RetrogeneDB ID: retro_nleu_2131

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397330.1:7369099..7370177(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC86
• Ensembl ID: ENSNLEG00000013582
• Aliases: None
• Description: None

Sequence

>retro_nleu_2131
ATGGATACACTGCCAAGGCGCAGACGACGGCTGGAAGGCCTAGGGCCTGAATCCCCCGAGAGCCTCACCTCAGTTTCGCA
GGGGAGACGGGCCCTTGTGGAGTTCAAGTCGGACCCAGAAGGAACCAGGGAGCCCGGGTCTCCTCCGAGTGTGCAATAAG
CTGGCCTGGGGCCCCCGAAAGGACACTGGAGAGAAGCCCAGGATCACCCAGTCTTTGCAGCAGGGTGCAGGCTTGGAGTC
CCCCCAAGGGCGGCCAGAATCAGGCCCAGGGTCCCCCCAGCGTCAGCAAGACCTACACCTGGAGTCGCCTCAAAGACAAC
TGGAGTCCAGTCCTGAATCCGCACGATGTCAGCCGAAGCCAAGTGAGGAGGCACCCAAGTGTTCTCAGGGCCAGGGAGTA
CCTGGCCTCGGAGTTGGCCCAAAGTAAGGAGGAGCTGATCCCAGGGGGCCCCCCAGCATCAGCTACTGCCGGGCCCAGGA
TCACCAGAGCCTTAACCCCAGTCAGCAAGCTCCGGGTCTGGAGCCCTCTCAGCCACTACTGCAGCCGGCACTCGAGGCAC
CTGGCTTCCCCCGGGGTCAGCACGAGCAGAGCAAACCACCTCCAGCTGGGGAGACGGTGACAGACGGCTTCGGGGCAAAG
AAGCCAAAGGGTTCTTCATCCCAGGCCCCAGCGTCCAAGAAGCTGAAGGAGGAGCAGCTTCCTGTAATCCCGAAGGGGAA
GCCCAAATCGGGGCAAGTGTGGAAGGACAGCTCCAAGAAAAGATTCTCTCAGATGCTTCAGGACAAGCCCCTGCGTACAT
CGTGGCAGCGGAAGATGAAGCAGGAGAGGAAGCTGGCCGAGGACTTTGCCCGTCACCTGGAGGAGGAGTAGGAGAGGCGC
CGCCAGGAGAAGAAACAGCGTCGGGCCGAGAACCTGAAATGCCGCCTGGAGAATGAGCGGAAGGTGGAGATCGTCCAAGT
GATCCGAAACCCTGCCAAGCTCAAGCGGGCAAAGCAGCAGCAGCTGCGCTCCATTGAGAAGCGGGACACCCTGGCCCTGC
TGCAGAAGCAGCCGCCCTAGCGGCCGGCAGCCAAGATC

Alignment

ORF - retro_nleu_2131 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MDTPLRRSRRLGGLRPESPESLISVARARRTLVEFESNPEETREPGSPPSVQQAGLGSPERPPKTSPGSP
          MDT..RR.RRL.GL.PESPESL.SV...RR.LVEF.S.PE.TREPGSPPSVQ.AGLG.P..........P
Retrocopy MDTLPRRRRRLEGLGPESPESLTSVSQGRRALVEFKSDPEGTREPGSPPSVQ*AGLGPPKGHWREAQDHP

Parental  -RLQQGAGLESPQRQPEPGAGSPQRRQDLHLESPQRQPESSPESPRCQPKPSEEAPKCSQDQGV-LASEL
          ..LQQGAGLESPQ..PE.G.GSPQR.QDLHLESPQRQ.ESSPES.RCQPKPSEEAPKCSQ.QGV.LASEL
Retrocopy >SLQQGAGLESPQGRPESGPGSPQRQQDLHLESPQRQLESSPESARCQPKPSEEAPKCSQGQGV>LASEL

Parental  AQSKEEL-TSGVPQHQLPPGPTSPEP-YPGQQAPGPEPSQPLLELTPRAPGAPRGQHEPSKPPPAGETVT
          AQSKEEL...G.PQHQL.PGP.SPEP..P.QQAPG.EPSQPLL.....APG.PRGQHE.SKPPPAGETVT
Retrocopy AQSKEEL>SQGAPQHQLLPGPGSPEP>NPSQQAPGLEPSQPLLQPALEAPGFPRGQHEQSKPPPAGETVT

Parental  GGFGAKKRKGFSSQAPASKKLNKEELPVIPKGKPKSGRVWKDRSKKRFSQMLQDKPLHTSWQRKMKERQE
          .GFGAKK.KG.SSQAPASKKL..E.LPVIPKGKPKSG.VWKD.SKKRFSQMLQDKPL.TSWQRKMK..QE
Retrocopy DGFGAKKPKGSSSQAPASKKLKEEQLPVIPKGKPKSGQVWKDSSKKRFSQMLQDKPLRTSWQRKMK--QE

Parental  RKLAKDFARHLEEEKERRRQEKKQRRAENLKRRLENERKAEVVQVIRNPAKLKRAKKKQLRSIEKRDTLA
          RKLA.DFARHLEEE.ERRRQEKKQRRAENLK.RLENERK.E.VQVIRNPAKLKRAK..QLRSIEKRDTLA
Retrocopy RKLAEDFARHLEEE*ERRRQEKKQRRAENLKCRLENERKVEIVQVIRNPAKLKRAKQQQLRSIEKRDTLA

Parental  LLQKQPPQRPAAKI
          LLQKQPP.RPAAKI
Retrocopy LLQKQPP*RPAAKI

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_2131 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000110104	2 retrocopies	retro_hsap_3276, retro_hsap_3834,
Gorilla gorilla	ENSGGOG00000013670	1 retrocopy	retro_ggor_2582,
Macaca mulatta	ENSMMUG00000000019	1 retrocopy	retro_mmul_1622,
Nomascus leucogenys	ENSNLEG00000013582	1 retrocopy	retro_nleu_2131 ,
Pongo abelii	ENSPPYG00000003205	1 retrocopy	retro_pabe_2818,
Pan troglodytes	ENSPTRG00000003721	2 retrocopies	retro_ptro_2216, retro_ptro_2610,