RetrogeneDB ID: retro_pabe_432

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:115401056..115401286(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTS
• Ensembl ID: ENSPPYG00000003880
• Aliases: None
• Description: 6-pyruvoyltetrahydropterin synthase [Source:HGNC Symbol;Acc:9689]

Sequence

>retro_pabe_432
GGTGCTAGAAGCCACCAAGTGCTAGTGTACAGCCTCCACTCCTTCAGCACTAAGCCACCGGCTGGCACAGCAAATCTCTG
AGTATCAAAGAAACCATCAAACAGTTTTAGAACTGCAACAATGCAAATGTCCATGAACATGATTATAAAGTTGTATTTAT
AGTATATGGAGGGATTGATCCAGTTACAGGAATGGTTATGAATATGATCAACCTCATAAAGTATATGGAG

Alignment

ORF - retro_pabe_432 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.13 %
• Parental protein coverage: 67.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GGRRCQAQVSRRISFSA-SHRL-YSKFLSDEENLKLFGKCSNPNGHGHNYKVVVTVHGEIDPATGMVMNL
          G.R..Q..V....SFS..SHRL..SK.LS..E..K.F..C.N.N.H.H.YKVV..V.G.IDP.TGMVMN.
Retrocopy GARSHQVLVYSLHSFST>SHRL>HSKSLSIKETIKQF*NCNNANVHEHDYKVVFIVYGGIDPVTGMVMNM

Parental  ADLKKYME
          ..L.KYME
Retrocopy INLIKYME

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	0.11 RPM	2.71 RPM
SRP007412_cerebellum	0.00 RPM	1.46 RPM
SRP007412_heart	0.00 RPM	1.23 RPM
SRP007412_kidney	0.00 RPM	3.25 RPM
SRP007412_liver	0.03 RPM	7.56 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_432 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_432 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_432 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_337

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000013	2 retrocopies	retro_chof_1925, retro_chof_2556,
Callithrix jacchus	ENSCJAG00000012437	2 retrocopies	retro_cjac_2534, retro_cjac_2853,
Dasypus novemcinctus	ENSDNOG00000014823	1 retrocopy	retro_dnov_1747,
Echinops telfairi	ENSETEG00000008145	2 retrocopies	retro_etel_1924, retro_etel_2039,
Homo sapiens	ENSG00000150787	1 retrocopy	retro_hsap_3408,
Macaca mulatta	ENSMMUG00000015255	1 retrocopy	retro_mmul_995,
Nomascus leucogenys	ENSNLEG00000007299	1 retrocopy	retro_nleu_1856,
Otolemur garnettii	ENSOGAG00000017191	3 retrocopies	retro_ogar_1718, retro_ogar_2790, retro_ogar_609,
Pongo abelii	ENSPPYG00000003880	1 retrocopy	retro_pabe_432 ,
Pan troglodytes	ENSPTRG00000004288	3 retrocopies	retro_ptro_2315, retro_ptro_2979, retro_ptro_337,