RetrogeneDB ID: retro_pabe_2552

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:117449065..117449410(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WRB
• Ensembl ID: ENSPPYG00000011427
• Aliases: None
• Description: tail-anchored protein insertion receptor WRB [Source:RefSeq peptide;Acc:NP_001126525]

Sequence

>retro_pabe_2552
ATGGGCACGGCCAAGGCTAACCCCTGGGCGTGGCTGCTGGTGCTCAGATTCCTGTTTGGGTGCGGTGTCCTTCAGATCCT
ACTCCTGTCCTTCTCTTTTATGTCCAGGGTGCAGCACAAGGATGCAGAACAGGAGTCGCAGATAAAAGCAGAGATCCAGG
ATATGAAGCAAGAGTTATCCGCGGTCAATATGATGGACAAGTTTGCCAGATCCACCAGGCTGGAAAGAAAGATCAACAAG
ATGACGAATAAGTTCAAAACTCATGTGAAAGCACAGACAGCTCAATCAGGAATGATAAAATGGGTTATAAGTGTTGCTTT
CTACAAATTGCCAAGTACCATGATC

Alignment

ORF - retro_pabe_2552 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.28 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSAAADHWAWLLVLSFVFGCNVLRILLPSFSSFMSRVLQKDAEQESQMRAEIQDMKQELSTVNMMDEFA
          M..A.A..WAWLLVL.F.FGC.VL.ILL.SFS.FMSRV..KDAEQESQ..AEIQDMKQELS.VNMMD.FA
Retrocopy MGTAKANPWAWLLVLRFLFGCGVLQILLLSFS-FMSRVQHKDAEQESQIKAEIQDMKQELSAVNMMDKFA

Parental  RYARLERKINKMTDKLKTHVKARTAQLAKIKWVISVAFYVLQAALM
          R..RLERKINKMT.K.KTHVKA.TAQ...IKWVISVAFY.L.....
Retrocopy RSTRLERKINKMTNKFKTHVKAQTAQSGMIKWVISVAFYKLPSTMI

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	18.19 RPM
SRP007412_cerebellum	0.12 RPM	24.81 RPM
SRP007412_heart	0.03 RPM	5.51 RPM
SRP007412_kidney	0.00 RPM	6.30 RPM
SRP007412_liver	0.00 RPM	3.58 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2552 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2552 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2552 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3080
Pan troglodytes	retro_ptro_2078
Macaca mulatta	retro_mmul_1966

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005714	2 retrocopies	retro_cjac_2153, retro_cjac_3208,
Dasypus novemcinctus	ENSDNOG00000024987	1 retrocopy	retro_dnov_1496,
Homo sapiens	ENSG00000182093	1 retrocopy	retro_hsap_3080,
Gorilla gorilla	ENSGGOG00000013144	1 retrocopy	retro_ggor_2116,
Microcebus murinus	ENSMICG00000015808	1 retrocopy	retro_mmur_1275,
Macaca mulatta	ENSMMUG00000020654	2 retrocopies	retro_mmul_1966, retro_mmul_853,
Mus musculus	ENSMUSG00000023147	1 retrocopy	retro_mmus_1452,
Nomascus leucogenys	ENSNLEG00000013146	1 retrocopy	retro_nleu_2014,
Otolemur garnettii	ENSOGAG00000026761	1 retrocopy	retro_ogar_2691,
Pongo abelii	ENSPPYG00000011427	1 retrocopy	retro_pabe_2552 ,
Pan troglodytes	ENSPTRG00000013915	1 retrocopy	retro_ptro_2078,
Ictidomys tridecemlineatus	ENSSTOG00000012736	1 retrocopy	retro_itri_1744,
Tursiops truncatus	ENSTTRG00000015373	1 retrocopy	retro_ttru_1711,