RetrogeneDB ID: retro_nleu_2476

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397359.1:495438..497415(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DSE
• Ensembl ID: ENSNLEG00000013106
• Aliases: None
• Description: None

Sequence

>retro_nleu_2476
ATGAAGACTCACACACAGGGGTTCTCCCAGTGTGTTTTTCATATATTTGCTTTGCGTTGTGTCAGCCTACATCACCGACA
AGAACCCAGAAGTCATGATTCCCTTCACCAATGCCAACTACGACAGCCACCCCATGCTGTACTTCAGGGCAGAGGTGGCA
GAGCTGCAGCTCAGGGTGGCCAGCTCGCAGGAGCACATTGCAGCCCGCCTCACGGAGGCTGTGCACATGATGCTGTGCGG
CCCCTTGGAATACCTCCCTCCCTGGGATCCCAAGGATTACAGTGCCCACTAGAATGAAATCTATGGAAACAACTTGGTTG
CCTTGGCAATGTTCTGTGTGCTGTATCCTGAGAACACTGAAGCCCGAGACATGGCCAAAGTCCACATGGAGAGGATGGCA
GTGCAGCCCAGTTGGTTGGTGAAAGATGCTCCTCGGGATGAGGTCCCGCATGCTCATTCCCTGGTTGGTTTTGCCACTGC
TTATGACTTCTTGAACAACTACCTGAGCAAGACACAACAGAAGTTTCTTGAAGTGATTGCCGGTGCCTCAGGGTATATGT
ATGAAACTTCATACAGGAGAGGACAGGAATTTTAATACCTGCACAATCATCAGCCCACCAACTGCATGGCTTGGCTCACA
GGAAGCCTAGTCCTGACGAATCAAGGATATCTTCAAGAAGCCTGCTTATGGACCAAACAAGTTCTGACCATCATGGAGAA
ATCTCTGGTCTTGCTCAGGGAGATGATGGATGGCTCCCTCTATGAAAGAGTTGTGTATGGCAGCTACACCACTAGATAAC
TCTTCCAATACATGTTTCTCATCCAGAGGCACTTCAACATCAACCGCGTTGGCCATCCGTGGCTTAAACAGCACTTTGCC
TTTATGGGTAGAACCATCCTGCCAGGGTTTTAAAGGACTGTGGCTATTGCGGACTCAAATTACAACTGGTTTTATGGTCC
AGAAAGCCAATTAGTGTTCCTTGATAAATTTGTCATGCGTAACAGCAATGGTAACTGGCTAGCTGACCAAATCAGAAGGA
ACTGTGTGGTGGAAGGTCCAGGAACACTGTCCAAAGGGCATCGCTGGTGCACTTTGCACACAGAATTTCTCTGGTATGAT
GCCAGCTTGAAATCAGTTCCTCCTCCAGACTGTGGCACCCCTACACTGCATCATTTTGAAGACCGGGTGTCGTGACTTAT
GGAAGTGCACTACCTGCTGAAATCAATAAATCTTTCCTCTCTTTCAAGTCTGGAAAACTGAGGGGACATGCAATATGTGA
CATTGTCCACAGAAACAAATACAAAGATTGGATCAAAGGGTGGAGAAACTGTAATGCAGGGCATGAACGTTATGATGAAA
ACTCACTTCCTTTTGCTCCCAGTTGTGTGCCTTTCATCACTGAGGCTCTGTACAGGCCAAAGTACACTTTCTTCAACAAT
GTTTTGATGTTTTCTGCAGCTGTGTCAAAGAGCTGCTTTTCTCCCTGGAAGGGTCAAGTCACAGAAGACTGTTCATCAAA
ATGGTCTAAATACCAGCATGACCTGGCAGCTAGCTGTCAAGGGAGAGTGGTTGCAGCAGAGGAGAAAAATGGGGTAGTTT
TCATCTGAGGAGAAGGTGTGGGAGCTTATAACCCCCAGCTCAGCCTAAAGAATGTTCAGAGGAATCTGATCCTCCTACAT
CCACAGCTGCTTCTCCTTGTAGACCAAATACACCTGGAAGAGGAGAGTTCCCTGGAGACAGCAGTGAGCTTCTTCCACAA
TGTGGATGTTCCTTTTGAGGAAACTGTTGTAGATGGTGTCCATGGGGCTTTCATCAGGTAGAGAGATGGTCTCTATATAA
AGTACTGATGGACAATACTGGCTACAGCAAGAAAGCAACATTTGCCTCAGTGACATATCCTGGGAGCTATCCCCTACAAC
GGGACAAACTATGTGAATGTCACCATGCACCTCCGAAGTCCCATCACCAGGCCAGCT

Alignment

ORF - retro_nleu_2476 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.37 %
• Parental protein coverage: 69. %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MRTHT-RGAPSVFFIYLLCFVSAYITDENPEVMIPFTNANYDSHPMLYFSRAEVAELQRRAASSHEHIAA
          M.THT.RG.PSVFFIYLLC.VSAYITD.NPEVMIPFTNANYDSHPMLYF.RAEVAELQ.R.ASS.EHIAA
Retrocopy MKTHT>RGSPSVFFIYLLCVVSAYITDKNPEVMIPFTNANYDSHPMLYF-RAEVAELQLRVASSQEHIAA

