RetrogeneDB ID: retro_ggor_1491

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 19:51671406..51671985(-)
• Located in intron of: ENSGGOG00000027839

Retrocopy information

• Ensembl ID: ENSGGOG00000025810
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS9
• Ensembl ID: ENSGGOG00000027839
• Aliases: None
• Description: None

Sequence

>retro_ggor_1491
ATGCCAGTGGCCTGGAGCTGGGTTTGTCGCAAAACTTATGTGACCCCGCGGAGACCCTTCGAGAAATCTCGTCTCGACCA
AGAGCTGAAGCTGATCGGCGAGTATGGGCTCCGGAACAAACGGGAGGTCTAGAGGGTCAAATTTACCTTGGCCAACATCC
GCAAGGCCGCCCGGGAACTGCTGACGCTTGATGAGAAGGACCCACGGCGTCTGTTCGAAGGCAACGTCCTGCTGCGGCGG
CTGCTCCGCATTGGGGTGCTGGATGAGGGCAAGACGAAGCTGGATTACATCCTGGGCCTGAAGACAGAGGATTTCTTAGA
GAGACGCCTACAGACCCAGGTCTTCAAGCTGGGCTTGGCCAAGTCCATCCACCACGCTGGCGTGCTGATCCGCCAGCGCC
GTATCAGGGTCCGCAAGCAGGTGGTGAACATCCCGTCCTGCATTGTCCGCCTGGATTCCCAGAAGCCAATCGACTTGTCT
CTGCGCTCTCCCTATGGGGGTGGCCGCCCGGGCCGCGTGAAGAGGAAGAACGCCAAGAAGGGCCAGGGTGAGGGTGGGGC
TGGAGACGACGAGGAGGAG

Alignment

ORF - retro_ggor_1491 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.75 %
• Parental protein coverage: 99.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPRR
          MPVA.SWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREV.RVKFTLA.IRKAARELLTLDEKDPRR
Retrocopy MPVAWSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREV*RVKFTLANIRKAARELLTLDEKDPRR

Parental  LFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQ
          LFEGN.LLRRL.RIGVLDEGK.KLDYILGLK.EDFLERRLQTQVFKLGLAKSIHHA.VLIRQR.IRVRKQ
Retrocopy LFEGNVLLRRLLRIGVLDEGKTKLDYILGLKTEDFLERRLQTQVFKLGLAKSIHHAGVLIRQRRIRVRKQ

Parental  VVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEE
          VVNIPS.IVRLDSQK.ID.SLRSPYGGGRPGRVKRKNAKKGQG..GAGDDEEE
Retrocopy VVNIPSCIVRLDSQKPIDLSLRSPYGGGRPGRVKRKNAKKGQGEGGAGDDEEE

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	0.19 RPM	152.97 RPM
SRP007412_cerebellum	0.35 RPM	163.07 RPM
SRP007412_heart	0.25 RPM	172.27 RPM
SRP007412_kidney	0.41 RPM	228.90 RPM
SRP007412_liver	0.40 RPM	364.65 RPM
SRP007412_testis	0.31 RPM	162.96 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_1491 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1491 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001130	3 retrocopies	retro_cjac_2034, retro_cjac_2993, retro_cjac_719,
Cavia porcellus	ENSCPOG00000020893	2 retrocopies	retro_cpor_1457, retro_cpor_407,
Gorilla gorilla	ENSGGOG00000027839	4 retrocopies	retro_ggor_1491 , retro_ggor_160, retro_ggor_2190, retro_ggor_32,
Mustela putorius furo	ENSMPUG00000010394	1 retrocopy	retro_mputfur_128,
Mus musculus	ENSMUSG00000006333	2 retrocopies	retro_mmus_3082, retro_mmus_526,
Nomascus leucogenys	ENSNLEG00000006314	1 retrocopy	retro_nleu_91,
Pan troglodytes	ENSPTRG00000011449	1 retrocopy	retro_ptro_57,
Rattus norvegicus	ENSRNOG00000011355	7 retrocopies	retro_rnor_1298, retro_rnor_2577, retro_rnor_2849, retro_rnor_2902, retro_rnor_635, retro_rnor_663, retro_rnor_892,
Rattus norvegicus	ENSRNOG00000049813	3 retrocopies	retro_rnor_2082, retro_rnor_30, retro_rnor_78,