RetrogeneDB ID: retro_mmul_653

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 10:86835138..86835569(-)
• Located in intron of: ENSMMUG00000002229

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2450
• Ensembl ID: ENSMMUG00000019023
• Aliases: COA1, C3H7orf44
• Description: cytochrome oxidase assembly 1 [Source:RefSeq peptide;Acc:NP_001252565]

Sequence

>retro_mmul_653
TGGCAAAAGTATCCAGGAAGCAGGATGCCAGTGCCTCAAGGAAAAAATGGTCCTTTTCGGCAATGTGTTCAGTACTGGGG
GCTTGGCCCTTGTGTATTACCTCATACAAAAGACTTTTCCAGGGCTTCGTGTTACCAGTTGGCATTGGAGCAGGTGCATA
GCCATCCCAAGGCACAGGGTGCTCTGGGCCCTCTTCTCAACATTCAGTGTCTCAAACTCACCAACAAGCACAACTTCGTG
GACATTGCTGATGCCAAGTTGAAGATTCCTAGCTCTGGATCCAAGTCAGAGAGCCGTCTCCACATCAGCTCATCCAGAAG
TGCACCTTTCAGAGGTGGCACCTTGATGAGGTCTTCCTAGAGCCCAAGGATTGCCAGCAGATTCCTATGTTCAAGCTCAG
TGGGGAGAATGGTGAAGAAGTGAAAAAGAAG

Alignment

ORF - retro_mmul_653 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.07 %
• Parental protein coverage: 99.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  WQKYPGSRQSIPLGIK-VLFSGVFGAGGFALVYYLIQKFH-SRSLYYKLAVEQLQSHPEAQEALGPPLNI
          WQKYPGSR...P.G...VLF..VF..GG.ALVYYLIQK...SR...Y.LA.EQ..SHP.AQ.ALGP.LNI
Retrocopy WQKYPGSRMPVPQGKN>VLFGNVFSTGGLALVYYLIQKTF<SRASCYQLALEQVHSHPKAQGALGPLLNI

Parental  HYLKLTDRENFVDIADAKLKIPVSGSKSEGLLYVHSSRGGP-FQRWHLDEVFLELKDGQQIPVFKLSGEN
          ..LKLT...NFVDIADAKLKIP.SGSKSE..L...SSR..P.FQRWHLDEVFLE.KD.QQIP.FKLSGEN
Retrocopy QCLKLTNKHNFVDIADAKLKIPSSGSKSESRLHISSSRSAP<FQRWHLDEVFLEPKDCQQIPMFKLSGEN

Parental  GDEVKKE
          G.EVKK.
Retrocopy GEEVKKK

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	0.00 RPM	10.42 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	12.30 RPM
SRP007412_cerebellum	0.52 RPM	10.27 RPM
SRP007412_heart	0.12 RPM	10.30 RPM
SRP007412_kidney	0.23 RPM	10.68 RPM
SRP007412_liver	0.16 RPM	8.71 RPM
SRP007412_testis	0.08 RPM	5.73 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_653 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_653 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_653 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009377	1 retrocopy	retro_amel_1871,
Canis familiaris	ENSCAFG00000031110	1 retrocopy	retro_cfam_2115,
Callithrix jacchus	ENSCJAG00000007826	1 retrocopy	retro_cjac_656,
Homo sapiens	ENSG00000106603	1 retrocopy	retro_hsap_2595,
Gorilla gorilla	ENSGGOG00000034928	1 retrocopy	retro_ggor_1624,
Macaca mulatta	ENSMMUG00000019023	1 retrocopy	retro_mmul_653 ,
Mustela putorius furo	ENSMPUG00000018149	1 retrocopy	retro_mputfur_1572,
Nomascus leucogenys	ENSNLEG00000003316	1 retrocopy	retro_nleu_1527,
Pongo abelii	ENSPPYG00000017606	1 retrocopy	retro_pabe_1914,
Pan troglodytes	ENSPTRG00000019125	1 retrocopy	retro_ptro_1520,