RetrogeneDB ID: retro_pabe_2306

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:54136796..54137333(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000013638
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPAT
• Ensembl ID: ENSPPYG00000029568
• Aliases: None
• Description: phosphoribosyl pyrophosphate amidotransferase [Source:HGNC Symbol;Acc:9238]

Sequence

>retro_pabe_2306
TGTGGACTTTCATATGTGGAGGTGCTGTGTAAAAACCGATATGTAGGGAGAACTTTCATTCAGCCAAACATGAGGTTAAG
ACAACTTGGTGTTGCAAAAAAATTTGGAGTATTGTCAGACAACTTTAAAGGCAAAAGAATTGTTCTTGTAGATGATTCAG
TTGTGAGAGGCAATACCATCTCACCTATAATAAAATTGCTCAAAGAATCTGGTGCAAAAGAGGTACACATTTGAGTAGCT
TCACCACCAATTAAATATCCATGCTTCATGGGAATAAACATTCCTACAAAAGAAGAGCTCATTGCCAATAAACCAGAATT
TGATCACCTTGCAGGATATCTAGGAGCAAACAGTGTTGTGTATCTGTCAGTACAAGGACTGGTTTCATCTGTACAAGAAG
GGATAAAGTTTAAAAAACGGAAAGAGAAAAAGCACGATATTATGATCCAAGAAAATGGAAATGGTCTAGAATGTTTTGAA
AAGAGTGGTCATTGTACAGCTTGTTTCACTGGAAAATAACCTGTAGAATTAGAATGG

Alignment

ORF - retro_pabe_2306 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.85 %
• Parental protein coverage: 89.95 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CGLPYVEVLCKNRYVGRTFIQPNVRLRQLGVAKKFGVLSDNFKGKRIVLVDDSIVRGNTILPIIKLLKES
          CGL.YVEVLCKNRYVGRTFIQPN.RLRQLGVAKKFGVLSDNFKGKRIVLVDDS.VRGNTI.PIIKLLKES
Retrocopy CGLSYVEVLCKNRYVGRTFIQPNMRLRQLGVAKKFGVLSDNFKGKRIVLVDDSVVRGNTISPIIKLLKES

Parental  GAKEVHIRVASPPIKYPCFMGINIPTKEELIANKPEFDHLAEYLGANSVVYLSVEGLVSSVQEGIKFKKQ
          GAKEVHI.VASPPIKYPCFMGINIPTKEELIANKPEFDHLA.YLGANSVVYLSV.GLVSSVQEGIKFKK.
Retrocopy GAKEVHI*VASPPIKYPCFMGINIPTKEELIANKPEFDHLAGYLGANSVVYLSVQGLVSSVQEGIKFKKR

Parental  KEKKHDIMIQENGNGLECFAKSGHCTACLTGKYPVELEW
          KEKKHDIMIQENGNGLECF.KSGHCTAC.TGK.PVELEW
Retrocopy KEKKHDIMIQENGNGLECFEKSGHCTACFTGK*PVELEW

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	5.97 RPM
SRP007412_cerebellum	0.00 RPM	6.08 RPM
SRP007412_heart	0.06 RPM	2.89 RPM
SRP007412_kidney	0.07 RPM	4.01 RPM
SRP007412_liver	0.09 RPM	1.62 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2306 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2306 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2306 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000023644	2 retrocopies	retro_ecab_1113, retro_ecab_270,
Homo sapiens	ENSG00000128059	1 retrocopy	retro_hsap_2809,
Gorilla gorilla	ENSGGOG00000004608	1 retrocopy	retro_ggor_1953,
Monodelphis domestica	ENSMODG00000020693	1 retrocopy	retro_mdom_1487,
Nomascus leucogenys	ENSNLEG00000008762	1 retrocopy	retro_nleu_431,
Pongo abelii	ENSPPYG00000029568	1 retrocopy	retro_pabe_2306 ,
Pan troglodytes	ENSPTRG00000016080	1 retrocopy	retro_ptro_1903,
Tursiops truncatus	ENSTTRG00000010928	1 retrocopy	retro_ttru_794,