RetrogeneDB ID: retro_nleu_911

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397276.1:24995869..24997771(+)
• Located in intron of: ENSNLEG00000005523

Retrocopy information

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

Parental gene information

• Parental gene symbol: CENPC1
• Ensembl ID: ENSNLEG00000009058
• Aliases: None
• Description: None

Sequence

>retro_nleu_911
GTCAGTTCCACTAAAGAACCCTTTTCTTGCAGTTTTGTTGTAGAAACCAAGTGAAGCCACCAACAGATCAGTTCAAGGCC
CATGAAGTTCGTCAGAAAATTTCTGGCACTGATGTTGGTCGTCCAAAAATACACTGACTCGAAAAAAATGTCAAGTAGAA
ACATAAATGATCATCACAGTGAAGCTGATGAAGAATTTTACTTATCTGTTGGCTCACTTTCTGTTCTCTTGGATGCAAAA
ACATCTGTATTGCAAAATGTTATTCCATCTAGTGCCCAAAAGAGAGAGACTTACACTTTTGAAAATTCAGTAAATATGCT
GCCTTCAAGTACAGAGGTGTCACTTAAAACCAAAAAAAGGTTAAACTTTGAAGATAAAGTAAATTTAAGGAAAATAGAAA
TAGATAATAAAGTATCAGATGAAGAGGATAAAACATCAGAAGGACAAGAAAGAAAACCATCAGGATCATCTCAGAATAGA
ATACGAGATTCGGAATATGAAATTCAATGACAAGCTAAAAAAAGTTTTTCAACATTGTTTTTAGAAACAGTAAAATGAGA
AAGTGAATCCAGTCCCATTGTCAGGCATGGAGCAATAGCTCCACCTCATTCGTGTCCTCCCGATGATATGAAGTTGATAG
AGGATGAATTTATAATTGATGAGCCAGATCAAAGTTTTGCCAGTAGATCTTGGATTACTATACCAAGAAAGGCAGGGCCT
CTGAAACAAAGCACCATATCCCCAGCTGAGAGCACTGCACTCCTTCAAGATAGAAAGTCAAGAGAAAAGTATCATAATAT
ATTAGCTAAGACTTTGGCAAATGACAAACATTTCCATAAACCTCACCTAGTAGAGACATCTCAGCCCTCTGATAAAACAG
TACTGGATACAAGTTATGCTTTGACAGGTGAAACAGAAAATGACTGTAGATCTACAAAATATGAAATGTATTCCAAGAAT
GCAGAAAAATCATCTAGAAGCAAAAGGACTATAAAACAAAACCAGAGAAGAAAATTTATGGCTAAACCGGCTGACGAACA
GCTTGATGTGGGACAGTCTAAAGATGAAAACATACATACGTCACATATTACCTAAGACAAATTTCAAAGAAATTCAGACA
GAAATATGGAAGAGCGCGAAGAGATGGGAAATGATTGTGCCTCCAAAAAACAGATGCCACCTGTGGGAAGCAAGAAAAGT
AGCACTAGAAAAGATAAGGAAGAATCTAAAAAGCAGCACTTTTCCCGTGAGTCCAAGAACAAACTTGTACCTGAAGAAGT
GACTTCAACTGTCACAAGAAGTCGAAGAATTTCCAGGCATCCATCTAATTGGTGGGTGGTAAAATCAGAGGAGAGTCCTG
TTTATAGCAATTCGTCAATAAGAAATGCATTACCAGTGCATCACACCAGTAGGCAAAAATCTGCTAAGAAAACAAATCAG
TCATCTAAGAATATTGGGAAAAAAACTATTCCACTTAAAAGGCAGAAGACAGCAACTAAAGACAGCCAAAGAGTACAGAA
GTTTTTAAATGCTAAAGGTTCTGGAGGTATCATTGGTCATGATGAAATTTCCAGTTGTTCGCTGAGTGAGCCATTGGAAA
GTGATGAGGCAGACTTGGCTAAGAAGAAAAATCTGGATTGTTCTAGATCTACAGGAAGCTCAAAGAATGAAGATAATATT
ATTACTGCACAAAATGTTCCCCTAAAGCCTCAGACCAGTGGATATACATGTAATACACCAACAGAGTCAAACTTGGATTC
TGGAGAGCATAAGGCTTCAGTTTTAGAGCAAAGTGGACCTTCCAGGCTCAATAATAATTATTTAATGTCTGGAAAGAATA
ACAATGATGTGGATGATGAGGAAGTTCATGGAAGTTCAGATGACTCAAAACGATCTAAAGTG

Alignment

ORF - retro_nleu_911 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.58 %
• Parental protein coverage: 66.91 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VSSRKKEASLQFVVE-PSEATNRSVQ-AHEVHQ-KILATDVSSKNTPDSKKKSSRNTNDHHSKADEEFYL
          VSS.K...S..FVVE.PSEATNRSVQ.AHEV.Q.K.LA.........DSKK.SSRN.NDHHS.ADEEFYL
Retrocopy VSSTKEPFSCSFVVE>PSEATNRSVQ>AHEVRQ>KFLALMLVVQKYTDSKKMSSRNINDHHSEADEEFYL

