RetrogeneDB ID: retro_pabe_492

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:208993898..208994168(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1R11
• Ensembl ID: ENSPPYG00000029642
• Aliases: None
• Description: protein phosphatase 1, regulatory (inhibitor) subunit 11 [Source:HGNC Symbol;Acc:9285]

Sequence

>retro_pabe_492
TCCGAGGCAGGGGCTGGGCTGAGCGAGACTGTCACTGAGACAACGGTTACCGTGACAACCGAGCCCGAGAACCGGAGCCT
TACCATCAAACTTCCGAAATGGAAGCCAGAGAAAAAGGTGGAATGGACAAGCGACACTGTGGACAATGAACGCATGCGCT
GCCGCTCATCAAAATGCTGCTGTATTTATGAAAAACCCCCGGCCTTTGGCGAGAGCTCCACGGAAAGTGATGAGGAGGAA
GAAGAGGGCTGTGGTCATACACACTGTGTA

Alignment

ORF - retro_pabe_492 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.11 %
• Parental protein coverage: 86.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AEAGAGLSETVTETTVTVTTEPENRSLTIKLRKRKPEKKVEWTSDTVDNEHMGRRSSKCCCIYEKPRAFG
          .EAGAGLSETVTETTVTVTTEPENRSLTIKL.K.KPEKKVEWTSDTVDNE.M..RSSKCCCIYEKP.AFG
Retrocopy SEAGAGLSETVTETTVTVTTEPENRSLTIKLPKWKPEKKVEWTSDTVDNERMRCRSSKCCCIYEKPPAFG

Parental  ESSTESDEEEEEGCGHTHCL
          ESSTESDEEEEEGCGHTHC.
Retrocopy ESSTESDEEEEEGCGHTHCV

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	40.97 RPM
SRP007412_cerebellum	0.00 RPM	26.27 RPM
SRP007412_heart	0.00 RPM	8.07 RPM
SRP007412_kidney	0.00 RPM	26.12 RPM
SRP007412_liver	0.00 RPM	13.13 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_492 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_492 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_492 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_359

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000013592	1 retrocopy	retro_fcat_1794,
Gorilla gorilla	ENSGGOG00000026830	1 retrocopy	retro_ggor_80,
Macropus eugenii	ENSMEUG00000006493	2 retrocopies	retro_meug_715, retro_meug_933,
Monodelphis domestica	ENSMODG00000016021	1 retrocopy	retro_mdom_98,
Otolemur garnettii	ENSOGAG00000001598	1 retrocopy	retro_ogar_1458,
Pongo abelii	ENSPPYG00000029642	1 retrocopy	retro_pabe_492 ,
Pan troglodytes	ENSPTRG00000017915	1 retrocopy	retro_ptro_2969,
Pteropus vampyrus	ENSPVAG00000008330	1 retrocopy	retro_pvam_894,
Ictidomys tridecemlineatus	ENSSTOG00000003632	1 retrocopy	retro_itri_159,