RetrogeneDB ID: retro_mmul_1917

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:146726109..146726749(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MEP50
• Ensembl ID: ENSMMUG00000003311
• Aliases: WDR77, MEP50
• Description: WD repeat domain 77 [Source:RefSeq peptide;Acc:NP_001182372]

Sequence

>retro_mmul_1917
ATGGCAACATTGTGTCTACCCTCAGCGTTCTTAGCTGTCAACGGCAGCAAAGGCTTCAGCATCAAGGATTGGGACCTTGC
TCAGCAGGCGGCACTGAATTCACACTGATCTCATGTTGGGCAGGACACCTGTACTCCTTCCTCTCTCCGCAAGGACTCTG
TGTTTCTTTCCTGCAGTGAGGACTGTAGAATTTTATTCTGGCATACTCTGTGTCCCAAGCCGGCGTCACAGGTGGGCTGC
AGTGTCTCTGGCTGCCTTCCCACCTCACTAGCTTGGCATCCTCAGCAAAGTGAAGTCTTCATCTTTGTGATGGGAATGAG
ACAGTCTCCCTTGTGGACTCCAAGAGAGGCAGAGGTGCTCTTGGCTCAGTTGTACGAGACCAATGTGTCATTGGGCTGGT
GTTTTCCTTGCACCGTGTTCCCTTCCTAGCCTCTCACAGAGAAGATGGCTCACTGGCTGTGCTGGACTCCAGCCTTTCTA
AGGCGTTTAGAAGCCAAGGCCACAGCTACTTTGCGAGAGATGCTGCTTGATCCCCATTCAGTCACTTTCTGCTTACCACA
ATGGGCCAGGACCATCAGTTCGTCTGCCACAAGTGTCCACAGAACCTCTCCCAGCCCCTGGACCTGAGAACGTTGCTGAG

Alignment

ORF - retro_mmul_1917 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.98 %
• Parental protein coverage: 62.87 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VSTVCVLSSGTQAVSGSKDFCIKVWDLAQQVVLNSYRAHAAQVTCVAASPHKDSVFLSCSEDNRILLWDT
          ..T.C.L.S...AV.GSK.F.IK.WDLAQQ..LNS...H..Q.TC...S..KDSVFLSCSED.RIL.W.T
Retrocopy MATLC-LPSAFLAVNGSKGFSIKDWDLAQQAALNSH*SHVGQDTCTPSSLRKDSVFLSCSEDCRILFWHT

Parental  RCPKPASQIGCSAPGYLPTSLAWHPQQSEVFVF-GDENGTVSLVDTKSTSCVLSSAVHSQCVTGLVFSPH
          .CPKPASQ.GCS..G.LPTSLAWHPQQSEVF.F..D.N.TVSLVD.K.....L.S.V..QCV.GLVFS.H
Retrocopy LCPKPASQVGCSVSGCLPTSLAWHPQQSEVFIF<CDGNETVSLVDSKRGRGALGSVVRDQCVIGLVFSLH

Parental  SVPFLASLSEDCSLAVLDSSLSEVFRSRAHRDFVRDATWSPLNHSLLTTVGWDHQVVHHIVP-TEPLPAP
          .VPFLAS..ED.SLAVLDSSLS..FRS..H..F.RDA..SP..H.LLTT.G.DHQ.V.H..P.TEPLPAP
Retrocopy RVPFLASHREDGSLAVLDSSLSKAFRSQGHSYFARDAA*SPFSHFLLTTMGQDHQFVCHKCP<TEPLPAP

Parental  GPASVTE
          GP..V.E
Retrocopy GPENVAE

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	21.40 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	26.73 RPM
SRP007412_cerebellum	0.06 RPM	20.21 RPM
SRP007412_heart	0.00 RPM	19.79 RPM
SRP007412_kidney	0.00 RPM	18.66 RPM
SRP007412_liver	0.00 RPM	12.43 RPM
SRP007412_testis	0.04 RPM	73.39 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1917 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1917 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1917 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2995
Pan troglodytes	retro_ptro_2026
Pongo abelii	retro_pabe_2482

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014102	1 retrocopy	retro_btau_1342,
Choloepus hoffmanni	ENSCHOG00000013829	1 retrocopy	retro_chof_2618,
Callithrix jacchus	ENSCJAG00000013344	2 retrocopies	retro_cjac_1166, retro_cjac_3063,
Dasypus novemcinctus	ENSDNOG00000006521	1 retrocopy	retro_dnov_695,
Homo sapiens	ENSG00000116455	1 retrocopy	retro_hsap_2995,
Gorilla gorilla	ENSGGOG00000005208	1 retrocopy	retro_ggor_2076,
Macaca mulatta	ENSMMUG00000003311	1 retrocopy	retro_mmul_1917 ,
Mus musculus	ENSMUSG00000000561	1 retrocopy	retro_mmus_1120,
Nomascus leucogenys	ENSNLEG00000003918	1 retrocopy	retro_nleu_746,
Oryctolagus cuniculus	ENSOCUG00000007801	1 retrocopy	retro_ocun_535,
Pongo abelii	ENSPPYG00000001033	1 retrocopy	retro_pabe_2482,
Pan troglodytes	ENSPTRG00000001098	1 retrocopy	retro_ptro_2026,
Tupaia belangeri	ENSTBEG00000010325	1 retrocopy	retro_tbel_2253,