RetrogeneDB ID: retro_mmul_1968

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:109297187..109297382(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000003422
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: COX7AH
• Ensembl ID: ENSMMUG00000000250
• Aliases: COX7AH, COX7A1
• Description: cytochrome c oxidase subunit 7AH [Source:RefSeq peptide;Acc:NP_001035368]

Sequence

>retro_mmul_1968
AGAACCATAAGCACTACTTCCCACAGGCATTTTAAAAATAAAGTTCCAGAGAAACAAAAACTGTTCCAGGAGGATGATGG
AATTCCACTGTATCTAAAGGGTGGGATATTTCATGTCCTCCTGTATAGAGCCACCATGATTCTTACAGTTGGTGGAACAG
CATATGCCATGTATCAGCTGTCTGTGGCTGCATTT

Alignment

ORF - retro_mmul_1968 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.92 %
• Parental protein coverage: 82.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RSFSSTARNRFQNRVPEKQKLFQEDNDIPLYLKGGFVDNILYRVTMALGLGGSVYSLYCLGWASF
          R..S.T....F.N.VPEKQKLFQED..IPLYLKGG.....LYR.TM.L..GG..Y..Y.L..A.F
Retrocopy RTISTTSHRHFKNKVPEKQKLFQEDDGIPLYLKGGIFHVLLYRATMILTVGGTAYAMYQLSVAAF

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	0.56 RPM	2.47 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	5.71 RPM
SRP007412_cerebellum	0.90 RPM	2.58 RPM
SRP007412_heart	0.12 RPM	127.19 RPM
SRP007412_kidney	1.53 RPM	15.73 RPM
SRP007412_liver	0.28 RPM	31.59 RPM
SRP007412_testis	1.58 RPM	3.51 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1968 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1968 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1968 has 0 orthologous retrocopies within eutheria group .

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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,
Macaca mulatta	ENSMMUG00000016278	1 retrocopy	retro_mmul_110,
Monodelphis domestica	ENSMODG00000025577	1 retrocopy	retro_mdom_1288,
Pan troglodytes	ENSPTRG00000010888	1 retrocopy	retro_ptro_125,