RetrogeneDB ID: retro_pabe_3236

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7_random:12765739..12765981(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000018258
• Aliases: None
• Description: None

Sequence

>retro_pabe_3236
TGTCCACAAGTCGGCCTCTCAAGGCCCAGCTCCTGGCTTTTGTTGGCGTCTCCAGGCCCAGCTTCTGCCCCCACGTGGCC
TCTACAGGCCGTGCTCTTTCTTCTGACTGTGTGTGGAGGTCCAACTCCTGCCTCAGAACAACCTCTTCTGGCTCAGCTCC
CGCCCAGCTCCTAGTGGCCTTTGTAGGCCCCAAACTGCCTCAAGTCAAGCTTTCCAGGCCCACCTTCTGCCTCCCAATGG
CC

Alignment

ORF - retro_pabe_3236 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.1 %
• Parental protein coverage: 61.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CP--GMSSPGLKLPFS-LSSPSYCL-LASPGPALPPGCVYRPGSCVTATALDSAPAQLLVAFGGPKLPQA
          CP..G.S.P...L.....S.PS.C...AS.G.AL...CV.R..SC...T...SAPAQLLVAF.GPKLPQ.
Retrocopy CPQVGLSRPSSWLLLA<VSRPSFCPHVASTGRALSSDCVWRSNSCLRTTSSGSAPAQLLVAFVGPKLPQV

Parental  KLCRPAFCLPVA
          KL.RP.FCLP.A
Retrocopy KLSRPTFCLPMA

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	0.06 RPM	0.11 RPM
SRP007412_cerebellum	0.12 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.03 RPM
SRP007412_kidney	0.23 RPM	0.23 RPM
SRP007412_liver	0.12 RPM	0.06 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3236 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3236 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3236 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000000034	1 retrocopy	retro_mmul_1610,
Pongo abelii	ENSPPYG00000018258	4 retrocopies	retro_pabe_133, retro_pabe_3119, retro_pabe_3126, retro_pabe_3236 ,