RetrogeneDB ID: retro_nleu_1101

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397281.1:6196868..6198112(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NOLC1
• Ensembl ID: ENSNLEG00000015012
• Aliases: None
• Description: nucleolar and coiled-body phosphoprotein 1 [Source:HGNC Symbol;Acc:15608]

Sequence

>retro_nleu_1101
CCAGGTCCCTAAAGTTCAGTGCCCCCCTCCTGCTCCTCCATCAAAGAAGTCCTTGTGAACCCAGCCTCCCAAGAAAGCTA
TGGAGAAGAAACAGCCTTCCGAAAGCATTGAAGACAGCAGCAGTGAGTCTGACTGAAGTTTGGAGGAAGAGGATGAACTC
TTGCTAAGTCAGTCATCTCTAAAGCAAATACTAAACAACCTCCAGCAAAGAAAGCAGCAGAGAGCTCGCTCTTCAGACAT
CTCGTATTCCAACAGTTCCGAGGATGATGAAGCTCCTTCCAAGCTAGCCAGTACCAGCAAGAATTCCTCAAATAAGCCAG
CTGCCACTACCAAGTCACCTGCAGCGGAGCCAGCTGCAACTCTCAAGCAACCTGCAAGCAGTGGCCAGAAACCTCTGACG
AGAAAGGCTGACAGCAGTTCCAGTGAGAAAGAGAGCAGTTCCAGTGAGGAGGAGAAGACAAAGATGACTGTGGCCCCCCT
TAAGCCCAAGATAACTGACAAAGCAGCTCCATATCTGCCTGCCAAGCAGGCTCCTGAGGGTGGTAAGGACAGCAGCTCTC
ATTCAGACAGCTCCAGCAGTGAGGAGGAGGAGGAGGAAGAGAAGACATCTAAATCCCCAGTTAAGAAGAAGTTGCAGAAG
GCAGCAGGAGGGACAGCCCCTTCCAAGCCAGCCTCCACAAAGAAAGGAAAGGTCGAGAGCAGCAGCAATTCTTCCTCTGA
TGACTCCAGTGAGGAAGAGGAAGCAAAGCCCAAGGGCAAGGACTCTCCAAGACCACAAGTCCCCAAGGCCAATGGCACCT
CTGGACTGACTGCCCAGAATGGAAAAGCAGCTAAGAACAGTGAGGAGGAGGAAGAGGAGGAAGAAGAAAAGAAAAAGGCA
GCAGTGGTAGTTTCCAAGCTGGGTTCAGGAAAGAAGTGGAAGCAGCTGAGACTGCCAAAGAGGCAGAGACTCCTCCAGCC
GAGAAAATAAAGCTTCAGACCCCTAACACATTTCCAAAAAGGAAGAAAGAAGAAAAAAGGGCATGATCCACATTCTTAAG
GGTCAGGGAGGAGGAAATTGAGGTGGCAGACAACTCCACTGATGCCAACTGAGGTGCAGCCGGAGACTGGGGGAACAAGC
CAATGAGGTTTTGAGGTTCACCAAAGGCAAATCTTTCTGGCATGAGAAAACCAAGAAGAAGCAGGGCATCTCTTGGGGAG
GCTCAATCTCTGTCCAGGTCAATTCTATTAATTTTGACAGTGAG

Alignment

ORF - retro_nleu_1101 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.35 %
• Parental protein coverage: 59.06 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PGPYSSVP-PPSAPPPKKSLGTQPPKKAVEKQQPVESSEDSSDESDSSSEEEKK-PPTKAVISKATTKPP
          PGP.SSVP.PP.APP.KKSL.TQPPKKA.EK.QP.ES.EDSS.ESD.S.EEE......K.VISKA.TK.P
Retrocopy PGP*SSVP>PP-APPSKKSL*TQPPKKAMEKKQPSESIEDSSSESD*SLEEEDE<TLAKSVISKANTKQP

Parental  PA-KKAAES-SSDSSDSDSSEDDEAPSKPGGTTKNSSNKPAVTTKSPAAKPAAAPKQPVGGGQKLPTRKA
          PA.K.A..S.SSD.S.S.SSEDDEAPSK...T.KNSSNKPA.TTKSPAA.PAA..KQP...GQK..TRKA
Retrocopy PAKKAAESS>SSDISYSNSSEDDEAPSKLASTSKNSSNKPAATTKSPAAEPAATLKQPASSGQKPLTRKA

Parental  DSSSSEEESSSSEEDKTKKMVATTKPKATAKAAPPLPAKQAPQGSRDSSSDSDSSSSEEEEE--KTSKST
          DSSSSE.ESSSSEE.KTK..VA..KPK.T.KAAP.LPAKQAP.G..DSSS.SDSSSSEEEEE..KTSKS.
Retrocopy DSSSSEKESSSSEEEKTKMTVAPLKPKITDKAAPYLPAKQAPEGGKDSSSHSDSSSSEEEEEEEKTSKSP

Parental  VKKKPQKVAGGVAPSKPAFAKKGKAESSSSSSSDDSSEEEEEKPKGKGSPRPQAPKANGISALTAQNGKA
          VKKK.QK.AGG.APSKPA..KKGK.ESSS.SSSDDSSEEEE.KPKGK.SPRPQ.PKANG.S.LTAQNGKA
Retrocopy VKKKLQKAAGGTAPSKPASTKKGKVESSSNSSSDDSSEEEEAKPKGKDSPRPQVPKANGTSGLTAQNGKA

Parental  AKNSE--EEEEEKKKAA-VVVSKSGSLKKRKQ-NEAAKEAETPQAKKIKLQTPNTFPKRKKGEKRASSPF
          AKNSE........KK.A.VVVSK.GS.KK.KQ..E.AKEAETP.A.KIKLQTPNTFPKRKK.EKRA.S.F
Retrocopy AKNSEXXXXXXXEKKKAAVVVSKLGSGKKWKQ<AETAKEAETPPAEKIKLQTPNTFPKRKKEEKRA*STF

Parental  RRVREEEIEVDSRVADNSFDAKRGAAGDW-GERANQVLKFTKGKSFRHEKTKKKRGSYRGGSISVQVNSI
          .RVREEEIEV....ADNS.DA..GAAGDW.GE.AN.VL.FTKGKSF.HEKTKKK.G...GGSISVQVNSI
Retrocopy LRVREEEIEV----ADNSTDAN*GAAGDW<GEQANEVLRFTKGKSFWHEKTKKKQGISWGGSISVQVNSI

Parental  KFDSE
          .FDSE
Retrocopy NFDSE

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_1101 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010062	1 retrocopy	retro_cfam_1047,
Callithrix jacchus	ENSCJAG00000017832	2 retrocopies	retro_cjac_4136, retro_cjac_4187,
Homo sapiens	ENSG00000166197	1 retrocopy	retro_hsap_4781,
Nomascus leucogenys	ENSNLEG00000015012	1 retrocopy	retro_nleu_1101 ,
Pongo abelii	ENSPPYG00000002595	1 retrocopy	retro_pabe_3721,
Pan troglodytes	ENSPTRG00000023882	1 retrocopy	retro_ptro_3182,
Tursiops truncatus	ENSTTRG00000014974	1 retrocopy	retro_ttru_155,