RetrogeneDB ID: retro_ptro_125

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:99328025..99328268(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000018353
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: COX7A1
• Ensembl ID: ENSPTRG00000010888
• Aliases: None
• Description: cytochrome c oxidase subunit VIIa polypeptide 1 (muscle) [Source:HGNC Symbol;Acc:2287]

Sequence

>retro_ptro_125
ATGCTGTGGAATCTGCTGGCTCTTCATCAGATTGGGCAGAGGACCATAAGCACTGCTTCCCACAGGCATTTTAAAAATAA
AGTTCCAGAGAAACAAAAACTGTTCCAGGAGGATGATGGAATTCCACTGTATCTAAAGGGTGGGATAGCTGATGCCCTCC
TTCATAGAGCCACCATGATTCTTACAGTTGGTGGAACAGCATATGCCATATATCAGCTGGCTGTGGCTTCATTTCCCAAT
AAA

Alignment

ORF - retro_ptro_125 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.58 %
• Parental protein coverage: 83.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RSFSSTARNRFQNRVREKQKFFQEDNDIPLYLKGGIVDNILYRVTMTLCLGGTVYSLYSLGWASFP
          R..S......F.N.V.EKQK.FQED..IPLYLKGGI.D..L.R.TM.L..GGT.Y..Y.L..ASFP
Retrocopy RTISTASHRHFKNKVPEKQKLFQEDDGIPLYLKGGIADALLHRATMILTVGGTAYAIYQLAVASFP

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	0.05 RPM	46.42 RPM
SRP007412_cerebellum	0.32 RPM	8.50 RPM
SRP007412_heart	0.64 RPM	319.27 RPM
SRP007412_kidney	0.39 RPM	75.84 RPM
SRP007412_liver	0.29 RPM	3.54 RPM
SRP007412_testis	5.16 RPM	0.84 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_125 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_125 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_125 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2961
Gorilla gorilla	retro_ggor_2051
Pongo abelii	retro_pabe_2456

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012840	1 retrocopy	retro_chof_305,
Echinops telfairi	ENSETEG00000007654	1 retrocopy	retro_etel_2078,
Myotis lucifugus	ENSMLUG00000012331	1 retrocopy	retro_mluc_187,
Macaca mulatta	ENSMMUG00000000250	3 retrocopies	retro_mmul_1665, retro_mmul_1968, retro_mmul_2489,
Monodelphis domestica	ENSMODG00000025577	1 retrocopy	retro_mdom_1288,
Pan troglodytes	ENSPTRG00000010888	1 retrocopy	retro_ptro_125 ,
Pan troglodytes	ENSPTRG00000011865	1 retrocopy	retro_ptro_575,