RetrogeneDB ID: retro_mmul_2067

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:18943097..18943338(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4310
• Ensembl ID: ENSMMUG00000007202
• Aliases: None
• Description: COX19 cytochrome c oxidase assembly homolog [Source:RefSeq peptide;Acc:NP_001244763]

Sequence

>retro_mmul_2067
ATGTCCACAGCCATAAATCTTAGGACCAAGACCTTCCAGGCATGGCCCCTGGGCACGGGCAGTTTCCCACTGAATCTTTT
CAATGAATATGAAAGCTTAAAGAGAAATTATGAAGTGTCTTCATGATAATAAATGTGAAAATATTTTGCAGAAGAATAAA
TCAAAAGCATATTCAGAATGCAGAATGGAGAGACAATGAAAGGCATAAAAACCAACAGGACTACTGGGATTTGGAGGTTT
G

Alignment

ORF - retro_mmul_2067 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.01 %
• Parental protein coverage: 90.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSTAMNFGTKSFQPRPPEKGSFPLDHLGECKSF-KDKF-MKCLYDNHFENALCRNESKEYLECRMERKLM
          MSTA.N..TK.FQ..P...GSFPL....E..S..K.K..MKCL.DN..EN.L..N.SK.Y.ECRMER...
Retrocopy MSTAINLRTKTFQAWPLGTGSFPLNLFNEYESL<KEKL<MKCLHDNKCENILQKNKSKAYSECRMERQ*K

Parental  LQEPLEKLGFGDL
          ...P...LGFG.L
Retrocopy A*KPTGLLGFGGL

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	3.92 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	5.39 RPM
SRP007412_cerebellum	0.00 RPM	4.46 RPM
SRP007412_heart	0.00 RPM	9.07 RPM
SRP007412_kidney	0.00 RPM	11.27 RPM
SRP007412_liver	0.00 RPM	2.45 RPM
SRP007412_testis	0.00 RPM	9.95 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2067 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2067 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2067 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3300
Pan troglodytes	retro_ptro_2168
Gorilla gorilla	retro_ggor_1312

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015253	1 retrocopy	retro_btau_671,
Homo sapiens	ENSG00000240230	1 retrocopy	retro_hsap_3300,
Gorilla gorilla	ENSGGOG00000034907	1 retrocopy	retro_ggor_1312,
Macaca mulatta	ENSMMUG00000007202	1 retrocopy	retro_mmul_2067 ,
Pan troglodytes	ENSPTRG00000041621	1 retrocopy	retro_ptro_2168,
Pteropus vampyrus	ENSPVAG00000002192	1 retrocopy	retro_pvam_409,
Tursiops truncatus	ENSTTRG00000011489	2 retrocopies	retro_ttru_1140, retro_ttru_1270,