RetrogeneDB ID: retro_nleu_1538

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397298.1:2107970..2108453(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNPC3
• Ensembl ID: ENSNLEG00000015566
• Aliases: None
• Description: RNA-binding region (RNP1, RRM) containing 3 [Source:HGNC Symbol;Acc:18666]

Sequence

>retro_nleu_1538
GATGCATCCAACATAGGATTTGCAAGAATCTTTCCCAAAGCTAATTTGAACATCACAGAAGAGATTAAAGAAGACTCTGA
TGAAATGTCATCAGAATGTATTTCTAGAAGGGAATTAGAAAAGGACAGAATTTCTAGAGAAGAAATGGAAACACTTTCAG
TTTTCATAAGTTATGAACCTGGTGAACCAAACTGTAGAATTTATGTAAAGAATTTAGCTAAACATGTTCAAGAAAAGGAC
CTTAAATATATTTTTGGAAGATATGTTGACTTTTCATCAGAAACACAGTGGATCATGTTTGATATACGTTTGACGAAACG
TCGTATGAAAGGATAAGCTTTCATTGGACTTCCTAACGTAAAAGCAGCAGCAAAAGCCTTAAAGGAAGCTAATGGATATG
TGCTTTTTGGAAAATGCATGGTGGTTCAATTTGCTCGATCTGCTAGACCAAAACAAGATCCTAAGGAAGGAAAAAGACAG
TGT

Alignment

ORF - retro_nleu_1538 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.74 %
• Parental protein coverage: 61.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DASNIGFGKIFPKPNLDITEEIKEDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVK
          DASNIGF..IFPK.NL.ITEEIKEDSDEM.SECISRRELEK.RISREEMETLSVF.SYEPGEPNCRIYVK
Retrocopy DASNIGFARIFPKANLNITEEIKEDSDEMSSECISRRELEKDRISREEMETLSVFISYEPGEPNCRIYVK

Parental  NLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP
          NLAKHVQEKDLKYIFGRYVDFSSETQ.IMFDIRL.K..RMKG.AFIGLPN.KAAAKALKEANGYVLFGK.
Retrocopy NLAKHVQEKDLKYIFGRYVDFSSETQWIMFDIRLTKR-RMKG*AFIGLPNVKAAAKALKEANGYVLFGKC

Parental  MVVQFARSARPKQDPKEGKRKC
          MVVQFARSARPKQDPKEGKR.C
Retrocopy MVVQFARSARPKQDPKEGKRQC

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_1538 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
Callithrix jacchus	ENSCJAG00000035686	1 retrocopy	retro_cjac_1397,
Homo sapiens	ENSG00000185946	1 retrocopy	retro_hsap_2800,
Macaca mulatta	ENSMMUG00000018039	1 retrocopy	retro_mmul_1435,
Nomascus leucogenys	ENSNLEG00000012013	1 retrocopy	retro_nleu_1539,
Nomascus leucogenys	ENSNLEG00000015566	1 retrocopy	retro_nleu_1538 ,
Pongo abelii	ENSPPYG00000001102	1 retrocopy	retro_pabe_2224,
Pan troglodytes	ENSPTRG00000033902	1 retrocopy	retro_ptro_1897,