGAGCTGGCCCT
CAGCAGCCCCGGACCCCTGTCCCCTTCGGGCATGAAGGGGGCCTCCCAGTACTACCCCTCCTACGCCAGCAGCTCCGCCG
GAGAGAGGCGGACAGCGGCCTGGACATGCAGCCCAGGAAGGTTGGGAAGGTCCCGTCTGGTCTTCCATCTTTGGCGTACC
TGCTCAGCTCAGGTGAGGACTACGGTAGGGATGCTGCCGCCTACCCATCCGCCAAGACCCCGCCTACCCGTCCGCCTATC
CTGCCCCCTTCTACATGGCAGATAGCAGCCTGCACCTCTAAGCCGACCTCTGGAGTTACCCGGGCCAGGCGGGCTTCGGC
CCCATGCTGGGCAGGGGCTCCCCCTCTGTCCCTCCCGCACGGCAGCGGCCCCGTGGGCAGTGGCGGAGGCAGCAGCACGT
TTGGTGGCCTGCACCAGCACGAGCGCATAGGCTACCAGCTGCACGGAGCAGAAGTGAACGGTGGGCTTCGGGCTGCATCC
ACCTTCTCCTTGGCCCCCGGAGCCGCGTATGGCAGCGTCTCCAGCCACATGCCTGTCAGCAGGGCCAACAGCCTCCTGGG
CTCCCGAGAGACCACAGCCAGCAGCTCCGGGGACGCCCTTGGGAAGGCCTGGCCTCAGTCTACTCCCCGGATCACTCAAG
CAATAACTTCTGGTCCAGCCCCTCCACCGCCGTGGGCTCCCCCCAGGGCCTGGGAGGGACGTCGCACTGGCCCGGAGTAG
GAGTCCCCGGTGCCTTATCACCCAGCTATGACGGGGGTCTCTACGGCCTGGAGAGTAAGATAGAAAACCACCTGAACGAG
GGCATCCACGTGCTCTGCAGCCACGCCGTGGGCACTGCTGGCAACGTGTACACGCTGCTGCCTGGCCACGGGGCGCTGGC
CTTGGGCTTCTCCGGCCCCATGCTGCTGGTGGGGGCAGCACGCAGGACTGGTTGGAGACGAACACCCTGAGGACGGCCCT
GCGGGCAGCGCCAGCCTCATGCACATCCATGTGGCCCTCTCCAGCTAGTCAGGCGCCCTCCCCGACCTCTCTTGGCCTCC
CGACTCCTACAGTGGGCTAGGGCGAGCAGGCCACTGGCGAAATCAAGCGGGAAGAGGAGGATGAGGAGAACACATCGGCA
GCTGACCACTCAAGAGGAGGAGGAGGAGCTGAAGGACCCCCGGGCCCGGACTAGCCCAGACGAGGACGAGGAGGAAGATG
ACCTTTTCTCCCCAGAGTAGAAGGCCGAGTGGGAGAAGGAGGTGGCCAATAACGCCAGGGAGCGGCTGCGGGTC

Alignment

ORF - retro_nleu_2472 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.46 %
• Parental protein coverage: 70.52 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  GAYASFGRDTGVGGLTQAGFLSGELALSSPGPLSPSGMKGASQYYPSYSSSS-RRRAADGSLDTQPKKVR
          GAY.SFGRD.GV.GLTQAGFL.GELALSSPGPLSPSGMKGASQYYPSY.SSS.RRR.AD..LD.QP.KV.
Retrocopy GAYSSFGRDAGVRGLTQAGFLPGELALSSPGPLSPSGMKGASQYYPSYASSS<RRREADSGLDMQPRKVG

Parental  KVPPGLPSSVYPPSSGEDYGRDAAAY-PSAKTPS--SAYPAPFYMADGSLHPSAELWSPTGQAGFG-PML
          KVP.GLPS..Y..SSGEDYGRDAAAY.P....P...SAYPAPFYMAD.SLH..A.LWS..GQAGFG.P..
Retrocopy KVPSGLPSLAYLLSSGEDYGRDAAAY<PIRQDPAYPSAYPAPFYMADSSLHL*ADLWSYPGQAGFG<PHA

Parental  G-AGSSPLPLPPGSGPVGSSGSSSTFGGLHQHERMGYQLHGAEVNGGLPAASSFSSAPGATYGGVSSHTP
          G.AG..PL.LP.GSGPVGS.G.SSTFGGLHQHER.GYQLHGAEVNGGL.AAS.FS.APGA.YG.VSSH.P
Retrocopy G<AGAPPLSLPHGSGPVGSGGGSSTFGGLHQHERIGYQLHGAEVNGGLRAASTFSLAPGAAYGSVSSHMP

Parental  PVSGADSLLGSRGTTAGSSGDALGKA-LASIYSPDHSSNNFSSSPSTPVGSPQGLAGTSQWPRAGAPGAL
          .VS.A.SLLGSR.TTA.SSGDALGKA.LAS.YSPDHSSNNF.SSPST.VGSPQGL.GTS.WP..G.PGAL
Retrocopy -VSRANSLLGSRETTASSSGDALGKA<LASVYSPDHSSNNFWSSPSTAVGSPQGLGGTSHWPGVGVPGAL

Parental  SPSYDGGLHGLQSKIEDHLDEAIHVLRSHAVGTAGDMHTLLPGHGALASAFTGPMSL-GGRHAGLVGGSH
          SPSYDGGL.GL.SKIE.HL.E.IHVL.SHAVGTAG...TLLPGHGALA..F.GPM.L..G.HAGLVG..H
Retrocopy SPSYDGGLYGLESKIENHLNEGIHVLCSHAVGTAGNVYTLLPGHGALALGFSGPMLL>WGQHAGLVGDEH

Parental  PEDGLAGSTSLMHNHAALPSQPGALPDLSRPPDSYSGLGRAG-ATAAAGEIKREEKEDEENTSAADHSEE
          PEDG.AGS.SLMH.H.AL.S..GALPDLS.PPDSYSGLGRAG...A......R........T......E.
Retrocopy PEDGPAGSASLMHIHVALSS*SGALPDLSWPPDSYSGLGRAG<PLAKSSGKRRMRRTHRQLTTQEEEEE-

Parental  EKKELKAPRARTSPDEDEDDLLPPEQKAEREKERRVANNARERLRV
          ..K...A........E..DDL..PE.KAE.EKE..VANNARERLRV
Retrocopy -LKDPRARTSPDEDEEE-DDLFSPE*KAEWEKE--VANNARERLRV

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_2472 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	ENSG00000071564	1 retrocopy	retro_hsap_4123,
Gorilla gorilla	ENSGGOG00000003667	1 retrocopy	retro_ggor_2770,
Macaca mulatta	ENSMMUG00000009017	1 retrocopy	retro_mmul_1194,
Nomascus leucogenys	ENSNLEG00000001742	1 retrocopy	retro_nleu_2472 ,