RetrogeneDB ID: retro_mmul_566

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:185418475..185419130(-)
• Located in intron of: ENSMMUG00000013882

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2373
• Ensembl ID: ENSMMUG00000011125
• Aliases: None
• Description: 26S proteasome non-ATPase regulatory subunit 7 [Source:RefSeq peptide;Acc:NP_001244743]

Sequence

>retro_mmul_566
CTATATCAAGATTATTTGGAAAACATGTATGGAATGTTTAAGAAGGTAAATGCCAGAGAAAGAATATTTGAGTGGCACCA
CACAGGCCATAAACTTTACAAGAATGCCATTGCCATCAGTGAAGTAATGAAATGATACTGCCCTAACTCTTGTTTTGGTC
ATTATTGATGTGAAACCCAAGGACCTGAGCCTGCCAACAGAAGCATATATTTCAGTGGAAGAAGTTCATGTGGATAGAAC
TACAACCATAAAAACATTTGAGCTTGTGACCAGTGAAACCAGAGCAGAGGAAGCTGAGGAAGTCAGAGTCAAACGCTTGT
TATGAGACATCAAAGACACTACCGTGGGCACTCTTTCCCAGCAGATTATAAACCAAGTCTCTGCATGGCTTGAAGGGACT
GAACTCCATGCTTCTGGATATCAGGAGCTACCAGGTAAAAGTAGTGACAGGCAGGCTACCCATAGACCATCAGATCATCC
ACCTGCTGTAGGATGTCTTCAGCCTGCTGCCAGATGTCAGCCCTGATGAGTTTGTCAAGGCCTTTCACCTGAAGACCGAC
AACCAAATGGAGGTGATGTACGTGGCCTTGCTCATCTGTTTTTGGCTGCCCTGCACAGCCTTATCAACAACAAGATTGCC
AACCAGGATGCAGAG

Alignment

ORF - retro_mmul_566 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.21 %
• Parental protein coverage: 67.39 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LDHDYLENMYGMFKKVNARERIVGWYHTGPKLHKNDIAINELMKRYCPNS-VLVIIDVKPKDLGLPTEAY
          L..DYLENMYGMFKKVNARERI..W.HTG.KL.KN.IAI.E.MK.YCPNS.VLVIIDVKPKDL.LPTEAY
Retrocopy LYQDYLENMYGMFKKVNARERIFEWHHTGHKLYKNAIAISEVMK*YCPNS>VLVIIDVKPKDLSLPTEAY

Parental  ISVEEVHDDGTPTSKTFEHVTSEIGAEEAEEVGVEHLLRDIKDTTVGTLSQRITNQVHG-LKG-LNSKLL
          ISVEEVH.D.T.T.KTFE.VTSE..AEEAEEV.V..LL.DIKDTTVGTLSQ.I.NQV...L.G.LNS.LL
Retrocopy ISVEEVHVDRTTTIKTFELVTSETRAEEAEEVRVKRLL*DIKDTTVGTLSQQIINQVSAWLEG>LNSMLL

Parental  DIRSYLEKVATGKLPINHQIIYQLQDVFNLLPDVSLQEFVKAFYLKTNDQMVVVYLASLI-RSVVALHNL
          DIRSY..KV.TG.LPI.HQII..L.DVF.LLPDVS..EFVKAF.LKT..QM.V.Y.A.LI.....ALH.L
Retrocopy DIRSYQVKVVTGRLPIDHQIIHLL*DVFSLLPDVSPDEFVKAFHLKTDNQMEVMYVALLI<LFLAALHSL

Parental  INNKIANRDAE
          INNKIAN.DAE
Retrocopy INNKIANQDAE

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	37.42 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	40.62 RPM
SRP007412_cerebellum	0.06 RPM	31.00 RPM
SRP007412_heart	0.24 RPM	26.68 RPM
SRP007412_kidney	0.12 RPM	28.87 RPM
SRP007412_liver	0.32 RPM	26.56 RPM
SRP007412_testis	0.15 RPM	46.55 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_566 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_566 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_566 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015129	2 retrocopies	retro_cjac_1520, retro_cjac_2910,
Homo sapiens	ENSG00000103035	2 retrocopies	retro_hsap_1781, retro_hsap_234,
Gorilla gorilla	ENSGGOG00000009774	1 retrocopy	retro_ggor_2235,
Myotis lucifugus	ENSMLUG00000005416	1 retrocopy	retro_mluc_505,
Macaca mulatta	ENSMMUG00000011125	4 retrocopies	retro_mmul_1242, retro_mmul_372, retro_mmul_417, retro_mmul_566 ,
Macaca mulatta	ENSMMUG00000013440	1 retrocopy	retro_mmul_387,
Macaca mulatta	ENSMMUG00000015010	1 retrocopy	retro_mmul_412,
Nomascus leucogenys	ENSNLEG00000005608	1 retrocopy	retro_nleu_1310,
Otolemur garnettii	ENSOGAG00000014868	1 retrocopy	retro_ogar_388,
Procavia capensis	ENSPCAG00000014356	1 retrocopy	retro_pcap_399,
Pongo abelii	ENSPPYG00000025918	1 retrocopy	retro_pabe_418,
Pan troglodytes	ENSPTRG00000008343	2 retrocopies	retro_ptro_1192, retro_ptro_205,
Tupaia belangeri	ENSTBEG00000016950	1 retrocopy	retro_tbel_4135,