RetrogeneDB ID: retro_ptro_2673

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:15119591..15119916(+)
• Located in intron of: ENSPTRG00000020031

Retrocopy information

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

Parental gene information

• Parental gene symbol: C8H8orf46
• Ensembl ID: ENSPTRG00000020307
• Aliases: None
• Description: Pan troglodytes chromosome 8 open reading frame 46 ortholog (C8H8orf46), mRNA. [Source:RefSeq mRNA;Acc:NM_001251906]

Sequence

>retro_ptro_2673
CCCAAAGCATCGAATCTGTATAGGAATCAAGCACATGGAAAAATCTTTGATTCCTCCAGTGTCTTGGATCTCAATGAAAG
CTCCAGCCTCAGCCTTGGTGGAGGCAGCAGCCCCGGGCTCAGAGAAGGAAGGTATTCAGATGACAGGATTCAGACATCTC
AGGATGACCAAAGAGTATCCAACCATTCACCAAGGAGCAGAAGCTTCCCTACCACTGACAGGCAGTACTTCCTGCGGTGT
CCCCAGCATCCCCCAGAAACTGTGGACAAGGCACAAGAAGAAGTCTGAATATGTGAAAGCCAGCAACAGTGCCTTTGAGG
CCGAC

Alignment

ORF - retro_ptro_2673 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.18 %
• Parental protein coverage: 52.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PKTSNLCGNRAYGK-SLIPPVPRISVKTSASASLEATAMGTEKGAVLMRGSRHLKKMTEEYPALPQGAEA
          PK.SNL..N.A.GK.SLIPPV..IS.K..ASA..EA.A.G.EK....M.G.RHL..MT.EYP...QGAEA
Retrocopy PKASNLYRNQAHGK>SLIPPVSWISMKAPASALVEAAAPGSEKEGIQMTGFRHLR-MTKEYPTIHQGAEA

Parental  SLPLTGSASCGVPGILRKMWTRHKKKSEYVGATNSAFEAD
          SLPLTGS.SCGVP.I..K.WTRHKKKSEYV.A.NSAFEAD
Retrocopy SLPLTGSTSCGVPSIPQKLWTRHKKKSEYVKASNSAFEAD

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	0.04 RPM	123.07 RPM
SRP007412_cerebellum	0.04 RPM	7.35 RPM
SRP007412_heart	0.03 RPM	0.26 RPM
SRP007412_kidney	0.00 RPM	1.41 RPM
SRP007412_liver	0.13 RPM	0.10 RPM
SRP007412_testis	0.11 RPM	0.32 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2673 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2673 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2673 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3937
Gorilla gorilla	retro_ggor_2646
Macaca mulatta	retro_mmul_2280

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000169085	1 retrocopy	retro_hsap_3937,
Gorilla gorilla	ENSGGOG00000008516	1 retrocopy	retro_ggor_2646,
Macaca mulatta	ENSMMUG00000022419	1 retrocopy	retro_mmul_2280,
Nomascus leucogenys	ENSNLEG00000010728	1 retrocopy	retro_nleu_634,
Pongo abelii	ENSPPYG00000018639	2 retrocopies	retro_pabe_3245, retro_pabe_3378,
Pan troglodytes	ENSPTRG00000020307	1 retrocopy	retro_ptro_2673 ,
Tupaia belangeri	ENSTBEG00000014906	1 retrocopy	retro_tbel_1795,