RetrogeneDB ID: retro_mmul_1291

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 17:55282043..55282801(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RIOK3
• Ensembl ID: ENSMMUG00000021478
• Aliases: None
• Description: None

Sequence

>retro_mmul_1291
AATCTGGCAGGAGTAACATTGTCTAAGCCCAAGCCAGCAGTGGGCTGGGGGACCCAGTAAGTGTCCATGGGCTATCCTTC
AAATGACAACATCTTGTTCTTTGGCTGATACAATGAGTGAACAGTTGGTCAAAGAACTGCAGTTAGAGGTAGAAACTGTC
ACTTTTCCTCAAGTAGCTATTGCTAAAAGGCCATTTATTACTGGAGAAAACATTGACACTTCCAGTGACCTAATGTTGGC
TCAGATACTACAGATGGAATTTGGCAAAGAATATGATGCACAACTTAGGCATAAAGAAAAAAAGATTCAATGGAGATAAA
AAAAAAATGTCCATGTCCTTTGAAAACTATTGAAAAGTCCATCCTGATGAAGACAGTGATAGCTCTGAAGATGAGGCTGA
CTGCCAGGGTACTCATGATGATCTCTACTGACTAGCAAAACCAGTTCCCACTCCCAAAAAGGGTTTTATTGGAAAAGGAA
AGGGCATTACCACCAAACATCATGAAGTAGTATGTGGGAGAAAGAATCCAGCAAGAATGGAAAATCTTGCACCTGCATTT
CAGGTAGAAGACAGAATGGATTTAAAACTACCAAACAAAGTTTTTGAGGCTTCAAAACAACATACCTACTCAGAAGAACA
TCAAAGTGCCTTCCTCCACAAGAAAAAGGAGCACTCTACCAAAGAAAATGCAGTTGATCCTGAGACATGTTTTTTTATGT
ATGAAAAGGTCAACTCCAGAATGTTTGAGACAATCACT

Alignment

ORF - retro_mmul_1291 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.88 %
• Parental protein coverage: 93.36 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DLVGVASPEPGPAAAWG-PSKCPWAIPQNTISCSLADVMSEQLAKELQLEEEAAVFPEVAVAEGPFITGE
          .L.GV....P.PA..WG.PSKCPWAI.Q.T.SCSLAD.MSEQL.KELQLE.E...FP.VA.A..PFITGE
Retrocopy NLAGVTLSKPKPAVGWG>PSKCPWAILQMTTSCSLADTMSEQLVKELQLEVETVTFPQVAIAKRPFITGE

Parental  NIDTSSDLMLAQMLQMEYDREYDAQLRREEKK-FNGD-SKVSISFENYRKVHPYEDSDSSEDEVDWQDTR
          NIDTSSDLMLAQ.LQME...EYDAQLR..EKK.FNGD....S.SFENY.KVHP.EDSDSSEDE.D.Q.T.
Retrocopy NIDTSSDLMLAQILQMEFGKEYDAQLRHKEKK>FNGDXXXXSMSFENY*KVHPDEDSDSSEDEADCQGTH

Parental  DDPYRPAKPVPTPKKGFIGKGKDITTKHDEVVCGRKNTARMENFAPEFQVGDGIGMDLKLSNHVFNALKQ
          DD.Y..AKPVPTPKKGFIGKGK.ITTKH.EVVCGRKN.ARMEN.AP.FQV.D...MDLKL.N.VF.A.KQ
Retrocopy DDLY*LAKPVPTPKKGFIGKGKGITTKHHEVVCGRKNPARMENLAPAFQVED--RMDLKLPNKVFEASKQ

Parental  HAYSEERRSARLHEKKEHSTAEKAVDPKTRLLMYKMVNSGMLETIT
          H.YSEE..SA.LH.KKEHST.E.AVDP.T...MY..VNS.M.ETIT
Retrocopy HTYSEEHQSAFLHKKKEHSTKENAVDPETCFFMYEKVNSRMFETIT

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	9.30 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	9.28 RPM
SRP007412_cerebellum	0.00 RPM	11.88 RPM
SRP007412_heart	0.00 RPM	10.95 RPM
SRP007412_kidney	0.00 RPM	13.73 RPM
SRP007412_liver	0.00 RPM	12.03 RPM
SRP007412_testis	0.04 RPM	44.86 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1291 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1291 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1291 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_1011

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008343	1 retrocopy	retro_chof_1788,
Callithrix jacchus	ENSCJAG00000020556	1 retrocopy	retro_cjac_2617,
Echinops telfairi	ENSETEG00000003689	1 retrocopy	retro_etel_2181,
Macropus eugenii	ENSMEUG00000006292	1 retrocopy	retro_meug_1278,
Macaca mulatta	ENSMMUG00000021478	1 retrocopy	retro_mmul_1291 ,
Ochotona princeps	ENSOPRG00000004803	2 retrocopies	retro_opri_1034, retro_opri_946,
Pongo abelii	ENSPPYG00000009062	1 retrocopy	retro_pabe_1011,