RetrogeneDB ID: retro_nleu_1493

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397296.1:20163373..20164117(+)
• 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_1493
ATGGAGGGCCGGGAGGACGGCGGAGGGAGCCCTGCAGCGCGAGTCCACGAGGGTCCGTCGGCACCGGAAGCCAGGGTGCA
CTTTCGCGTGGCGATGTTCATTATGGAGGTAGGTGTCAAGCTAGGGATGCGGTCCATTCCCATTGCCACTGCTTGCACCA
TTTACCGTAAGTTCTTCTGCGAGACCAACCTGGACGCCTATGACCCTTACCTGATTGCCATGTCTTCCATTTACTTGGCG
GGCAAAGTGGAAGAGCAGCACCTGCGGGCTCGTGACATCATCAATGTGTCCAACAGGTACTTCAACCCAAGCAGTGGGCC
CCTGGAATTGGACTCCCGCTTCTGGGAGCTCCAGGACAGCATTGTGCAGTGTGAGCTTCTCATGCTGAGAGTTCTGCGCT
TCCAGGTCTCCTTCCAGCATCCACACAAGTACCTGCTCCACTACTTGGTTTCCCTCAAGAACTGGCTGAACCGCAACGGC
TGGCAGCGGACCCCAGTTGCCGTCACTGCCTGGGCCCTGCTGTGGGACAGCTACCACGGGGGACTGTGCCTCCGCTTCCA
GGCCCAGCACATCGCCGTGGCGGTGCTCTCCCTGGCCCTGCAGGTCTACGGAGTCGAGGTGCCCGCCAAGGTCGAGGCTG
AGAGGCCGTGGTGGCAGGTGTTTAGTGACGACCTTACCAAGCCAATCATTGATAATATTGTGTCTGATCTCATTCAGATT
TATACCATAGACACAGAGATCCCC

Alignment

ORF - retro_nleu_1493 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.73 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEAPEGGGGGPAARCPEGQPAPEARVHFRVARFIMEAGVKLGMRSIPIATACTIYHKFFCETNLDAYDPY
          ME..E.GGG.PAAR..EG..APEARVHFRVA.FIME.GVKLGMRSIPIATACTIY.KFFCETNLDAYDPY
Retrocopy MEGREDGGGSPAARVHEGPSAPEARVHFRVAMFIMEVGVKLGMRSIPIATACTIYRKFFCETNLDAYDPY

Parental  LIAMSSIYLAGKVEEQHLRTRDIINVSNRYFNPGGEPLELDSRFWELRDSIVQCELLMLRVLRFQVSFQH
          LIAMSSIYLAGKVEEQHLR.RDIINVSNRYFNP...PLELDSRFWEL.DSIVQCELLMLRVLRFQVSFQH
Retrocopy LIAMSSIYLAGKVEEQHLRARDIINVSNRYFNPSSGPLELDSRFWELQDSIVQCELLMLRVLRFQVSFQH

Parental  PHKYLLHYLVSLKNWLNRHSWQRTPVAVTAWALLRDSYHGGLCLRFQAQHIAVAVLYLALQVYGVEVPAE
          PHKYLLHYLVSLKNWLNR..WQRTPVAVTAWALL.DSYHGGLCLRFQAQHIAVAVL.LALQVYGVEVPA.
Retrocopy PHKYLLHYLVSLKNWLNRNGWQRTPVAVTAWALLWDSYHGGLCLRFQAQHIAVAVLSLALQVYGVEVPAK

Parental  VEAEKPWWQVFSDDLTKPIIDNIVSDLIQIYTMDTEIP
          VEAE.PWWQVFSDDLTKPIIDNIVSDLIQIYT.DTEIP
Retrocopy VEAERPWWQVFSDDLTKPIIDNIVSDLIQIYTIDTEIP

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_1493 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,