Parental  RLTEAVHTMLSSPLEYLPPWDPKDYSARWNEIYGNNLGALAMFCVLYPENIEARDMAKDYMERMAAQPSW
          RLTEAVH.ML..PLEYLPPWDPKDYSA..NEIYGNNL.ALAMFCVLYPEN.EARDMAK..MERMA.QPSW
Retrocopy RLTEAVHMMLCGPLEYLPPWDPKDYSAH*NEIYGNNLVALAMFCVLYPENTEARDMAKVHMERMAVQPSW

Parental  LVKDAPWDEVPLAHSLVGFATAYDFLYNYLSKTQQEKFLEVIANASEYMYETSYRRGWGFQYLHNHQPTN
          LVKDAP.DEVP.AHSLVGFATAYDFL.NYLSKTQQ.KFLEVIA.AS.YMYETSYRRG..F.YLHNHQPTN
Retrocopy LVKDAPRDEVPHAHSLVGFATAYDFLNNYLSKTQQ-KFLEVIAGASGYMYETSYRRGQEF*YLHNHQPTN

Parental  CMALLTGSLVLMNQGYLQEAYLWTKQVLTIMEKSLVLLREVTDGSLYEGVAYGSYTTRSLFQYMFLVQRH
          CMA.LTGSLVL.NQGYLQEA.LWTKQVLTIMEKSLVLLRE..DGSLYE.V.YGSYTTR.LFQYMFL.QRH
Retrocopy CMAWLTGSLVLTNQGYLQEACLWTKQVLTIMEKSLVLLREMMDGSLYERVVYGSYTTR*LFQYMFLIQRH

Parental  FNINHFGHPWLKQHFAFMYRTILPGFQRTVAIADSNYNWFYGPESQLVFLDKFVMRNGSGNWLADQIRRN
          FNIN..GHPWLKQHFAFM.RTILPGF.RTVAIADSNYNWFYGPESQLVFLDKFVMRN..GNWLADQIRRN
Retrocopy FNINRVGHPWLKQHFAFMGRTILPGF*RTVAIADSNYNWFYGPESQLVFLDKFVMRNSNGNWLADQIRRN

Parental  RVVEGPGTPSKGQRWCTLHTEFLWYDASLKSVPPPDFGTPTLHYFEDW-GVVTYGSSLPAEINRSFLSFK
          .VVEGPGT.SKG.RWCTLHTEFLWYDASLKSVPPPD.GTPTLH.FED..GVVTYGS.LPAEIN.SFLSFK
Retrocopy CVVEGPGTLSKGHRWCTLHTEFLWYDASLKSVPPPDCGTPTLHHFEDR<GVVTYGSALPAEINKSFLSFK

Parental  SGKLGGRAIYDIVHRNKYKDWIKGWRNFNAGHEHPDQNSFTFAPNGVPFITEALYGPKYTFFNNVLMFSP
          SGKL.G.AI.DIVHRNKYKDWIKGWRN.NAGHE..D.NS..FAP..VPFITEALY.PKYTFFNNVLMFS.
Retrocopy SGKLRGHAICDIVHRNKYKDWIKGWRNCNAGHERYDENSLPFAPSCVPFITEALYRPKYTFFNNVLMFSA

Parental  AVSKSCFSPWEGQVTEDCSSKWSKYKHDLAASCQGRVVAAEEKNGVVFIRGEGVGAYNPQLNLKNVQRNL
          AVSKSCFSPW.GQVTEDCSSKWSKY.HDLAASCQGRVVAAEEKNGVVFI.GEGVGAYNPQL.LKNVQRNL
Retrocopy AVSKSCFSPWKGQVTEDCSSKWSKYQHDLAASCQGRVVAAEEKNGVVFI*GEGVGAYNPQLSLKNVQRNL

Parental  ILLHPQLLLLVDQIHLGEESPLETAASFFHNVDVPFEETVVDGVHGAFMRQRDGLYKMY-WMDDTGYSEK
          ILLHPQLLLLVDQIHL.EES.LETA.SFFHNVDVPFEETVVDGVHGAF.R.RDGLY..Y..MD.TGYS.K
Retrocopy ILLHPQLLLLVDQIHLEEESSLETAVSFFHNVDVPFEETVVDGVHGAFIR*RDGLYIKY<LMDNTGYSKK

Parental  ATFASVTYPRGY-PYNGTNYVNVTMHLRSPITRAA
          ATFASVTYP..Y.PYNGTNYVNVTMHLRSPITR.A
Retrocopy ATFASVTYPGSY>PYNGTNYVNVTMHLRSPITRPA

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_2476 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 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013791	1 retrocopy	retro_acar_15,
Callithrix jacchus	ENSCJAG00000004530	1 retrocopy	retro_cjac_1174,
Homo sapiens	ENSG00000111817	1 retrocopy	retro_hsap_4178,
Gorilla gorilla	ENSGGOG00000026746	2 retrocopies	retro_ggor_1419, retro_ggor_2802,
Nomascus leucogenys	ENSNLEG00000013106	1 retrocopy	retro_nleu_2476 ,
Pongo abelii	ENSPPYG00000016948	2 retrocopies	retro_pabe_3418, retro_pabe_3517,
Pan troglodytes	ENSPTRG00000018529	1 retrocopy	retro_ptro_2833,
Sorex araneus	ENSSARG00000010799	1 retrocopy	retro_sara_560,
Takifugu rubripes	ENSTRUG00000006239	1 retrocopy	retro_trub_32,
Xenopus tropicalis	ENSXETG00000032776	1 retrocopy	retro_xtro_8,