RetrogeneDB ID: retro_ptro_324

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:101159503..101160298(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C5orf15
• Ensembl ID: ENSPTRG00000017234
• Aliases: None
• Description: chromosome 5 open reading frame 15 [Source:HGNC Symbol;Acc:20656]

Sequence

>retro_ptro_324
ATGGTTGCTGCTGCCCTGAGGAGGATGAGGGGGCCCGCACAAGCAAAACTTCTGCCCAGGTCGGCCATCCAAGCCTTTGC
GGGGCTGGTGGGGCCGCTGGTCTTGGCGCTCCTCCTTGTGTCCGCCACTCTATCCAGTGTTGTATCATGGACTGATTCAC
TGATTCAATCTGTACTCAACTCAGATATTTCTACCCCAAATGTGAATGCTTTAACACATGAAAAACAAACCAAATCTTCT
ATTTCCCAAATCAGTACCACCCTCCCTCCCACAATGAGTACTGAGAAAAGTGGAGGAGCATCTGTGGCCCCTCATCCCTC
ACCTACACCTCTGTCTCAAGAGGAAGCTGATAACAATGAAGATCCTAGCACAGAGGAGGAGGATCTTCTCACGCTGAACA
GTTCTCCATCCACAGCCAAAGACACTCTGGACAGTGGCAATTATGGAGAACCAGACTATGACTGGACCACGGGCCACAGG
GATGACGACGAGTCTGATGACACCTTGGAAGAAAACAGGGGTTACATGGAAATTGAACAGTCAGTGAAATCTTTTAAGAT
GCCATCCTCAAATATAGAAGAGGAAGACAGCCATTTCTTTTTTCATCTTATTATTTTTGCTTTTTGCATTGCTATTGTCT
ACATTACATACCACAAAAAAAGGAAGATTTTTCTTCTGGTTCAAAGCAGAAAATGGCGTGATGGCCTTTGTTCCAAAACA
GTGGAATACCATTGCCTAGATCAGAATGTTAGTGAGGCAATGTCTTCTTTGAAGATTACCAATAATTATATTTTT

Alignment

ORF - retro_ptro_324 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.68 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAVPKRMRGPAQAKLLPGSAIQALVGLARPLVLALLLVSAALSSVVSRTDSPSPTVLNSHISTPNVNA
          M.AA...RMRGPAQAKLLP.SAIQA..GL..PLVLALLLVSA.LSSVVS.TDS....VLNS.ISTPNVNA
Retrocopy MVAAALRRMRGPAQAKLLPRSAIQAFAGLVGPLVLALLLVSATLSSVVSWTDSLIQSVLNSDISTPNVNA

Parental  LTHENQTKPSISQISTTLPPTTSTKKSGGASVAPHPSPTPLSQEEADNNEDPSIEEEDLLTLNSSPSTAK
          LTHE.QTK.SISQISTTLPPT.ST.KSGGASVAPHPSPTPLSQEEADNNEDPS.EEEDLLTLNSSPSTAK
Retrocopy LTHEKQTKSSISQISTTLPPTMSTEKSGGASVAPHPSPTPLSQEEADNNEDPSTEEEDLLTLNSSPSTAK

Parental  DTLDNGDYGEPDYDWTTGPRDDDESDDTLEENRGYMEIEQSVKSFKMPSSNIEEEDSHFFFHLIIFAFCI
          DTLD.G.YGEPDYDWTTG.RDDDESDDTLEENRGYMEIEQSVKSFKMPSSNIEEEDSHFFFHLIIFAFCI
Retrocopy DTLDSGNYGEPDYDWTTGHRDDDESDDTLEENRGYMEIEQSVKSFKMPSSNIEEEDSHFFFHLIIFAFCI

Parental  AVVYITYHNKRKIFLLVQSRKWRDGLCSKTVEYHRLDQNVNEAMPSLKITNDYIF
          A.VYITYH.KRKIFLLVQSRKWRDGLCSKTVEYH.LDQNV.EAM.SLKITN.YIF
Retrocopy AIVYITYHKKRKIFLLVQSRKWRDGLCSKTVEYHCLDQNVSEAMSSLKITNNYIF

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	0.02 RPM	12.78 RPM
SRP007412_cerebellum	0.25 RPM	18.21 RPM
SRP007412_heart	0.09 RPM	15.27 RPM
SRP007412_kidney	0.21 RPM	33.13 RPM
SRP007412_liver	0.13 RPM	23.27 RPM
SRP007412_testis	0.11 RPM	23.18 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_324 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_324 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_324 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_416
Pongo abelii	retro_pabe_295

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000021947	1 retrocopy	retro_ggor_416,
Nomascus leucogenys	ENSNLEG00000008019	1 retrocopy	retro_nleu_1021,
Pongo abelii	ENSPPYG00000015780	1 retrocopy	retro_pabe_295,
Pan troglodytes	ENSPTRG00000017234	1 retrocopy	retro_ptro_324 ,
Pteropus vampyrus	ENSPVAG00000012421	1 retrocopy	retro_pvam_171,