RetrogeneDB ID: retro_ggor_911

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 13:952336..952912(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000027000
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_ggor_911
ATGGAGGCAAGTGTCAAGCTAGGGATGCGGTCCATTCCCATTGCCACTGCTTGCACCATTTACCGTAAGTTCTTCTGCGA
GACCAGCCTGGACGCCTGTGACCCTTACCTGATTGCCATGTTTTCCATTTACTTGGCCGGCAAAGTGGAAGAGCAGCACC
TGCAGACTCGTGACATCATCAATGTGTCCAACAAGTACTTTAACCCAAGCGGTGAGCCCCTGGAATTGGACTCCCGCTTC
CGGGAGCTCCGGGACAGCATTGTGCAGTGTCAGCTTCTCATGCTGAGAGTTCTGCGCTTCCAGGTCTCCTTCCAGCATCC
ACACAAGTACCTGCTCCACTACCTGGTTTCCCTCAAGAACTGGCTGAACCGCCACAGCTGGCAGCGGACCCCCGTTGCCG
TCACTGCCTGGGCCCTGCTGCGGGACAGCTACCACAGGGGTCTGTGCCTCCGCTTCCAGGACCAGCACATCGCCGTGGCG
GTGCTCTACCTGGCCCTGCAGGTCTACGGAGTTGAGGTGCCCGCTGAGGTCGAGGCTGAGAAGCCGTGGTGGCAGGTGTT
TGGTGACGACATTACC

Alignment

ORF - retro_ggor_911 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.62 %
• Parental protein coverage: 89.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSAGVKLGMRSIPIATACTIYHKFFCETNLDAYDPYLIAMSSIYLAGKVEEQHLRTRDIINVSNRYFNPS
          ..A.VKLGMRSIPIATACTIY.KFFCET.LDA.DPYLIAM.SIYLAGKVEEQHL.TRDIINVSN.YFNPS
Retrocopy MEASVKLGMRSIPIATACTIYRKFFCETSLDACDPYLIAMFSIYLAGKVEEQHLQTRDIINVSNKYFNPS

Parental  GEPLELDSHFWELRDSIVQCELLMLRVLRFQVSFQHPHKYLLHYLVSLKNWLNRHSWQRTPVAVTAWALL
          GEPLELDS.F.ELRDSIVQC.LLMLRVLRFQVSFQHPHKYLLHYLVSLKNWLNRHSWQRTPVAVTAWALL
Retrocopy GEPLELDSRFRELRDSIVQCQLLMLRVLRFQVSFQHPHKYLLHYLVSLKNWLNRHSWQRTPVAVTAWALL

Parental  RDSYHGALCLRFQAQHIAVAVLYLALQVYGVEVPAEVEAEKAWWQVFNDDLT
          RDSYH..LCLRFQ.QHIAVAVLYLALQVYGVEVPAEVEAEK.WWQVF.DD.T
Retrocopy RDSYHRGLCLRFQDQHIAVAVLYLALQVYGVEVPAEVEAEKPWWQVFGDDIT

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	0.14 RPM	23.98 RPM
SRP007412_cerebellum	0.04 RPM	14.97 RPM
SRP007412_heart	0.06 RPM	12.51 RPM
SRP007412_kidney	0.04 RPM	13.41 RPM
SRP007412_liver	0.00 RPM	7.04 RPM
SRP007412_testis	0.00 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_911 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_911 has 0 orthologous retrocopies within eutheria group .

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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,