RetrogeneDB ID: retro_pabe_3245

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:18478115..18478440(+)
• Located in intron of: ENSPPYG00000018396

Retrocopy information

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

Parental gene information

• Parental gene symbol: C8H8orf46
• Ensembl ID: ENSPPYG00000018639
• Aliases: None
• Description: None

Sequence

>retro_pabe_3245
CCCAAAGCATCAAATCTGTATAGGAATCGAGCACATGGAAAAATCTTTGATTCCTCCAGTGTCTTGGATCTCAATGAAAG
CTCCAGCCTCAGCCTTGGTGGAGGCAGCAGCCCTGGGCTCAGAGAAGGAAGGTATTCAGACGACAGGATTCAGACATCTC
AGGATGACCAAAGAGTATCCAACCATTCACCAAGGATCAGAAGCTTCCCTATCGCTGACAGGCAGTACTTCCTGCAGTGT
TCCCAGCAACCCCCGGAAACTGTGGACAAGGCACAAGAAGAAGTCTGAATATGTGAGAGCCACCAACAGTGCCTTTGAGG
CCGAC

Alignment

ORF - retro_pabe_3245 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.36 %
• 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..NRA.GK.SLIPPV..IS.K..ASA..EA.A.G.EK......G.RHL..MT.EYP...QG.EA
Retrocopy PKASNLYRNRAHGK>SLIPPVSWISMKAPASALVEAAALGSEKEGIQTTGFRHLR-MTKEYPTIHQGSEA

Parental  SLPLTGSASCGVPGILRKMWTRHKKKSEYVGATNSAFEAD
          SL.LTGS.SC.VP...RK.WTRHKKKSEYV.ATNSAFEAD
Retrocopy SLSLTGSTSCSVPSNPRKLWTRHKKKSEYVRATNSAFEAD

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	77.19 RPM
SRP007412_cerebellum	0.00 RPM	38.43 RPM
SRP007412_heart	0.00 RPM	0.21 RPM
SRP007412_kidney	0.00 RPM	2.09 RPM
SRP007412_liver	0.06 RPM	1.04 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3245 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3245 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3245 has 0 orthologous retrocopies within eutheria group .

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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,