RetrogeneDB ID: retro_mmul_2434

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 9:24851774..24852230(-)
• Located in intron of: ENSMMUG00000016123

Retrocopy information

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

Parental gene information

• Parental gene symbol: COQ10B
• Ensembl ID: ENSMMUG00000010488
• Aliases: None
• Description: coenzyme Q-binding protein COQ10 homolog B, mitochondrial [Source:RefSeq peptide;Acc:NP_001182715]

Sequence

>retro_mmul_2434
AGAAGGGTGGTCTCGGGATGCCATCCAAAGTTGATGACAGTGGTCGGAGCCCTGGCTCCAGCATAGGGGCCTGAGCAGAA
CATCAGATATTTAGCTTACTGTGGTATACTGATGAGCAGAGCTCTTCCGCTACATACGTCAATTTTGATTAAGGAGATAT
GTGCAGTAACTTTCTTCAAAATCGCTGCACCATTGATAAACAAAAGAAAATATTCAGAGAGGAGGATTTTAGGCTATTTA
ATGCAGAAAGTATATGATATTATATTGGGAATGGAGGATTGTAAGCATTTCATTCCTTGGTGCAAAAAATCTGATATAAT
ATCAAAGAGATCTGGATATTATAAAACACTATTAGAAACTGAGTTTCCACCAGTGTTGGATTGATATTCAGCAATAACCT
TGGCAAAACCTCATTTGGTAAAGGTATCCTGTACTGATGGGAGACTTTTCAAGCAT

Alignment

ORF - retro_mmul_2434 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 63.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RRVFSGCLPKSATAACAPARALAPVRNGRYLASCGILMSRTLPRHTSILPKEICVRTFFKITAPLINKRK
          RRV.SGC.PK..T...A.A.A..P..N.RYLA.CGILMSR.LP.HTSIL.KEIC..TFFKI.APLINKRK
Retrocopy RRVVSGCHPKLMTVVGALAPA*GPEQNIRYLAYCGILMSRALPLHTSILIKEICAVTFFKIAAPLINKRK

Parental  EYSERRILGYSMQEMYDVVSGVEDYKHFVPWCKKSDVISKRSGYCKTRLEIGFPPVLERYTSVVTLVKPH
          .YSERRILGY.MQ..YD...G.ED.KHF.PWCKKSD.ISKRSGY.KT.LE..FPPVL..Y.S..TL.KPH
Retrocopy -YSERRILGYLMQKVYDIILGMEDCKHFIPWCKKSDIISKRSGYYKTLLETEFPPVLD*Y-SAITLAKPH

Parental  LVKASCTDGRLFNH
          LVK.SCTDGRLF.H
Retrocopy LVKVSCTDGRLFKH

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	8.96 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	6.43 RPM
SRP007412_cerebellum	0.13 RPM	7.56 RPM
SRP007412_heart	0.00 RPM	6.07 RPM
SRP007412_kidney	0.12 RPM	10.21 RPM
SRP007412_liver	0.04 RPM	2.26 RPM
SRP007412_testis	0.00 RPM	17.30 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2434 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2434 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2434 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_569
Pongo abelii	retro_pabe_576

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004659	2 retrocopies	retro_btau_1595, retro_btau_1832,
Choloepus hoffmanni	ENSCHOG00000005807	1 retrocopy	retro_chof_1504,
Callithrix jacchus	ENSCJAG00000003971	1 retrocopy	retro_cjac_1836,
Dasypus novemcinctus	ENSDNOG00000003229	2 retrocopies	retro_dnov_1571, retro_dnov_2203,
Dipodomys ordii	ENSDORG00000004090	1 retrocopy	retro_dord_508,
Erinaceus europaeus	ENSEEUG00000001626	1 retrocopy	retro_eeur_401,
Felis catus	ENSFCAG00000022385	1 retrocopy	retro_fcat_1487,
Homo sapiens	ENSG00000115520	1 retrocopy	retro_hsap_3349,
Gorilla gorilla	ENSGGOG00000023373	2 retrocopies	retro_ggor_2270, retro_ggor_569,
Myotis lucifugus	ENSMLUG00000000865	1 retrocopy	retro_mluc_1236,
Macaca mulatta	ENSMMUG00000010488	1 retrocopy	retro_mmul_2434 ,
Monodelphis domestica	ENSMODG00000012281	1 retrocopy	retro_mdom_600,
Mus musculus	ENSMUSG00000025981	1 retrocopy	retro_mmus_3224,
Nomascus leucogenys	ENSNLEG00000006871	1 retrocopy	retro_nleu_1172,
Ochotona princeps	ENSOPRG00000010091	3 retrocopies	retro_opri_1020, retro_opri_173, retro_opri_664,
Pongo abelii	ENSPPYG00000013045	2 retrocopies	retro_pabe_2758, retro_pabe_576,
Pan troglodytes	ENSPTRG00000012772	1 retrocopy	retro_ptro_2137,
Rattus norvegicus	ENSRNOG00000014456	1 retrocopy	retro_rnor_1620,
Tarsius syrichta	ENSTSYG00000012642	2 retrocopies	retro_tsyr_1213, retro_tsyr_1666,