RetrogeneDB ID: retro_ptro_340

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:126585672..126585846(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COA5
• Ensembl ID: ENSPTRG00000012267
• Aliases: None
• Description: cytochrome c oxidase assembly factor 5 [Source:HGNC Symbol;Acc:33848]

Sequence

>retro_ptro_340
CTGAAGGAGGACCTGGGCGTGTGTCTGTTGCAGTCCAACTGTGTGGTCCAGGAAGGAAAATCCCCTCTGCAGTGTTTGAA
GGAAGGATACTGCAAAGCTTTGAAATACTCATTTTTTGAGTATAAAAGATCAGTGTTGGATATCAGATCAAGAACCAGAG
GAAGAAAGGGATAT

Alignment

ORF - retro_ptro_340 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.76 %
• Parental protein coverage: 78.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LKEDLGACLLQSDCVVQEGKSPRQCLKEGYCNSLKYAFFECKRSVLDNRARFRGRKGY
          LKEDLG.CLLQS.CVVQEGKSP.QCLKEGYC..LKY.FFE.KRSVLD.R.R.RGRKGY
Retrocopy LKEDLGVCLLQSNCVVQEGKSPLQCLKEGYCKALKYSFFEYKRSVLDIRSRTRGRKGY

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	23.18 RPM
SRP007412_cerebellum	0.00 RPM	24.66 RPM
SRP007412_heart	0.00 RPM	18.10 RPM
SRP007412_kidney	0.00 RPM	23.72 RPM
SRP007412_liver	0.00 RPM	12.50 RPM
SRP007412_testis	0.00 RPM	45.31 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_340 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_340 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_340 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_204
Gorilla gorilla	retro_ggor_278
Pongo abelii	retro_pabe_435

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007139	1 retrocopy	retro_cjac_1382,
Cavia porcellus	ENSCPOG00000009263	1 retrocopy	retro_cpor_270,
Equus caballus	ENSECAG00000004183	1 retrocopy	retro_ecab_295,
Echinops telfairi	ENSETEG00000013626	1 retrocopy	retro_etel_757,
Felis catus	ENSFCAG00000004424	1 retrocopy	retro_fcat_201,
Homo sapiens	ENSG00000183513	1 retrocopy	retro_hsap_204,
Gorilla gorilla	ENSGGOG00000006019	1 retrocopy	retro_ggor_278,
Myotis lucifugus	ENSMLUG00000013167	2 retrocopies	retro_mluc_1336, retro_mluc_1760,
Monodelphis domestica	ENSMODG00000001197	1 retrocopy	retro_mdom_1413,
Nomascus leucogenys	ENSNLEG00000001998	1 retrocopy	retro_nleu_1854,
Ochotona princeps	ENSOPRG00000002972	3 retrocopies	retro_opri_1198, retro_opri_1203, retro_opri_391,
Pongo abelii	ENSPPYG00000012085	1 retrocopy	retro_pabe_435,
Pan troglodytes	ENSPTRG00000012267	1 retrocopy	retro_ptro_340 ,
Pteropus vampyrus	ENSPVAG00000001578	1 retrocopy	retro_pvam_460,
Sorex araneus	ENSSARG00000006275	1 retrocopy	retro_sara_61,