RetrogeneDB ID: retro_pabe_3624

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:28095614..28095963(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000007306
• Aliases: None
• Description: None

Sequence

>retro_pabe_3624
ATGGAGAGTACTTGGGGGAACCCCGGCTGGGCGCGGCTCGCGCTCTGCCTGGCTGACTTAGTGCTGTCGCTCTACGCGCG
CTGCACGTGAAGGCGGAGCGCGCGCCCGGGACCGGGATTACCGCGCTCTCTGCGACGTGGGCACCGCCATTAGCTGTCCG
CGCGTCTTCTCCTACAGGTAGGGCAGGGGCTTCGGGCTGGTGGAGCACGTGCTGGGACAGGACAGCATCCTCAATCAATC
CAATAACATATTCCTTTGCATCTTCTACACACCACAGCTGTTAGGTTGCCTGCGGACGCACTGGGCCTCTGTCCTGCGGC
TGCTGAGCTCCCTGCTGTCTCTCGCTGGC

Alignment

ORF - retro_pabe_3624 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.88 %
• Parental protein coverage: 71.17 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGSTW-GSP-GWVRLALCLTGLVLSLYALHVKAARARDRDYRALCDVGTAISCSRVFSSRWGRGFGLVEH
          M.STW.G.P.G.......LT....S..A.....ARARDRDYRALCDVGTAISC.RVFS.R.GRGFGLVEH
Retrocopy MESTW>GTPAGRGSRSAWLT*CCRSTRAAREGGARARDRDYRALCDVGTAISCPRVFSYR*GRGFGLVEH

Parental  VLGQDSILNQSNSIFGCIFYTLQLLLGCLRTRWASVLMLLSSLVSLAG
          VLGQDSILNQSN.IF.CIFYT.Q.LLGCLRT.WASVL.LLSSL.SLAG
Retrocopy VLGQDSILNQSNNIFLCIFYTPQ-LLGCLRTHWASVLRLLSSLLSLAG

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	18.19 RPM
SRP007412_cerebellum	0.00 RPM	15.44 RPM
SRP007412_heart	0.00 RPM	8.13 RPM
SRP007412_kidney	0.00 RPM	36.26 RPM
SRP007412_liver	0.00 RPM	204.54 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3624 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3624 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3624 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_4049

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003097	1 retrocopy	retro_cjac_4049,
Homo sapiens	ENSG00000167397	1 retrocopy	retro_hsap_4664,
Oryctolagus cuniculus	ENSOCUG00000002289	1 retrocopy	retro_ocun_1423,
Ochotona princeps	ENSOPRG00000016146	3 retrocopies	retro_opri_1124, retro_opri_1164, retro_opri_70,
Pongo abelii	ENSPPYG00000007306	1 retrocopy	retro_pabe_3624 ,
Pan troglodytes	ENSPTRG00000008031	1 retrocopy	retro_ptro_3099,