RetrogeneDB ID: retro_mmul_491

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:51209960..51210990(-)
• Located in intron of: ENSMMUG00000009282

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1R8
• Ensembl ID: ENSMMUG00000006933
• Aliases: None
• Description: nuclear inhibitor of protein phosphatase 1 [Source:RefSeq peptide;Acc:NP_001253391]

Sequence

>retro_mmul_491
ATGGTGGCAGTTGCAAACTCTGGCTCCAGCCTCACGCTGCTCCACTGTCCAACCTGGGCGGGTAAGCCCCCTCCTGGTCG
ACATCTGGATGCAGTCAAATGAGACAAACTAATTGAGAAACTGATTATTGGTGAAAGTAAGTATTACTTATTTGGGAGAA
ACCTTGATTTGTGTGACTTTACCACTGAACACCAGTCTTGCACTCGGGTCCATGCTGCATTTGTCTACCACAAGCATCTG
AGGAGAGTTTTCCTAATAGATCTCAACAGTACACACAGCACTTTCTTGGGTCACCTTCGGTTGGAACCTCACAAGCCTCA
GCAAATTCCTATCAATTCCAGGGTCTCATTGACGCATCCACAAGGGCATACACTCTGTGTGAGACACTTCAGCCATTGCC
ATTGGCTGTGAAAGGAGTTGAGAAGATGGGTGAAGAGGATGATGAACTCAAGGGCTTACTGGGGCTTCCAGAGAAGGAAA
CTAAGCTTGATAACCTGACATAGTTCAACACTGCCCACAACAAGTGGATTTCCACCCTTACCATTGAGGAGGGAAATCTA
GGCATTCCAAGACCAAAGAGGAAGAGGAAGAACTCATGGGTGACATTCAGTGAGGATGATGAGATCATTAACTCAGAGGA
TGTGGATCCCTCAGTTGGTCGATTCAGGAACTTAGTGCAAACTGCAGGGGTCTCAGTCCAGAAGAAGCAGGGGAGGGCCC
TGGCTCCTTGGGCCTGGAGGAATCAGGGAGAAGGCGCATGCAGAACTTTGCCTTCAACGGAGGACATCCCCCACACACAG
TGAAGCAGACTCCCAGCTTCCATGAGACAGCACTCATCGGTGGCTTGTTTATGCCATACCCAAACCTTGCCTCTGATGTG
GACTTGACTCCTGTTGTGCCGGCAGCAGTGAACACGAACCCTGCACCAAACCTTGCCGTTCATAACCCTGAAACTGTAAA
TGAACCCAAGAAGAAGAAATATGCAAAAGAGACTTGGCCAGGCAAGAATCCCACATCTTCCTTACTGATT

Alignment

ORF - retro_mmul_491 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.04 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAAANSGSSLPLFDCPTWAGKPPPGLHLDVVKGDKLIEKLIIDEKKYYLFGRNPDLCDFTIDHQSCSRV
          M.A.ANSGSSL.L..CPTWAGKPPPG.HLD.VK.DKLIEKLII.E.KYYLFGRN.DLCDFT..HQSC.RV
Retrocopy MVAVANSGSSLTLLHCPTWAGKPPPGRHLDAVK*DKLIEKLIIGESKYYLFGRNLDLCDFTTEHQSCTRV

Parental  HAALVYHKHLKRVFLIDLNSTHGTFLGHIRLEPHKPQQIPIDSTVSF-GASTRAYTLREKPQTLPSAVKG
          HAA.VYHKHL.RVFLIDLNSTH.TFLGH.RLEPHKPQQIPI.S.VS...ASTRAYTL.E..Q.LP.AVKG
Retrocopy HAAFVYHKHLRRVFLIDLNSTHSTFLGHLRLEPHKPQQIPINSRVSL<DASTRAYTLCETLQPLPLAVKG

Parental  DEKMGGEDDELKGLLGLPEEETELDNLTEFNTAHNKRISTLTIEEGNLDIQRPKRKRKNSRVTFSEDDEI
          .EKMG.EDDELKGLLGLPE.ET.LDNLT.FNTAHNK.ISTLTIEEGNL.I.RPKRKRKNS.VTFSEDDEI
Retrocopy VEKMGEEDDELKGLLGLPEKETKLDNLT*FNTAHNKWISTLTIEEGNLGIPRPKRKRKNSWVTFSEDDEI

Parental  INPEDVDPSVGRFRNMVQTAVVPVKKKRV-EGPGSLGLEESGSRRMQNFAFSGGLYGGLPPTHSEAGSQP
          IN.EDVDPSVGRFRN.VQTA.V.V.KK...EGPGSLGLEESG.RRMQNFAF.....GG.PP.......Q.
Retrocopy INSEDVDPSVGRFRNLVQTAGVSVQKKQG<EGPGSLGLEESGRRRMQNFAFN----GGHPP---HTVKQT

Parental  HGIHGTALIGGLPMPYPNLAPDVDLTPVVPSAVNMNPAPNPAVYNPEAVNEPKKKKYAKEAWPGKKPTPS
          ...H.TALIGGL.MPYPNLA.DVDLTPVVP.AVN.NPAPN.AV.NPE.VNEPKKKKYAKE.WPGK.PT.S
Retrocopy PSFHETALIGGLFMPYPNLASDVDLTPVVPAAVNTNPAPNLAVHNPETVNEPKKKKYAKETWPGKNPTSS

Parental  LLI
          LLI
Retrocopy LLI

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	23.87 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	22.29 RPM
SRP007412_cerebellum	0.00 RPM	30.61 RPM
SRP007412_heart	0.00 RPM	12.48 RPM
SRP007412_kidney	0.00 RPM	18.19 RPM
SRP007412_liver	0.04 RPM	9.06 RPM
SRP007412_testis	0.41 RPM	27.55 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_491 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_491 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_491 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_380
Pan troglodytes	retro_ptro_296

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012023	1 retrocopy	retro_cfam_334,
Homo sapiens	ENSG00000117751	1 retrocopy	retro_hsap_380,
Gorilla gorilla	ENSGGOG00000012062	1 retrocopy	retro_ggor_387,
Loxodonta africana	ENSLAFG00000017834	1 retrocopy	retro_lafr_1173,
Macaca mulatta	ENSMMUG00000006933	1 retrocopy	retro_mmul_491 ,
Pan troglodytes	ENSPTRG00000000417	1 retrocopy	retro_ptro_296,
Ictidomys tridecemlineatus	ENSSTOG00000004381	2 retrocopies	retro_itri_1611, retro_itri_1704,