RetrogeneDB ID: retro_ptro_678

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:24826078..24826370(+)
• Located in intron of: ENSPTRG00000005173

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: MRPS25
• Ensembl ID: ENSPTRG00000014658
• Aliases: None
• Description: Pan troglodytes mitochondrial ribosomal protein S25 (MRPS25), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001251923]

Sequence

>retro_ptro_678
CCTTGGATGCAGATCATGATGTTTAAGAACACAATACCATTACCCTTCCTACAATTCTGTTTATATTATGAAGAGCAGGT
CCTGGTGGATATAGAGATCAAGATGAATAAGGAGATTATGGAACACATCAAAAAAATCGTGGGGAAGAATGAGGACACAA
GAAAGGAGAGCAGGAGAAAAAGCAGCTCTCTCACCCAGCTCATTTTGGCCTTCAAAGTAGTTCTGATGGGAATCTACCTG
TGAAGTTAAAGAGCAGGTGCCCTATCCAGGCCTAATGGCATTAGGAGAAGAC

Alignment

ORF - retro_ptro_678 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.38 %
• Parental protein coverage: 57.23 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PWVQIMMFKNMTPSPFLRFYLDSGEQVLVDVETKSNKEIMEHIRKILGKNEETLRE-EEEEKKQLSHPAN
          PW.QIMMFKN..P.PFL.F.L...EQVLVD.E.K.NKEIMEHI.KI.GKNE.T..E.E.E.KKQLSHPA.
Retrocopy PWMQIMMFKNTIPLPFLQFCLYYEEQVLVDIEIKMNKEIMEHIKKIVGKNEDTRKE<EQE-KKQLSHPAH

Parental  FG-PRKYCLRECICEVEGQVPCPSLVPLPKE
          FG.P.K....E..CEV..QVP.P.L..L...
Retrocopy FG<PSK*F*WESTCEVKEQVPYPGLMALGED

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	0.00 RPM	31.12 RPM
SRP007412_cerebellum	0.07 RPM	32.77 RPM
SRP007412_heart	0.03 RPM	36.58 RPM
SRP007412_kidney	0.05 RPM	66.16 RPM
SRP007412_liver	0.07 RPM	40.16 RPM
SRP007412_testis	0.42 RPM	59.23 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_678 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_678 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_678 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1127
Gorilla gorilla	retro_ggor_880
Pongo abelii	retro_pabe_932
Macaca mulatta	retro_mmul_874
Callithrix jacchus	retro_cjac_3303

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017160	1 retrocopy	retro_cjac_3303,
Homo sapiens	ENSG00000131368	1 retrocopy	retro_hsap_1127,
Gorilla gorilla	ENSGGOG00000011005	1 retrocopy	retro_ggor_880,
Latimeria chalumnae	ENSLACG00000009006	1 retrocopy	retro_lcha_49,
Macaca mulatta	ENSMMUG00000005157	2 retrocopies	retro_mmul_1946, retro_mmul_874,
Nomascus leucogenys	ENSNLEG00000005218	1 retrocopy	retro_nleu_184,
Pongo abelii	ENSPPYG00000013409	1 retrocopy	retro_pabe_932,
Pelodiscus sinensis	ENSPSIG00000008882	1 retrocopy	retro_psin_36,
Pan troglodytes	ENSPTRG00000014658	1 retrocopy	retro_ptro_678 ,
Rattus norvegicus	ENSRNOG00000010912	1 retrocopy	retro_rnor_1184,
Ictidomys tridecemlineatus	ENSSTOG00000027997	1 retrocopy	retro_itri_984,