RetrogeneDB ID: retro_mmul_1141

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:34613262..34613742(+)
• Located in intron of: ENSMMUG00000016675

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP3R1
• Ensembl ID: ENSMMUG00000017460
• Aliases: None
• Description: WD repeat-containing protein 92 [Source:RefSeq peptide;Acc:NP_001248066]

Sequence

>retro_mmul_1141
ATGTGCGCCCACTTTGACAATGATGAAATTAAAAGGCTGGGCAGGAGGTTTCGGAAGTTGGACTTGGACAAATCAGGCTC
TCTGAGCGTGGAGGAGTTCATGTCCCTGCCGGAGCTGCGCCACAACCCGTTGGTGCGGCGAGTGATCGACGTCTTCGACA
CCAACGGCGATGGAGAAGTGGACTTCAAGGAATTCATCCTGGGGACCTCTCAGTTCAGCGTCAAGGGCGACGAGGAGCAG
AAGTTGAGGTTTGCGTTTAGCATTTACGACATGGATAAAGATGGCTACATTTCCAACGGGGAGCTCTTCCAGGTGCTGAA
GATGATGGTGGGCAACAACCTGCCGGACTGGCAGCTCCAGCAGCTGGTCGACAAAACCATCCTCATCCTGGACAAGGATG
GCGATGGGAAGATATCCTTTGAGGAATTCAGTGCTGTGGTCAGAGACCTGGAGATCCACAAGAAGCTGGTCCTCATCGTG

Alignment

ORF - retro_mmul_1141 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.88 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MCSHFDADEIKRLGKRFKKLDLDNSGSLSVEEFMSLPELQQNPLVQRVIDIFDTDGNGEVDFKEFIEGVS
          MC.HFD.DEIKRLG.RF.KLDLD.SGSLSVEEFMSLPEL..NPLV.RVID.FDT.G.GEVDFKEFI.G.S
Retrocopy MCAHFDNDEIKRLGRRFRKLDLDKSGSLSVEEFMSLPELRHNPLVRRVIDVFDTNGDGEVDFKEFILGTS

Parental  QFSVKGDKEQKLRFAFRIYDMDKDGYISNGELFQVLKMMVGNNLKDTQLQQIVDKTIINADKDGDGRISF
          QFSVKGD.EQKLRFAF.IYDMDKDGYISNGELFQVLKMMVGNNL.D.QLQQ.VDKTI...DKDGDG.ISF
Retrocopy QFSVKGDEEQKLRFAFSIYDMDKDGYISNGELFQVLKMMVGNNLPDWQLQQLVDKTILILDKDGDGKISF

Parental  EEFCAVVGGLDIHKKMVVDV
          EEF.AVV..L.IHKK.V..V
Retrocopy EEFSAVVRDLEIHKKLVLIV

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	0.22 RPM	140.40 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	70.68 RPM
SRP007412_cerebellum	0.13 RPM	81.95 RPM
SRP007412_heart	0.00 RPM	12.72 RPM
SRP007412_kidney	0.12 RPM	15.61 RPM
SRP007412_liver	0.00 RPM	8.75 RPM
SRP007412_testis	153.11 RPM	18.70 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1141 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1141 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1141 has 7 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3
Pan troglodytes	retro_ptro_2909
Callithrix jacchus	retro_cjac_624
Oryctolagus cuniculus	retro_ocun_272
Bos taurus	retro_btau_1660
Sus scrofa	retro_sscr_86
Equus caballus	retro_ecab_651

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010619	1 retrocopy	retro_btau_1660,
Callithrix jacchus	ENSCJAG00000006498	1 retrocopy	retro_cjac_624,
Dipodomys ordii	ENSDORG00000019760	1 retrocopy	retro_dord_404,
Equus caballus	ENSECAG00000009627	1 retrocopy	retro_ecab_651,
Felis catus	ENSFCAG00000028482	1 retrocopy	retro_fcat_1639,
Homo sapiens	ENSG00000221823	1 retrocopy	retro_hsap_3,
Loxodonta africana	ENSLAFG00000022682	1 retrocopy	retro_lafr_1014,
Macaca mulatta	ENSMMUG00000017092	2 retrocopies	retro_mmul_1809, retro_mmul_2088,
Macaca mulatta	ENSMMUG00000017460	1 retrocopy	retro_mmul_1141 ,
Mustela putorius furo	ENSMPUG00000006250	1 retrocopy	retro_mputfur_537,
Nomascus leucogenys	ENSNLEG00000026538	1 retrocopy	retro_nleu_1049,
Oryctolagus cuniculus	ENSOCUG00000027562	1 retrocopy	retro_ocun_272,
Otolemur garnettii	ENSOGAG00000034876	1 retrocopy	retro_ogar_1011,
Pan troglodytes	ENSPTRG00000041941	1 retrocopy	retro_ptro_2909,
Rattus norvegicus	ENSRNOG00000043210	1 retrocopy	retro_rnor_1932,
Sus scrofa	ENSSSCG00000022362	1 retrocopy	retro_sscr_86,
Ictidomys tridecemlineatus	ENSSTOG00000025985	1 retrocopy	retro_itri_1569,
Tarsius syrichta	ENSTSYG00000019531	2 retrocopies	retro_tsyr_326, retro_tsyr_41,
Tursiops truncatus	ENSTTRG00000021395	1 retrocopy	retro_ttru_382,
Vicugna pacos	ENSVPAG00000015522	1 retrocopy	retro_vpac_3,
Drosophila melanogaster	FBgn0015614	1 retrocopy	retro_dmel_53,