RetrogeneDB ID: retro_ptro_575

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:111681692..111681989(+)
• Located in intron of: ENSPTRG00000004297

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX7A2L
• Ensembl ID: ENSPTRG00000011865
• Aliases: None
• Description: cytochrome c oxidase subunit VIIa polypeptide 2 like [Source:HGNC Symbol;Acc:2289]

Sequence

>retro_ptro_575
ATGTACTACAAATTTAGTGGCTTCACGTTCGAGTTGGTGGGAGCATGGACTTCAGAGGCCTATAGCCCATAAGGATTAAT
GCCTGTGGTTTCCACAGAAGCACCACCTATCATATTTGCCATACCAACTAAGCTGACCTCTGATTCCACTGCATATAATT
TTGCTAGGAAAAACAAAGTTCCAGAGCTGCAGAAGTTTCTCCAGAAAGCTGATGATGTGCCCATCCACCTGAAATGAGGC
TTCCCTGACCAAATGCTATACTGGACCACCATGGTGCTGACTGTGGGTGGGATACTG

Alignment

ORF - retro_ptro_575 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.79 %
• Parental protein coverage: 86.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MYYKFSGFTQKLAGAWASEAYSPQGLKPVVSTEAPPIIFATPTKLTSDSTVYDYAGKNKVPELQKFFQKA
          MYYKFSGFT..L.GAW.SEAYSP.GL.PVVSTEAPPIIFA.PTKLTSDST.Y..A.KNKVPELQKF.QKA
Retrocopy MYYKFSGFTFELVGAWTSEAYSP*GLMPVVSTEAPPIIFAIPTKLTSDSTAYNFARKNKVPELQKFLQKA

Parental  DGVPVYLKRGLPDQMLYRTTMALTVGGTI
          D.VP..LK.G.PDQMLY.TTM.LTVGG..
Retrocopy DDVPIHLK*GFPDQMLYWTTMVLTVGGIL

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	0.04 RPM	44.92 RPM
SRP007412_cerebellum	0.04 RPM	34.06 RPM
SRP007412_heart	0.06 RPM	47.07 RPM
SRP007412_kidney	0.03 RPM	72.99 RPM
SRP007412_liver	0.00 RPM	32.73 RPM
SRP007412_testis	0.00 RPM	34.67 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_575 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_575 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_575 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_825
Gorilla gorilla	retro_ggor_674
Pongo abelii	retro_pabe_737

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000011940	1 retrocopy	retro_etel_650,
Homo sapiens	ENSG00000115944	1 retrocopy	retro_hsap_825,
Gorilla gorilla	ENSGGOG00000010739	1 retrocopy	retro_ggor_674,
Macaca mulatta	ENSMMUG00000016278	1 retrocopy	retro_mmul_110,
Mustela putorius furo	ENSMPUG00000008875	1 retrocopy	retro_mputfur_97,
Mus musculus	ENSMUSG00000024248	2 retrocopies	retro_mmus_32, retro_mmus_926,
Nomascus leucogenys	ENSNLEG00000016666	1 retrocopy	retro_nleu_258,
Oryctolagus cuniculus	ENSOCUG00000027189	3 retrocopies	retro_ocun_1617, retro_ocun_1781, retro_ocun_28,
Otolemur garnettii	ENSOGAG00000016029	1 retrocopy	retro_ogar_114,
Pan troglodytes	ENSPTRG00000010888	1 retrocopy	retro_ptro_125,
Pan troglodytes	ENSPTRG00000011865	1 retrocopy	retro_ptro_575 ,
Ictidomys tridecemlineatus	ENSSTOG00000012922	1 retrocopy	retro_itri_21,