RetrogeneDB ID: retro_mmul_1728

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:140580195..140580900(-)
• Located in intron of: ENSMMUG00000012435

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_1728
GTTTTCACTACCGGCACAATCTCTCGGAGCCATGTGGAGTATGCTCCTGTAGCAGATCACACTGTTTACAAACTGCCTGA
AAAACTGGACTTTTAAACAAAATGCTGCCATTGGTATCCCATATGTTACTGCATATAGAGCTCTGATTCACAGTGTCTGT
ATGAAATCTGGAGACTGGGTTCTGGTTCATGGGGATAGTGGAGTTGCTGGAGTAGCAACATGCCAAATGGTTAGAGTTTA
TGCCTTAAAGGTTTGGGGCCCAGTTGGTATTGAGAGGGACAAAATGCTTTTGCAAAATGGAGCCCACAAAGTGTTTAATT
ACGAAGAAGTTAATTATGTTGACAAAATTAAGAAATGTGTGGTAAGAAAGGAACTGATGTGATTATTGAAATAATAGCTA
ATATAAATCTTAGTAAAGCTGTGAATTGTTTGTCATATGGAAGATGAGTAATAGGTGTTGGCAACAGTGGTGCTATTGAA
ATAAACCCATGGGACACTATGGCAAAAAAGTCTAGTAAAATTGTCGTTACTCTATTTTTCCCCAACCAAGGAGGAATCTC
AGCAATTTGCAGCAGCCTATCAAGCTGGAATGGAAATTGGTTGGCTGAAACTTGTAATAGGTTCTCACTATATGTTGGAG
AGGCCGCCCAGCCTCACAAAAATCTCTCTTACGGCAACGGGGCTACTGTAAAAATGATTCTTCTC

Alignment

ORF - retro_mmul_1728 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 71.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VFTSSTISGGYAEYALAADHTVYKLPEKLDF-KQGAAIGIPYFTACRALIHSARVKAGESVLVHGASGGV
          VFT..TIS....EYA..ADHTVYKLPEKLDF.KQ.AAIGIPY.TA.RALIHS...K.G..VLVHG.SG..
Retrocopy VFTTGTISRSHVEYAPVADHTVYKLPEKLDF>KQNAAIGIPYVTAYRALIHSVCMKSGDWVLVHGDSGVA

Parental  GLAACQIARAYGLKVLGTAGTEEGQKIVLQNGAHEVFNHREVNYIDKIKKYV-GEKGIDVIIEMLANVNL
          G.A.CQ..R.Y.LKV.G..G.E...K..LQNGAH.VFN..EVNY.DKIKK.V.G.KG.DVIIE..AN.NL
Retrocopy GVATCQMVRVYALKVWGPVGIER-DKMLLQNGAHKVFNYEEVNYVDKIKKCV<GKKGTDVIIEIIANINL

Parental  SKDLSLLSHGGRVIVVGNRGTIEINPRDTMAKESSIIGVTL-FSSTKEEFQQYAAALQAGMEIGWLKPVI
          SK....LS.G..VI.VGN.G.IEINP.DTMAK.SS.I.VTL.FS.TKEE.QQ.AAA.QAGMEIGWLK.VI
Retrocopy SKAVNCLSYGR*VIGVGNSGAIEINPWDTMAKKSSKIVVTL>FSPTKEESQQFAAAYQAGMEIGWLKLVI

Parental  GSQYPLEK-VAEAHKDIIHGSGATGKMILL
          GS.Y.LE...A..HK....G.GAT.KMILL
Retrocopy GSHYMLER<AAQPHKNLSYGNGATVKMILL

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	0.11 RPM	9.41 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	11.03 RPM
SRP007412_cerebellum	0.13 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	0.15 RPM	4.56 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1728 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1728 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1728 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3884
Pongo abelii	retro_pabe_3165

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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,