RetrogeneDB ID: retro_nleu_2491

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397361.1:5446693..5448445(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSNLEG00000026811
• Aliases: None
• Description: None

Sequence

>retro_nleu_2491
CAGCATGCTTACTCTGGCTTCTCCTCAGCTCACATGGGCAGTCACATTCCCCGCCCCAGCGCCAGGGTCATCACACTGTC
CAACCCCATGGCACCCTTGCCCTCCAGACGGACTGCACCCCGAAGTAAGTGGGGCAGTGTCCAGACCAGCGGGCGCAGCA
GTGGGCTTGGCACTGATATGGGCTCCTGGTTAGCTGGCAGAGACGTGCTGGCCCCACCCCAGGCAACAGGGCCCCCTCGC
CCACCCGGGCTTCCTGCGGCTGCAGCGAGCAGCCCTCTACATCCTCGGGAACAAAGCCCAGCTCAAAGGTATGCGGCCAG
ACCCCCTGCAGCAGTGGGAGCTGGTGCCCATTGAGGTATTCGAGGAACAGCAGGTGAAGGCCAACTTCAAGAAGCTGCTG
AAGGCATGTGTCCCAGGCTGCCCCGCTGCTGAGCCCAGCCCAGCCTCCTTCCTGCGCTCGCTGGAGGACTCGGAGCGGCT
GACCCCAATCCACAAGCTGCTGCAGGTGTCAGTGCTGGTGGTGGAGCCCCTGGATTCAGACTCCTCTGTGCCGGTGGGCC
TGGAGGATGGCTGGGACATCACCTCCCAGGTGGTATCTTTGGTGCAGCTGCTCTCAGACCCCTTCTACTGCACACTGGAG
GGCTTCCGCCTGCTAGTGGAGAAGAAGTGGTTGTCCTTCAGTCATCCCTTCAGCCACCGTGGAGCCCACACCCTGGCTGG
GCAGAGCATCGGCTTCACACCTGCCTTCCTGTAGTTCCTGGACTGCGTAACACCAGGTCCATCTGCAGTTCTCCGTGGAG
TTTGAGTTCAGCCAGTTCTACCTCAGGTTCCTCAGGTGCCACCATATGTCCCGCAGTTCCAGACCTTCCTACTTGACTCT
GACTCTGAGAGCATTGAGCTGGGGCTGCTATATGAGGAGAAAGGGGAACACAGGGGCTAGCTGCTGTGCAGGTCTTTGTG
GGAATATGTGGACCGGCTGAGCAAGAGGACACCCTCTACAATTACATGCATGTACCCGAGGACACAGAGCTCCTACAGCC
CTACAGCTACGTGTCCAATCTGAAGATGTGGGATTTCTACACTGAGGAGATGCTGGCCGAGAGCCATCCCTATGACTGGG
AACTGGCCCAGGGGCCCCCTGAGCCCCCAGAGGAAGAACGGTCTGACGGAGGCGCTCCCAGTACAGGTACCGCGTGGTGT
GGCCCTGCTACGACAGCTGCCCCTGACCCCAGCGTGATGCCATCTCACTCCTGCTGGAGGAGCTGCAGAGGCGGGAGACA
GAGCTGGGCTAATGCCCCCAGTGATGGAAGGACACCTGGGACCAGGTGAAGGCTGCACAGCGCCTGGAAGGCTGGCCAGA
CGGAAACGGCACCCCTAGCTCCCTTCTAGTGTCCACTGCCCCCCACCACCACCGTTTGCTGGGTGTGTGACTGCAGGAGG
GGCCCGTGCGCTCCACCGTGAGCCTTAGCCTGGACAGCGACCAGAGTAGTGGCTCAACAGCATCTGGCTCCTGCCAGGCT
GCCCGTCGCAGCACCAGCACCCTGTGCAGCCAGTTCCAGACAGCTGAGAGTGAGAACGGGTCCAACGAGGGCACTCTGTA
GAAGAAGGGGGTCTTCATGAAGGCTTGGAAGGCCCGCTGGTTCATGTTGGCCAAGACCAACACCAGCTGTGCTATTACAA
CCACCGTGTGGACACAAAGTGCAAGGGTGTCATCGACTGGTGGAGGTGGAGGCTGTGGCACCTGGCACGCCC

