RetrogeneDB ID: retro_ggor_2302

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 5:157305210..157305852(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000027327
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAM58A
• Ensembl ID: ENSGGOG00000027073
• Aliases: None
• Description: None

Sequence

>retro_ggor_2302
ATGGAGGCAGGTGTCAAGCTAGGGATGAGGTCCATTCCCATTGCCACTGCTTGCACCATTTACCATAAGTTCTTTTGCGA
TACCAACCTGGACGCTTATGACCCTTACCTGATTGCCGTGTCTTCCATTTACTTGGCCGGCAAAGCGGAAAAGCAGCACC
TGCGGACTCATGACATCATCAATGTGTCCAACAGGTACTTTAACCCGAGCGGTGAGCCCCTGGAATTGGACTCCCGCTTC
TGGGAGCTCCGGGACAGCATTGTGCAGTGTGAGCTTCTCATGCTGAGAGTTCTGCGCTTCCAGGTCTCCTTCCAGCATCC
ACACAAGTACCTGCTCCACTACCTGGTTTCCCTCAAAAACTGTCTGAACCGCCACAGCTGGCAGCGGACCCCGGTTGCCG
TCACTCCCTGGGCCCTGCTGCGGGACAGCTACCACGGGGGTCTGTGCCTCCGTTTCCAGGCCCAGCACATCGCGGTGGCG
GTGCTCTACCTGGCCCTGCAGGTCTACGGAGTTGAGGTGCCCGCCGAAGTTAAGGCTGAGAAGCCGTGGTGGCAGGTGTT
TGGTGACGACCTTACCAAGCCAATCATTGATAATATTGTGTCTGATCTCATTCAGATTTATACCATGGACACAGAGATCC
CC

Alignment

ORF - retro_ggor_2302 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.46 %
• Parental protein coverage: 99.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSAGVKLGMRSIPIATACTIYHKFFCETNLDAYDPYLIAMSSIYLAGKVEEQHLRTRDIINVSNRYFNPS
          ..AGVKLGMRSIPIATACTIYHKFFC.TNLDAYDPYLIA.SSIYLAGK.E.QHLRT.DIINVSNRYFNPS
Retrocopy MEAGVKLGMRSIPIATACTIYHKFFCDTNLDAYDPYLIAVSSIYLAGKAEKQHLRTHDIINVSNRYFNPS

Parental  GEPLELDSHFWELRDSIVQCELLMLRVLRFQVSFQHPHKYLLHYLVSLKNWLNRHSWQRTPVAVTAWALL
          GEPLELDS.FWELRDSIVQCELLMLRVLRFQVSFQHPHKYLLHYLVSLKN.LNRHSWQRTPVAVT.WALL
Retrocopy GEPLELDSRFWELRDSIVQCELLMLRVLRFQVSFQHPHKYLLHYLVSLKNCLNRHSWQRTPVAVTPWALL

Parental  RDSYHGALCLRFQAQHIAVAVLYLALQVYGVEVPAEVEAEKAWWQVFNDDLTKPIIDNIVSDLIQIYTMD
          RDSYHG.LCLRFQAQHIAVAVLYLALQVYGVEVPAEV.AEK.WWQVF.DDLTKPIIDNIVSDLIQIYTMD
Retrocopy RDSYHGGLCLRFQAQHIAVAVLYLALQVYGVEVPAEVKAEKPWWQVFGDDLTKPIIDNIVSDLIQIYTMD

Parental  TEIP
          TEIP
Retrocopy TEIP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.67 RPM	23.98 RPM
SRP007412_cerebellum	0.47 RPM	14.97 RPM
SRP007412_heart	0.19 RPM	12.51 RPM
SRP007412_kidney	0.53 RPM	13.41 RPM
SRP007412_liver	0.08 RPM	7.04 RPM
SRP007412_testis	1.04 RPM	4.97 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2302 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2302 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3403

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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,