RetrogeneDB ID: retro_mmul_1026

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 13:54291109..54291639(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2248
• Ensembl ID: ENSMMUG00000014593
• Aliases: None
• Description: quinone oxidoreductase [Source:RefSeq peptide;Acc:NP_001252740]

Sequence

>retro_mmul_1026
GAGGGTGTTCTGGTTCACGGGGCGACCGGAGAAGTTGGATTAACAGCATGCCAAATTACTAGAGTTTATGGCTTAAAGGT
TTTGGGCACTGCTGGTACTGAGGAAGGACAAAAGGTGGTTTTGCAAAATGGAATCCATTAAGTGTTCAATCACAGAGAAA
TTAATTATACTGATAAAATTAAGAAATATGTTGGTGAGAAAGGAATTGATGTAATTATTGAAATGTTAGCTAATGTAAAT
CTTAGTAAAGATTTGAGTCTTCTGTCACATAGAAGATGAGTGATAGTTGTTGGCAACAGAGTACTACTGAAATAAACCCA
CGGGACACCATGGCAAAGGAGTCGGGTATAATTGGAGTTACTCTCTTTTCCTCAACCAAGGAGGAATTTCAGCAATATGC
AGCCGCCCTTCAAGCTGGAATGGAAATTGGTTGGTTGAAACCTGTAATAGGTTCTCAATATCCACTGGAGAAGGTGGCCC
AGGCTCTAGAAACTACCATTCACGGCAGTGGGGCTACTGGAAAACGATTA

Alignment

ORF - retro_mmul_1026 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.96 %
• Parental protein coverage: 53.8 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ESVLVHGASGGVGLAACQIARAYGLKVLGTAGTEEGQKIVLQNGAHEVFNHREVNYIDKIKKYVGEKGID
          E.VLVHGA.G.VGL.ACQI.R.YGLKVLGTAGTEEGQK.VLQNG.H.VFNHRE.NY.DKIKKYVGEKGID
Retrocopy EGVLVHGATGEVGLTACQITRVYGLKVLGTAGTEEGQKVVLQNGIH*VFNHREINYTDKIKKYVGEKGID

Parental  VIIEMLANVNLSKDLSLLSHGGRVIVVGNR-GTIEINPRDTMAKESSIIGVTLFSSTKEEFQQYAAALQA
          VIIEMLANVNLSKDLSLLSH...VIVVGNR..T.EINPRDTMAKES.IIGVTLFSSTKEEFQQYAAALQA
Retrocopy VIIEMLANVNLSKDLSLLSHRR*VIVVGNR<STTEINPRDTMAKESGIIGVTLFSSTKEEFQQYAAALQA

Parental  GMEIGWLKPVIGSQYPLEKVAEAHKDIIHGSGATGKMI
          GMEIGWLKPVIGSQYPLEKVA.A....IHGSGATGK..
Retrocopy GMEIGWLKPVIGSQYPLEKVAQALETTIHGSGATGKRL

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	9.41 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	11.03 RPM
SRP007412_cerebellum	0.00 RPM	13.37 RPM
SRP007412_heart	0.00 RPM	29.62 RPM
SRP007412_kidney	0.00 RPM	164.43 RPM
SRP007412_liver	0.04 RPM	91.12 RPM
SRP007412_testis	0.08 RPM	4.56 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1026 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1026 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1026 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003162	1 retrocopy	retro_btau_1433,
Canis familiaris	ENSCAFG00000020404	1 retrocopy	retro_cfam_870,
Choloepus hoffmanni	ENSCHOG00000005167	1 retrocopy	retro_chof_1772,
Felis catus	ENSFCAG00000030626	1 retrocopy	retro_fcat_1907,
Homo sapiens	ENSG00000116791	1 retrocopy	retro_hsap_3884,
Loxodonta africana	ENSLAFG00000011371	1 retrocopy	retro_lafr_527,
Macaca mulatta	ENSMMUG00000014593	2 retrocopies	retro_mmul_1026 , retro_mmul_1728,
Mustela putorius furo	ENSMPUG00000010969	1 retrocopy	retro_mputfur_119,
Mus musculus	ENSMUSG00000028199	1 retrocopy	retro_mmus_1314,
Nomascus leucogenys	ENSNLEG00000009543	2 retrocopies	retro_nleu_1890, retro_nleu_3115,
Otolemur garnettii	ENSOGAG00000011586	1 retrocopy	retro_ogar_179,
Pongo abelii	ENSPPYG00000001235	2 retrocopies	retro_pabe_1909, retro_pabe_3165,
Pan troglodytes	ENSPTRG00000000865	1 retrocopy	retro_ptro_1598,
Tupaia belangeri	ENSTBEG00000016750	3 retrocopies	retro_tbel_1665, retro_tbel_2353, retro_tbel_3800,
Tarsius syrichta	ENSTSYG00000004193	2 retrocopies	retro_tsyr_1218, retro_tsyr_1884,
Tursiops truncatus	ENSTTRG00000010471	2 retrocopies	retro_ttru_555, retro_ttru_958,