Alignment

ORF - retro_nleu_2491 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.27 %
• Parental protein coverage: 65.04 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  RNTLSGFSSAHMGSHVPSPRARVTTLSNPMAASASRRTAPRGKWGSVRTSGRSSGLGTDVGSRLAGRDAL
          ....SGFSSAHMGSH.P.P.ARV.TLSNPMA...SRRTAPR.KWGSV.TSGRSSGLGTD.GS.LAGRD.L
Retrocopy QHAYSGFSSAHMGSHIPRPSARVITLSNPMAPLPSRRTAPRSKWGSVQTSGRSSGLGTDMGSWLAGRDVL

Parental  APPQANGGP-PDPGFLRPQRAALYILGDKAQLKGVRPDPLQQWELVPIEVFEARQVKASFKKLLKACVPG
          APPQA.G.P...PGFLR.QRAALYILG.KAQLKG.RPDPLQQWELVPIEVFE..QVKA.FKKLLKACVPG
Retrocopy APPQATGPP>AHPGFLRLQRAALYILGNKAQLKGMRPDPLQQWELVPIEVFEEQQVKANFKKLLKACVPG

Parental  CPAAEPSPASFLRSLEDSEWLIQIHKLMQVSVLVVELLDSGSSVLVGLEDGWDITTQVISLVQLLSDPFY
          CPAAEPSPASFLRSLEDSE.L..IHKL.QVSVLVVE.LDS.SSV.VGLEDGWDIT.QV.SLVQLLSDPFY
Retrocopy CPAAEPSPASFLRSLEDSERLTPIHKLLQVSVLVVEPLDSDSSVPVGLEDGWDITSQVVSLVQLLSDPFY

Parental  RTLEGFRLLVEKEWLSFGHRFSHRGAHTLAGQSSGFTPVFLQFLDCV-HQVHLQFPMEFEFSQFYLKFLG
          .TLEGFRLLVEK.WLSF.H.FSHRGAHTLAGQS.GFTP.FL.FLDCV.HQVHLQF..EFEFSQFYL.FL.
Retrocopy CTLEGFRLLVEKKWLSFSHPFSHRGAHTLAGQSIGFTPAFL*FLDCV>HQVHLQFSVEFEFSQFYLRFLR

Parental  YHHVSR-RFRTFLLDSDYERIELGLLYEEKGERRGQLPCRSVWEYVDRLSKKTPVFYNYVYAPEDAEVLR
          .HH.SR..F.TFLLDSD.E.IELGLLYEEKGE.RG.L.CRS.WEYVDRLSK.TP......Y.P.......
Retrocopy CHHMSR<QFQTFLLDSDSESIELGLLYEEKGEHRG*LLCRSLWEYVDRLSKRTPSTITCMY-PRTQSSYS

Parental  P-YSNVSNLKVWDFYTEETLAEGPPYDWELAQGPPEPPEEERSDGGAP-QSRRRVVWPCYDSCPRAQPDA
          P.YS.VSNLK.WDFYTEE.LAE..PYDWELAQGPPEPPEEERSDGGAP.Q.R.RVVWPCYDSCP..Q.DA
Retrocopy P<YSYVSNLKMWDFYTEEMLAESHPYDWELAQGPPEPPEEERSDGGAP<QYRYRVVWPCYDSCP*PQRDA

Parental  ISRLLEELQRLETELGRPPERWKDTWDRVKAAQRLEGRPDGRGTPSSLLVSTAPHHRRSLGVYLQEGPVG
          IS.LLEELQR.ETELG..P..WKDTWD.VKAAQRLEG.PDG.GTPSSLLVSTAPHH.R.LGV.LQEGPV.
Retrocopy ISLLLEELQRRETELG*CPQ*WKDTWDQVKAAQRLEGWPDGNGTPSSLLVSTAPHHHRLLGV*LQEGPVR

Parental  STLSLSLDSDQSSGSTASGSRQAARRSTSTLYSQFQTAESENRSYEGTLYKKGAFMKPWKARWFVLDKT-
          ST.SLSLDSDQSSGSTASGS.QAARRSTSTL.SQFQTAESEN.S.EGTL.KKG.FMK.WKARWF.L.KT.
Retrocopy STVSLSLDSDQSSGSTASGSCQAARRSTSTLCSQFQTAESENGSNEGTL*KKGVFMKAWKARWFMLAKT<

Parental  KHQLRYYDHRVDTECKGVID-LAEVEAVAPGAP
          .HQL.YY.HRVDT.CKGVID.L.EVEAVAPG.P
Retrocopy QHQLCYYNHRVDTKCKGVID<LVEVEAVAPGTP

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_2491 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000007138	1 retrocopy	retro_nleu_2239,
Nomascus leucogenys	ENSNLEG00000026811	2 retrocopies	retro_nleu_2491 , retro_nleu_557,