RetrogeneDB ID: retro_pabe_50

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:128287112..128287472(-)
• Located in intron of: ENSPPYG00000001116

Retrocopy information

• Ensembl ID: ENSPPYG00000001118
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: BRI3
• Ensembl ID: ENSPPYG00000025815
• Aliases: None
• Description: brain protein I3 [Source:HGNC Symbol;Acc:1109]

Sequence

>retro_pabe_50
CTGCTGCAAGAGCGGCCGCCCGCCTACAACCTGGAGGCTGGCCAGGGCGACTACGCGTGCGGCCAGCACGGCCACGGCGC
CATCCCCGCCGCGCCCCCGCAGCCGCCCTACTCCTACCTCGTCACAGGGACACCCACCCACCATCCCAGGGTCTACAACA
TCCACAGCCGGACCGTCACCCGCTATCCTACCAACTCTATCGTGGTCGTGGGAGGCTGTCCCGTCTGCAGGGTCGGGGTG
CTGCAGGACTGCTTCACTTTCCTGGGCATCTTCCTGGCCATCATCCTGTTCCCCTTTGGGTTCATCTGCTGTTTTGCCTT
GAGGAAGCGAAGATGCCCCAACTGTGGAGCCACCTTCGCT

Alignment

ORF - retro_pabe_50 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.24 %
• Parental protein coverage: 95.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLQRPP-YNLRPDQGDYACGPHGYGAIPAAPPPPPYPYLVTGIPTHHPRVYNIHSRTVTRYPANSIVVVG
          L..RPP.YNL...QGDYACG.HG.GAIPAAPP.PPY.YLVTG.PTHHPRVYNIHSRTVTRYP.NSIVVVG
Retrocopy LQERPPAYNLEAGQGDYACGQHGHGAIPAAPPQPPYSYLVTGTPTHHPRVYNIHSRTVTRYPTNSIVVVG

Parental  GCPVCRVGVLEDCFTFLGIFLAIVLFPFGFICCFALRKRRCPNCGATFA
          GCPVCRVGVL.DCFTFLGIFLAI.LFPFGFICCFALRKRRCPNCGATFA
Retrocopy GCPVCRVGVLQDCFTFLGIFLAIILFPFGFICCFALRKRRCPNCGATFA

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	2.27 RPM
SRP007412_cerebellum	0.00 RPM	0.85 RPM
SRP007412_heart	0.18 RPM	3.76 RPM
SRP007412_kidney	0.46 RPM	3.08 RPM
SRP007412_liver	0.18 RPM	3.21 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_50 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_50 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_50 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_195
Gorilla gorilla	retro_ggor_205

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015227	1 retrocopy	retro_cjac_2527,
Homo sapiens	ENSG00000164713	3 retrocopies	retro_hsap_1095, retro_hsap_1811, retro_hsap_195,
Gorilla gorilla	ENSGGOG00000009646	1 retrocopy	retro_ggor_205,
Microcebus murinus	ENSMICG00000002888	1 retrocopy	retro_mmur_372,
Macaca mulatta	ENSMMUG00000013275	2 retrocopies	retro_mmul_1248, retro_mmul_849,
Otolemur garnettii	ENSOGAG00000000638	1 retrocopy	retro_ogar_63,
Pongo abelii	ENSPPYG00000025815	3 retrocopies	retro_pabe_1484, retro_pabe_50 , retro_pabe_910,
Pan troglodytes	ENSPTRG00000019436	1 retrocopy	retro_ptro_698,
Tursiops truncatus	ENSTTRG00000015705	2 retrocopies	retro_ttru_706, retro_ttru_91,