RetrogeneDB ID: retro_nleu_2170

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397333.1:8133058..8133957(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000002480
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RBM39
• Ensembl ID: ENSNLEG00000010350
• Aliases: None
• Description: None

Sequence

>retro_nleu_2170
GAAAAAAACCGAGCTGCAGCCATGGCAAACAATGTACAAAAGGGAAGTGCTGGACCTAAGAGGCTTTATGTGGACTCATT
ACAATTTTAACATAACTGAAGATACACTTCGTGGGATCTTTGAGCCTTTCGGAAGGATTAAAAGTATCCAGCTGATGATA
GACAGTGAAACTGGTCGATCCAAGGGATATGGATTTATTACATTTTCTGATTCAGAATGTGCCAAAAAGGCTTTGGAACA
ATTTAATGGATTTGAACTAGCAGGGAGGCCAATGAAAGTTGGTCATGTTACTGAACCATGCTGATGCTTCGAGTACTAGT
TCATTTTTGGACAGTGATGAACTGGAAAGGACTAGAATTGATTTGAGAACAACTGGTCGTCTTCAGTTAGTGGCAAGACT
TGCAGAGGATACAGGTTTGCAGATTCCACCAGCAGCACAGCAAGCTCTACAAATGAGTGGCTCTTTGGCATTTGGTGCTG
TGGCAGAATTTTCTTTTGTTATGGATTTGCAAACAAGACTTTCCCAGCAGACTGAAGCTTCAGCTTTAGCTGCAGCTGCT
TCTGTTCAGCCACTTGCAACACAGTGTTTCCAACTCTCTAACATGTTTAACCCTCAAACAGAAGAAGTTGGATGGGATAC
AGAGATTAAGGGCGATGTGATTGAAGAATGTAATAAACATGGAGGAGTTATTCATATTTATAATGACAAAAATTCAGCTC
AGGGCAATGTGTATGTGAAGTGCCCATCAATTGCTGCAGCTATGGCTGCTGTCAATGCATTGCATGGCAGGTGGTTTGCT
GGTAAAATGATAACAGCAGCATATGTACCTCTTCCAACTTACCACAACCTGTTTTCCGATTCTATGACAGCAACACAACT
ACTGGTTCCAAGTAGACGA

Alignment

ORF - retro_nleu_2170 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.38 %
• Parental protein coverage: 99.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EKNRAAAMANNLQKGSAGPMRLYVGSL-HFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFS
          EKNRAAAMANN.QKGSAGP.RLYV.SL..FNITED.LRGIFEPFGRI.SIQLM.DSETGRSKGYGFITFS
Retrocopy EKNRAAAMANNVQKGSAGPKRLYVDSL>NFNITEDTLRGIFEPFGRIKSIQLMIDSETGRSKGYGFITFS

Parental  DSECAKKALEQLNGFELAGRPMKVGHVTE-RTDASSASSFLDSDELERTGIDLGTTGRLQLMARLAEGTG
          DSECAKKALEQ.NGFELAGRPMKVGHVTE...DASS.SSFLDSDELERT.IDL.TTGRLQL.ARLAE.TG
Retrocopy DSECAKKALEQFNGFELAGRPMKVGHVTE>HADASSTSSFLDSDELERTRIDLRTTGRLQLVARLAEDTG

Parental  LQIPPAAQQALQMSGSLAFGAVAEFSFVIDLQTRLSQQTEASALAAAASVQPLATQCFQLSNMFNPQTEE
          LQIPPAAQQALQMSGSLAFGAVAEFSFV.DLQTRLSQQTEASALAAAASVQPLATQCFQLSNMFNPQTEE
Retrocopy LQIPPAAQQALQMSGSLAFGAVAEFSFVMDLQTRLSQQTEASALAAAASVQPLATQCFQLSNMFNPQTEE

Parental  EVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPL
          .VGWDTEIK.DVIEECNKHGGVIHIY.DKNSAQGNVYVKCPSIAAA.AAVNALHGRWFAGKMITAAYVPL
Retrocopy -VGWDTEIKGDVIEECNKHGGVIHIYNDKNSAQGNVYVKCPSIAAAMAAVNALHGRWFAGKMITAAYVPL

Parental  PTYHNLFPDSMTATQLLVPSRR
          PTYHNLF.DSMTATQLLVPSRR
Retrocopy PTYHNLFSDSMTATQLLVPSRR

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_2170 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000003950	1 retrocopy	retro_ggor_2902,
Myotis lucifugus	ENSMLUG00000003000	1 retrocopy	retro_mluc_1152,
Macaca mulatta	ENSMMUG00000031284	1 retrocopy	retro_mmul_2491,
Nomascus leucogenys	ENSNLEG00000010350	1 retrocopy	retro_nleu_2170 ,
Otolemur garnettii	ENSOGAG00000011227	1 retrocopy	retro_ogar_267,
Ochotona princeps	ENSOPRG00000002183	2 retrocopies	retro_opri_55, retro_opri_913,