RetrogeneDB ID: retro_nleu_2811

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397437.1:1313318..1313867(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VTCN1
• Ensembl ID: ENSNLEG00000005256
• Aliases: None
• Description: None

Sequence

>retro_nleu_2811
GGCCTGATGGCAGTGCTTGCTGATCAATTGATAGTTGGCAATGCCTCTCTGCAGCTGAAAAACATACAACTCACAGATGC
TGGTACCTACAAATGTTATATCATCACTTCTAAAGGCAAGGGGAATGCTAACCTTGAGTATAAAATGAGGCTTCAGCATG
CCAGAAGTGAAGTAGACTATAATGCCAGCTCAGAGACCTTGCAATGTGAGGCTCCCTGATGGTTCCCCGAGCCCACAGTG
GTCTGAAGAGCCCTAGTTGACCAGGGAGCCAAATTCTCAGAAGTCTCCAATACCACCTTTGAGCTGAACTCTGAGGATGT
GACCATGAAGGTTTTGTCTGTGCTCTACAATGTTACGATCAACAACACATACTCCTGTATGATTGAAAATGACATTGCCA
AAGCAACAGGGGATATCAAAGGACAGAATCTGAGATCAAAAGGCGGAGTCACCTACAGCTGCTGAACTCAAAGGCTTCTC
TGTGTGTCTCTTCTTTTTTTTGCCATCAGCTGGACACTTGTGCTTCTCGCCCCTTACCTGATGCTAAAA

Alignment

ORF - retro_nleu_2811 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.91 %
• Parental protein coverage: 65.25 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GRTAVFADQVIVGNASLRLKNVQLTDAGTYKCYIITSKGKGNAN-LEYKTGAFSMPEVN-VDYNASSETL
          G..AV.ADQ.IVGNASL.LKN.QLTDAGTYKCYIITSKGKGNAN.L..K.G.FSMPEV..VDYNASSETL
Retrocopy GLMAVLADQLIVGNASLQLKNIQLTDAGTYKCYIITSKGKGNAN>LSIK*G-FSMPEVK<VDYNASSETL

Parental  RCEAPRWFPQPTVVWASQVDQGANFSEVSNTSFELNSENVTMKVVSVLYNVTINNTYSCMIENDIAKATG
          .CEAP.WFP.PTVV....VDQGA.FSEVSNT.FELNSE.VTMKV.SVLYNVTINNTYSCMIENDIAKATG
Retrocopy QCEAP*WFPEPTVV*RALVDQGAKFSEVSNTTFELNSEDVTMKVLSVLYNVTINNTYSCMIENDIAKATG

Parental  DIK-VTESEIKRRSHLQLLNSKASLCVS-SFFAISWALLPLTPYLMLK
          DIK..TESEIKRRSHLQLLNSKASLCVS....AISW.L..L.PYLMLK
Retrocopy DIK<RTESEIKRRSHLQLLNSKASLCVS>XXXAISWTLVLLAPYLMLK

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_2811 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005097	1 retrocopy	retro_chof_1322,
Dasypus novemcinctus	ENSDNOG00000013317	1 retrocopy	retro_dnov_1181,
Homo sapiens	ENSG00000134258	1 retrocopy	retro_hsap_2420,
Gorilla gorilla	ENSGGOG00000025814	1 retrocopy	retro_ggor_1505,
Macaca mulatta	ENSMMUG00000016964	1 retrocopy	retro_mmul_611,
Nomascus leucogenys	ENSNLEG00000005256	1 retrocopy	retro_nleu_2811 ,
Pan troglodytes	ENSPTRG00000001164	1 retrocopy	retro_ptro_1394,