Parental  SVGSPSVLLDAKTSASQNVIPSGAQKRETYTFENSVNILPSSTEVSVKTKKRLNFDDKVVLKKIEIDNKV
          SVGS.SVLLDAKTS..QNVIPS.AQKRETYTFENSVN.LPSSTEVS.KTKKRLNF.DKV.L.KIEIDNKV
Retrocopy SVGSLSVLLDAKTSVLQNVIPSSAQKRETYTFENSVNMLPSSTEVSLKTKKRLNFEDKVNLRKIEIDNKV

Parental  SDEEDKTSEGQERKPSGSSQNRIRDSEYEIQRQAKKSFSALFLETVKRKSESSPIVRHAATAPPHSCPPA
          SDEEDKTSEGQERKPSGSSQNRIRDSEYEIQ.QAKKSFS.LFLETVK..SESSPIVRH.A.APPHSCPP.
Retrocopy SDEEDKTSEGQERKPSGSSQNRIRDSEYEIQ*QAKKSFSTLFLETVK*ESESSPIVRHGAIAPPHSCPPD

Parental  DMKLVEDEFIIDESDQSFASRSWITIPRKAGPLKQRTISPAESTALLQGRKSREKHHNLLPKTLANDKHS
          DMKL.EDEFIIDE.DQSFASRSWITIPRKAGPLKQ.TISPAESTALLQ.RKSREK.HN.L.KTLANDKH.
Retrocopy DMKLIEDEFIIDEPDQSFASRSWITIPRKAGPLKQSTISPAESTALLQDRKSREKYHNILAKTLANDKHF

Parental  HKPHPVETSQPSDKTVLDTSYALTGETENNYRSTKYEMYSKNAEKPSRSKRTIKQKQRRKFMAKPAEEQL
          HKPH.VETSQPSDKTVLDTSYALTGETEN..RSTKYEMYSKNAEK.SRSKRTIKQ.QRRKFMAKPA.EQL
Retrocopy HKPHLVETSQPSDKTVLDTSYALTGETENDCRSTKYEMYSKNAEKSSRSKRTIKQNQRRKFMAKPADEQL

Parental  DVGQSKDENIHTSHITQDEFQRNSDRNMEEREEMGNDCVSKKQMPPVGSKKSSTRKDKEGSKKKRFSSES
          DVGQSKDENIHTSHIT.D.FQRNSDRNMEEREEMGNDC.SKKQMPPVGSKKSSTRKDKE.SKK..FS.ES
Retrocopy DVGQSKDENIHTSHIT*DKFQRNSDRNMEEREEMGNDCASKKQMPPVGSKKSSTRKDKEESKKQHFSRES

Parental  KNKLVPEEVTSTVTRSRRISRRPSDWWVVKSEESPVYSNSSIRNELPVHHNSRQKSAKKTNQSSKNIGKK
          KNKLVPEEVTSTVTRSRRISR.PS.WWVVKSEESPVYSNSSIRN.LPVHH.SRQKSAKKTNQSSKNIGKK
Retrocopy KNKLVPEEVTSTVTRSRRISRHPSNWWVVKSEESPVYSNSSIRNALPVHHTSRQKSAKKTNQSSKNIGKK

Parental  TIPLKRQKTATKGNQRVQKLLNAEGSGGTIGHDEISRRSLSEPLESDEADLAKKKNLDCSRSTGSSKNED
          TIPLKRQKTATK..QRVQK.LNA.GSGG.IGHDEIS..SLSEPLESDEADLAKKKNLDCSRSTGSSKNED
Retrocopy TIPLKRQKTATKDSQRVQKFLNAKGSGGIIGHDEISSCSLSEPLESDEADLAKKKNLDCSRSTGSSKNED

Parental  DIMTAQNVPLKPQTSGYTCNIPTESNLDSGEHKTSVLEESGPSRLNNNYLMSGK--NDVDDEEVHGSSDD
          .I.TAQNVPLKPQTSGYTCN.PTESNLDSGEHK.SVLE.SGPSRLNNNYLMSGK..NDVDDEEVHGSSDD
Retrocopy NIITAQNVPLKPQTSGYTCNTPTESNLDSGEHKASVLEQSGPSRLNNNYLMSGKNNNDVDDEEVHGSSDD

Parental  SKPSKV
          SK.SKV
Retrocopy SKRSKV

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_911 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	ENSG00000145241	1 retrocopy	retro_hsap_1038,
Mus musculus	ENSMUSG00000029253	1 retrocopy	retro_mmus_1910,
Nomascus leucogenys	ENSNLEG00000009058	1 retrocopy	retro_nleu_911 ,
Pongo abelii	ENSPPYG00000014736	1 retrocopy	retro_pabe_870,
Pan troglodytes	ENSPTRG00000016096	1 retrocopy	retro_ptro_708,