RetrogeneDB ID: retro_ptro_57

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 22:39782416..39783001(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000041697
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RPS9
• Ensembl ID: ENSPTRG00000011449
• Aliases: None
• Description: ribosomal protein S9 [Source:HGNC Symbol;Acc:10442]

Sequence

>retro_ptro_57
ATGCCAGTGGTCCGGAGCTGGGTTTGTCGCAAAACTTACGTGACCCCGCGGAGATCCTTTGAGAAATCTCGTCTCGACCA
AGAGCTGAAGCTGATCGGCGAGTATGGGCTCAGGAACAAACGTGAGGTCTGGAGGGTCAAATTTACCCTGGCCAAGATCC
GCAAGGCCGCCCGGGAACTGCTGACGCTTGATGAGAAGGACCCACGGCGTCTGTTCGAAGGCAATGCCCTGCTGCGGCGG
CTGGTCCGCATTGGGGTGCTGGATGAGGGCAAGATGAAGCTGGATTACATCCTGGGCCTGAAGATAGAGGATTTCTTAGA
GAGACGCCTACAGACCCAGGTCTTCAAGCTGGGCTTGGCCAAGTCCATCCACCACGCTCGCGTGCTGATCCGCCAGCGCC
ATATCAGGGTCCGCAAGCAGGTGGTGAACATCCCGTCCTTCATTGTCCGCCTGGATTCCCAGAAGCACATCGACTTCTCT
CTGTGCTCTCCCCATGGGGGTGGCCGCCCGGGCCGCGTGAAGAGGAAGAATGCCAAGAAGGGCCAGGGTGGGGCTGGGGC
TGGGGACCACAAGGAGGAGGATTAA

Alignment

ORF - retro_ptro_57 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.91 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPRR
          MPV.RSWVCRKTYVTPRR.FEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPRR
Retrocopy MPVVRSWVCRKTYVTPRRSFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPRR

Parental  LFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQ
          LFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQ
Retrocopy LFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQ

Parental  VVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED
          VVNIPSFIVRLDSQKHIDFSL.SP.GGGRPGRVKRKNAKKGQGGAGAGD..EED
Retrocopy VVNIPSFIVRLDSQKHIDFSLCSPHGGGRPGRVKRKNAKKGQGGAGAGDHKEED

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	4.92 RPM	199.19 RPM
SRP007412_cerebellum	31.76 RPM	111.60 RPM
SRP007412_heart	10.43 RPM	74.88 RPM
SRP007412_kidney	31.80 RPM	241.38 RPM
SRP007412_liver	45.76 RPM	194.47 RPM
SRP007412_testis	8.01 RPM	53.96 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_57 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_57 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_57 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_160
Pongo abelii	retro_pabe_1887

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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,