RetrogeneDB ID: retro_pabe_3232

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7_random:11617950..11618133(-)
• Located in intron of: ENSPPYG00000018268

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1R14C
• Ensembl ID: ENSPPYG00000017102
• Aliases: None
• Description: protein phosphatase 1, regulatory (inhibitor) subunit 14C [Source:HGNC Symbol;Acc:14952]

Sequence

>retro_pabe_3232
GAAGAGTAGATCCCAGAACTGGAGATTGACGTGGATGTGCTCCTGGACATGGAGACTGACGATGCCTGGGCTGCCAGGGT
CAAGGAGCTGCTGGTTGACTGTTACAAACCCACAGAGGCCTTCATCTCTGGCCTCCTGGACAAGATCCGGGGCATGCAGA
AGCTGAGCACACCCCAGAAGAAA

Alignment

ORF - retro_pabe_3232 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.3 %
• Parental protein coverage: 67.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEEMPEVEIDIDDLLDADSDEERASKLQEALVDCYKPTEEFIKELLSRIRGMRKLSPPQKK
          EE..PE.EID.D.LLD...D...A....E.LVDCYKPTE.FI..LL..IRGM.KLS.PQKK
Retrocopy EE*IPELEIDVDVLLDMETDDAWAARVKELLVDCYKPTEAFISGLLDKIRGMQKLSTPQKK

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	1.71 RPM	1.11 RPM
SRP007412_cerebellum	1.58 RPM	1.22 RPM
SRP007412_heart	0.75 RPM	4.30 RPM
SRP007412_kidney	2.68 RPM	1.56 RPM
SRP007412_liver	1.77 RPM	0.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3232 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3232 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3232 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000026586	2 retrocopies	retro_btau_161, retro_btau_571,
Dasypus novemcinctus	ENSDNOG00000017261	2 retrocopies	retro_dnov_1661, retro_dnov_80,
Myotis lucifugus	ENSMLUG00000023245	2 retrocopies	retro_mluc_1095, retro_mluc_499,
Mus musculus	ENSMUSG00000040653	2 retrocopies	retro_mmus_2089, retro_mmus_3721,
Pongo abelii	ENSPPYG00000017102	4 retrocopies	retro_pabe_1880, retro_pabe_2079, retro_pabe_3001, retro_pabe_3232 ,
Tarsius syrichta	ENSTSYG00000002873	1 retrocopy	retro_tsyr_245,