RetrogeneDB ID: retro_pabe_1484

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:18329424..18329781(-)
• Located in intron of: ENSPPYG00000008040

Retrocopy information

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

Parental gene information

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

Sequence

>retro_pabe_1484
CCACCTACAAACCTTAGGGGCCGGCCAGGGTGACTACGCATGCAGCTTGCATGGGCTACGGCATCATCCCTGCTTGCCCA
CCCCTTGCTGCTGGCCCGCCTTCCCCTTACCTCATCACAGGGATACCCAACCACCACCCCAGGGTCTACAATGACCACAG
CTGGACTATCACTTGGTACCCTGCCAATGCCATCGGATCAGCAATGAGAGGCTGTCCCGTCTGCAGGGATAGGGTGCTGG
GGGACTGCTTCACCTTCCTGGGAATCCTCCCTGGCCATCATCCTGTTCCCCTTTGGGTTCATCTGCTGTTTTGCCTTGAG
GAAGCAAAGATGCCCCAACTGCGGAGCAGCCTTTGCT

Alignment

ORF - retro_pabe_1484 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.9 %
• Parental protein coverage: 92.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PPYNLR-PDQGDYACGPHG-YGAIPAAPP---PPPYPYLVTGIPTHHPRVYNIHSRTVTRYPANSI-VVV
          PP.NLR...QGDYAC..HG.YG.IPA.PP....PP.PYL.TGIP.HHPRVYN.HS.T.T.YPAN.I....
Retrocopy PPTNLR>AGQGDYACSLHG>YGIIPACPPLAAGPPSPYLITGIPNHHPRVYNDHSWTITWYPANAIGSAM

Parental  GGCPVCRVGVLEDCFTFLGIF-LAIVLFPFGFICCFALRKRRCPNCGATFA
          .GCPVCR..VL.DCFTFLGI..LAI.LFPFGFICCFALRK.RCPNCGA.FA
Retrocopy RGCPVCRDRVLGDCFTFLGIL>LAIILFPFGFICCFALRKQRCPNCGAAFA

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	2.27 RPM
SRP007412_cerebellum	0.00 RPM	0.85 RPM
SRP007412_heart	0.00 RPM	3.76 RPM
SRP007412_kidney	0.10 RPM	3.08 RPM
SRP007412_liver	0.00 RPM	3.21 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1484 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1484 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1484 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1811

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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,