RetrogeneDB ID: retro_ptro_2772

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:84696822..84697227(-)
• Located in intron of: ENSPTRG00000020398

Retrocopy information

• Ensembl ID: ENSPTRG00000040162
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MIOX
• Ensembl ID: ENSPTRG00000014543
• Aliases: None
• Description: myo-inositol oxygenase [Source:HGNC Symbol;Acc:14522]

Sequence

>retro_ptro_2772
GTGAAGGTGACAGTGGACCCAGACCCTTCCCTGGTCTACCGACCTGAAGTGGACCCAGAGGCTGCCAAAGACAAGGCTGG
CTTCCAGAGCTACGTGTCGGGTCCCCTCCTGGACCACGTCTTTACCACCGACAAGCTCATGCACATGCACCACACAGTGG
ATTTCGTCAGGAGCAAGCACGCCTGGTTTGGGGACTTTTCCTACAAGAAAATGAAGGTCATGGAGGCCGTGGACCTGCTG
CATGGGCTGGTGGACGAATCAGACTCAGGTGTAGACTTCTCCCACTCCTTCCAAGCCTTCCAGATGGCGGAGGGCATCCG
AAAGCTCACCCGGGCAAGGACTGGTTCCAGCTTGTTGGGCTTCTATGACCTAGGGAAGGTCTTGGCCCTGTTGGGGGAGC
CCCAG

Alignment

ORF - retro_ptro_2772 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.54 %
• Parental protein coverage: 79.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKVTVGPDPSLVYRPDVDPEVAKDKASFRNYTSGPLLDRVFTTYKLMHTHQTVDFVRSKHAQFGGFSYKK
          .KVTV.PDPSLVYRP.VDPE.AKDKA.F..Y.SGPLLD.VFTT.KLMH.H.TVDFVRSKHA.FG.FSYKK
Retrocopy VKVTVDPDPSLVYRPEVDPEAAKDKAGFQSYVSGPLLDHVFTTDKLMHMHHTVDFVRSKHAWFGDFSYKK

Parental  MTVMEAVDLLDGLVDESDPDVDFPNSFHAFQTAEGIRK-AHPDKDWFH-LVGLLHDLGKVLALFGEPQ
          M.VMEAVDLL.GLVDESD..VDF..SF.AFQ.AEGIRK.AHP.KDWF..L.G...DLGKVLAL.GEPQ
Retrocopy MKVMEAVDLLHGLVDESDSGVDFSHSFQAFQMAEGIRK<AHPGKDWFQ>LLGF-YDLGKVLALLGEPQ

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	0.02 RPM	0.04 RPM
SRP007412_cerebellum	0.04 RPM	0.29 RPM
SRP007412_heart	0.03 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	564.51 RPM
SRP007412_liver	0.00 RPM	0.07 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2772 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2772 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2772 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000100253	1 retrocopy	retro_hsap_4087,
Gorilla gorilla	ENSGGOG00000013037	1 retrocopy	retro_ggor_2741,
Nomascus leucogenys	ENSNLEG00000000729	1 retrocopy	retro_nleu_1910,
Pan troglodytes	ENSPTRG00000014543	1 retrocopy	retro_ptro_2772 ,