RetrogeneDB ID: retro_pabe_435

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:118032311..118032533(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COA5
• Ensembl ID: ENSPPYG00000012085
• Aliases: COA5, C2orf64
• Description: Cytochrome c oxidase assembly factor 5 [Source:UniProtKB/Swiss-Prot;Acc:Q5RFJ0]

Sequence

>retro_pabe_435
ATGCCCCAGTATTACAAGGACAAGCTAGAGGGCTGCGTGTGCGCGGGTGTGAAGGAGGACCTGGGCGTGTGTCTGTTGCA
GTCCAACTGTGTGGTCCAGGAAGGAAAATCCCCTCTGCAGTGTTTGAAGGAAGGATACTGCAAAGCTTTGAAATACTCAT
TTTTTGAGTATAAAAGATCAGTGTTGGATACTAGGTCAAGAATCAGAGGAAGAAAGGGATAT

Alignment

ORF - retro_pabe_435 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.32 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPKYYEDKPQGGACGGLKEDLGACLLESDCVVQEGKSPRQCLKEGYCNSLKYAFFECKRSVLDNRARFRG
          MP.YY.DK..G..C.G.KEDLG.CLL.S.CVVQEGKSP.QCLKEGYC..LKY.FFE.KRSVLD.R.R.RG
Retrocopy MPQYYKDKLEGCVCAGVKEDLGVCLLQSNCVVQEGKSPLQCLKEGYCKALKYSFFEYKRSVLDTRSRIRG

Parental  RKGY
          RKGY
Retrocopy RKGY

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	20.84 RPM
SRP007412_cerebellum	0.00 RPM	26.39 RPM
SRP007412_heart	0.00 RPM	12.19 RPM
SRP007412_kidney	0.03 RPM	23.97 RPM
SRP007412_liver	0.00 RPM	17.99 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_435 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_435 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_435 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_204
Pan troglodytes	retro_ptro_340
Gorilla gorilla	retro_ggor_278

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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,