RetrogeneDB ID: retro_mmul_1224

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 16:30792479..30793280(+)
• Located in intron of: ENSMMUG00000005550

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP4R2
• Ensembl ID: ENSMMUG00000016959
• Aliases: None
• Description: None

Sequence

>retro_mmul_1224
GTTTGTCACGTAGCCAAGACTGGAAAAACAATGATTTAGGGGTCCCAATTTAAAGGCTATTTTATTTTCAAACTGGAGAA
AGTGATGGATGATTTCAGAACTTCAGCTCCTGAGCCAAGAGGTCCTCCCAACCCTAATGTCCAATATATTGCCTTTGACA
AAATGAAGGAAAGAATACTGAAAATTGTCGCTGGATTTAATGGTATCCCTTTTACTGTTCAGCGACTGTGTGAATTGTTA
ACAGATCCAAGGAGAAACTATACAGGAACAGACAAATTTCTTAGAGGAGTAGAAAAGAATGTGATGGTTATTAGCTGTGT
TTATCCTTCTTCAGAGAAAAACAATTCCAATAGTTTAAATCGAATGAATGGTGTTATGTTTCCTGGAAATTCACCAAGCT
ATACTGAGAGGTCTAATATAAATGGGCCTGGGACACCCAGGCCACTTAATCGATCAAAGATTTCTTTGTCAGCCCCCGTG
ACAAGAAATGGCTTGCCTGAGAGCACAGACAGCAAAGAGGCAAGTTTGCAGCAAAATGAGGAGAAAAATCACAGTGACTC
TTTGACATCTGAATCAGAAGTTTCCTCGGTGAGCCCTTTGAAAAATAAACATCCAGATGAATATGCTGTGGAAGCTGAGG
GGCATAAGGTAAAAAGACTCAAGTTTGACAAAGAAGGTGAAGTCGGAGAAACAGCCAGTCAAACGACTTCCAGCGAAATT
TCTTCAGCTATGGTAGAAAAAACAGAAGCATCATCATCTCAGGATAAAGACAAAGAAAGCCCTTGTACCCAGCAGCACTG
T

Alignment

ORF - retro_mmul_1224 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.55 %
• Parental protein coverage: 59.56 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LCHVAKTGETMIQWSQFKGYFIFKLEKVMDDFRTSAPEPRGPPNPNVEYIPFDEMKERILKIVTGFNGIP
          .CHVAKTG.TMI..SQFKGYFIFKLEKVMDDFRTSAPEPRGPPNPNV.YI.FD.MKERILKIV.GFNGIP
Retrocopy VCHVAKTGKTMI*GSQFKGYFIFKLEKVMDDFRTSAPEPRGPPNPNVQYIAFDKMKERILKIVAGFNGIP

Parental  FTIQRLCELLTDPRRNYTGTDKFLRGVEKNVMVVSCVYPSSEKNNSNSLNRMNGVMFPGNSPSYTERSNI
          FT.QRLCELLTDPRRNYTGTDKFLRGVEKNVMV.SCVYPSSEKNNSNSLNRMNGVMFPGNSPSYTERSNI
Retrocopy FTVQRLCELLTDPRRNYTGTDKFLRGVEKNVMVISCVYPSSEKNNSNSLNRMNGVMFPGNSPSYTERSNI

Parental  NGPGTPRPLNRPKVSLSAPMTTNGLPESTDSKETNLQQNEEKNHSDSSTSESQVSSVSPLKNKHPDEDAV
          NGPGTPRPLNR.K.SLSAP.T.NGLPESTDSKE..LQQNEEKNHSDS.TSES.VSSVSPLKNKHPDE.AV
Retrocopy NGPGTPRPLNRSKISLSAPVTRNGLPESTDSKEASLQQNEEKNHSDSLTSESEVSSVSPLKNKHPDEYAV

Parental  EAEGHEVKRLRFDKESEVRETASQTTSSEISSVMVEETEASSSSQDKDKESRCTRQHC
          EAEGH.VKRL.FDKE.EV.ETASQTTSSEISS.MVE.TEA.SSSQDKDKES.CT.QHC
Retrocopy EAEGHKVKRLKFDKEGEVGETASQTTSSEISSAMVEKTEA-SSSQDKDKESPCTQQHC

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	10.64 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	13.01 RPM
SRP007412_cerebellum	0.00 RPM	10.14 RPM
SRP007412_heart	0.00 RPM	4.12 RPM
SRP007412_kidney	0.00 RPM	9.39 RPM
SRP007412_liver	0.00 RPM	3.56 RPM
SRP007412_testis	0.19 RPM	10.89 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1224 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1224 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1224 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007954	3 retrocopies	retro_chof_1347, retro_chof_1914, retro_chof_2285,
Echinops telfairi	ENSETEG00000019946	2 retrocopies	retro_etel_1238, retro_etel_148,
Homo sapiens	ENSG00000163605	6 retrocopies	retro_hsap_2744, retro_hsap_2745, retro_hsap_2746, retro_hsap_2904, retro_hsap_3138, retro_hsap_3283,
Loxodonta africana	ENSLAFG00000000513	1 retrocopy	retro_lafr_603,
Macaca mulatta	ENSMMUG00000016959	1 retrocopy	retro_mmul_1224 ,
Mus musculus	ENSMUSG00000052144	3 retrocopies	retro_mmus_1068, retro_mmus_1157, retro_mmus_3474,
Oryctolagus cuniculus	ENSOCUG00000006235	1 retrocopy	retro_ocun_292,
Pan troglodytes	ENSPTRG00000015108	5 retrocopies	retro_ptro_1855, retro_ptro_1856, retro_ptro_2121, retro_ptro_2220, retro_ptro_2974,