RetrogeneDB ID: retro_nleu_2416

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397353.1:17130..17859(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM58A
• Ensembl ID: ENSNLEG00000013298
• Aliases: None
• Description: None

Sequence

>retro_nleu_2416
GGCGGTGGAGTGGGGCCCGCAGCGCGGGGCCCAGAAGGGCAGCAGGCGCCGGAAGCCAGGGTGTACTTCCGAGTGGCGAG
GTTCATCATGGAGGCAAGTGTCAAGCTAGGGATGCGCTCCGTTCCCATTGCCACTGCTTGCACCATTTACCATAAGTTCT
TCTGCGAGACCAGCCTGGACGCCTATGACCCTTACCTGATTGCCATGTCTTCCATTTACTTGGCTGGCGAAGTGGAAGAC
AAGCACCTGCGGACTCGTGACATCATCAGTGTGTCCAACAGGTACTTTAACCCAAGCGGTGAGCCCCTGGAATTGGACTC
CGCTTCTGGGAGCCCTGGGACAGCATTGTGCAGTGTGAGCTTCTCATGCTGAGAGTTCTGCGCTTCCAGGTCTCCTTCCA
GCATCCACACAAGTACCTGCTCCACTACCCGATTTCCCTCAAGAACTGGCTGAACGGCCACAGCTGGCAGCGGACCCCCT
TTGCCGTCACTGCCTGGGCCCTGCTGCAGGACAGATACCACGGGGGGACTGTGCCTCCGCTTCCAGGCCCAGCATATCGC
CGTGGCGGTGCTCTACCTGGCCCTGCGGGTCTACGGAGTTGAGGTGCCCGCCGAGGTGGAGGCTGAGAAGCCGTGGTGGC
AGGTGTTTGGTGACGACCTTACCAAGCCAATCATTGGTAATATTGTGTCTGATCGCATTCAGATTTATACTATGGACACA
GAGATCCCC

Alignment

ORF - retro_nleu_2416 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.39 %
• Parental protein coverage: 97.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GGGGGPAARCPEGQPAPEARVHFRVARFIMEAGVKLGMRSIPIATACTIYHKFFCETNLDAYDPYLIAMS
          GGG.GPAAR.PEGQ.APEARV.FRVARFIMEA.VKLGMRS.PIATACTIYHKFFCET.LDAYDPYLIAMS
Retrocopy GGGVGPAARGPEGQQAPEARVYFRVARFIMEASVKLGMRSVPIATACTIYHKFFCETSLDAYDPYLIAMS

Parental  SIYLAGKVEEQHLRTRDIINVSNRYFNPGGEPLELDS-RFWELRDSIVQCELLMLRVLRFQVSFQHPHKY
          SIYLAG.VE..HLRTRDII.VSNRYFNP.GEPLELDS.RFWE..DSIVQCELLMLRVLRFQVSFQHPHKY
Retrocopy SIYLAGEVEDKHLRTRDIISVSNRYFNPSGEPLELDS<RFWEPWDSIVQCELLMLRVLRFQVSFQHPHKY

Parental  LLHYLVSLKNWLNRHSWQRTPVAVTAWALLRDSYH-GGLCLRFQAQHIAVAVLYLALQVYGVEVPAEVEA
          LLHY..SLKNWLN.HSWQRTP.AVTAWALL.D.YH.GGLCLRFQAQHIAVAVLYLAL.VYGVEVPAEVEA
Retrocopy LLHYPISLKNWLNGHSWQRTPFAVTAWALLQDRYH>GGLCLRFQAQHIAVAVLYLALRVYGVEVPAEVEA

Parental  EKPWWQVFSDDLTKPIIDNIVSDLIQIYTMDTEIP
          EKPWWQVF.DDLTKPII.NIVSD.IQIYTMDTEIP
Retrocopy EKPWWQVFGDDLTKPIIGNIVSDRIQIYTMDTEIP

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_2416 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
Callithrix jacchus	ENSCJAG00000011407	1 retrocopy	retro_cjac_1814,
Dipodomys ordii	ENSDORG00000012846	1 retrocopy	retro_dord_420,
Gorilla gorilla	ENSGGOG00000027073	2 retrocopies	retro_ggor_2302, retro_ggor_911,
Macaca mulatta	ENSMMUG00000011480	1 retrocopy	retro_mmul_557,
Nomascus leucogenys	ENSNLEG00000013298	2 retrocopies	retro_nleu_1493, retro_nleu_2416 ,
Otolemur garnettii	ENSOGAG00000033279	1 retrocopy	retro_ogar_70,