RetrogeneDB ID: retro_nleu_312

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397263.1:22446406..22447116(+)
• Located in intron of: ENSNLEG00000006144

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDC
• Ensembl ID: ENSNLEG00000009404
• Aliases: None
• Description: None

Sequence

>retro_nleu_312
AAGTCAGAGATCCCAGGCCCCAGATCAAGGAGCTAACTGATGAAGAGGCAGAGAGTCTGCAGCTAGAGGCTGACCAGAAA
AAGGATGCAGAGAATCATGAGGCCCAGCTCAAGAATGTCAGCCTTGACTCCCCAGGGAAGTAGGAGACTGAGGAAGATGA
GGAGGAGGAAGATGAGAAGGACAAAGGAAAATTGAAGCCCAACTTAGGCAACAGGGCAGACCTGCCCAATTACCGCTGGA
CCAAGACCCTGTCGGAGCTGGACTTGGCGGTCCCTTTCCATGTGAACTTCCGGCTGAAACGGAAGGACGTGGTGGTGGAC
ATCCAGCGGCGGCACCTCAAGGTGGGGCTCAAGGGGCAGCCAGCGATCATCGATGGGGAGCTCTACAACGAAGTGAAGGT
GAAGAAGAGCTCATGGCTCATTGAGGACGGCAAGGTGGTGACTGTGCATCTGGAGAAAATCAATAATATGGAGTGGTAGA
GCCGCTTGGTGTCCAGTGACCCTGAGATCAATACCAAGAAGATTAACCCTGAGAATTCCAAGCTGTCAGACCTGGACAGT
GAGACTTGCAGCATGGTGGAAAAGATGATCTATGACCAGTGACAGAAGTCCATGGGGCTGCCAACCTCAGACGAACAGAA
GAAACAGGAGATTCTGAAGAAGTTCATGGATCAGCATCTGGAGATGGATTTTTCCAAGGCTAAATTCAAC

Alignment

ORF - retro_nleu_312 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.55 %
• Parental protein coverage: 71.39 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KSETSGP-QIKELTDEEAERLQLEIDQKKDAENHEAQLKNGSLDSPGKQETEEDEEEEDEKDKGKLKPNL
          KSE..GP.QIKELTDEEAE.LQLE.DQKKDAENHEAQLKN.SLDSPGK.ET...........KGKLKPNL
Retrocopy KSEIPGP<QIKELTDEEAESLQLEADQKKDAENHEAQLKNVSLDSPGK*ETXXXXXXXXXXXKGKLKPNL

Parental  GNGADLPNYRWTQTLSELDLAVPFRVNFRLKGKDVVVDIQRRHLRVGLKGQPAIIDGELYNEVKVEESSW
          GN.ADLPNYRWT.TLSELDLAVPF.VNFRLK.KDVVVDIQRRHL.VGLKGQPAIIDGELYNEVKV..SSW
Retrocopy GNRADLPNYRWTKTLSELDLAVPFHVNFRLKRKDVVVDIQRRHLKVGLKGQPAIIDGELYNEVKVKKSSW

Parental  LIEDGKVVTVHLEKINKMEWWSRLVSGDPEINTKKINPENSKLSDLDSETRSMVEKMMYDQRQKSMGLPT
          LIEDGKVVTVHLEKIN.MEW.SRLVS.DPEINTKKINPENSKLSDLDSET.SMVEKM.YDQ.QKSMGLPT
Retrocopy LIEDGKVVTVHLEKINNMEW*SRLVSSDPEINTKKINPENSKLSDLDSETCSMVEKMIYDQ*QKSMGLPT

Parental  SDEQKKQEILKKFMDQHPEMDFSKAKFN
          SDEQKKQEILKKFMDQH.EMDFSKAKFN
Retrocopy SDEQKKQEILKKFMDQHLEMDFSKAKFN

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_312 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 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000001291	1 retrocopy	retro_eeur_526,
Homo sapiens	ENSG00000090273	2 retrocopies	retro_hsap_2168, retro_hsap_2183,
Gorilla gorilla	ENSGGOG00000015314	2 retrocopies	retro_ggor_1720, retro_ggor_1730,
Microcebus murinus	ENSMICG00000015671	1 retrocopy	retro_mmur_457,
Mus musculus	ENSMUSG00000028851	1 retrocopy	retro_mmus_3181,
Nomascus leucogenys	ENSNLEG00000009404	2 retrocopies	retro_nleu_2545, retro_nleu_312 ,
Pongo abelii	ENSPPYG00000001673	2 retrocopies	retro_pabe_2055, retro_pabe_2064,
Pan troglodytes	ENSPTRG00000000395	2 retrocopies	retro_ptro_1655, retro_ptro_1661,
Pteropus vampyrus	ENSPVAG00000004408	1 retrocopy	retro_pvam_434,
Rattus norvegicus	ENSRNOG00000007399	2 retrocopies	retro_rnor_2009, retro_rnor_2108,