RetrogeneDB ID:

retro_mmus_3230

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:8:99145638..99148141(-)
Located in intron of:ENSMUSG00000036510
Retrocopy
information
Ensembl ID:ENSMUSG00000086842
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Ppp4r1
Ensembl ID:ENSMUSG00000061950
Aliases:Ppp4r1, 3110001J10Rik, Pp4r1
Description:protein phosphatase 4, regulatory subunit 1 [Source:MGI Symbol;Acc:MGI:1917601]


Retrocopy-Parental alignment summary:






>retro_mmus_3230
CTGGCAGACCTCTCACTGCTCCAGGAGGACCTGCTGGAAGGACGGGGACAGATCCCTGGACTTGGTCTCAGAAGATGAAA
AGTTGACACCCTTGGGGAGGCTAGACAAGTATGCTGCAAATGAGAAAGTATTAAAAAGACAAATGGTGGCCTGGAGTTTG
CTGGATACTCTAAGGGAAGTCTGCAATGATGAGAGAGACTGCATTGCTGTCTTGGAAAAAATCAGCCGATTAGCTGATGA
CTTGGAACCAACTGTGAGATTGGCGCTGATGGAACAAAACATTGCACTGTTTTGTCAAGAGAACCTGCCTTCTATCCCAT
ATGCTTTTTCCAAGTACATACTCCCAACTTTGGTTAGAGACCTTGAAGGCCAGAATAACCACATGAGGAAACCCAGTCAG
GCAGCATTGCTGGCTCCGTTGGAGCAAGACCTGATTGAGCGACTTGACTGACATGGAGACCATGGTGTGCCCTGTCCTCA
TAGACCTGACTGCCCCAGACAGCAATGATGATGTGAAGACAGAGGCTGTTGCTGTAATGTGCAAGGTGGTGCATGGTTGG
GAAGGACATTACTGAGCATTTCATCCTCCCCAGGTTTTGCGAGATGTGCTCTTACTGTTGAATGTTTCATGTCCAGAAGG
TCTGTACTGCCAATTTTGGAGATATTTGCAGTGACGTTGGCCAGCAAGCTACAGAAGAAATGTAGCTGCCCAGGTTCTTC
CAGCTGTGTTCTGATAATGTGTGGGGCATCCTACGCTGAGTGCTTCATGGCTGTCTCCTGTGCAACATGTCAAGAAATCC
GACGGACAAAGTTATCAGCACTATTTATTAACTCGATCAGTGATCCTTCGCATTGAGTTCACCAAGCAGCCTTTCATTCT
CTGGGGCCTTTCATATCCACGTTTGCTAATCCATTAAGCTTGGGCCAGGGCTTTAAAGATGAGAGCAAAAGCTCAGAAGA
CTCCTCAGTAGAATACAAAGATGGGATAAGAGACAATGATGTCGTAGAAGAATTGCATCACAGGCCAGAGGATGCTCCTA
TAGACCTCAGTGTCCCTCACTCCAGTGCCAGGCTGGAGAGTACACTCGAAGGCTATGCTGCCAAGACACCTGGGCACTCT
GCAGGTGAGGTGCATGCTCCAGTGGACAGCTCCTTACTCTGTACTTTGTCCTCAGAGTCTCCTCAGGAAGCAGCTAGCAA
GGATGAGAATGGCAGAAAGCCTGACACCAACAGCAAGTCTGCATCCAGGCCAGACACTGGCACCAGCTCCCCAGAGGCCA
CCCCCTTAGGACCAGGACATGTTCAATTCCTTGCATTTCTGGAAGGGCTCCTCTACCTAAAATAGATCTTGATAAAGAAC
TCCAACAGAACCCCGAGGAGAGACTCAGCCCAGAGAGAACAGGAGATGAACCTGCAAGCCCTGCACCAGGCTCTCCCAAT
ATCCCCATGGCTACCCGGAAGGAACTAGAAGAAATGATAGAAAACCTTGAGCCGCACATGGATGACCCGGATGTGAAAGC
ACAGGTGGAAGTGCTGTTGGCTGCCCTGCGTGCTTTCAGCTTGCATGCTCACCAAGAGACCAGTGGTGTAGAGCAGCAGA
GTGAGCTACAAGATGAAGTGCGTGTCCGTGATCTTCCAGGCTGTAACATAAATCACGACACTTGTGTGCCTTTGATCAGC
GCTGCTTAGGAGAATATGGAGGCCACTCCTGATTATGTCGATAGAAGTGCGGACCTAAGCCCCGGCGGGGGCTTCAGCCG
GGATGATGATAGGAGACCCAAAATCCAGGATGTTGTACCACAAGTGTTATTAGATCAGTGCTTGTCAATGACTGACCCTT
CTTGAGCACAAACAGTTGACACTGAGATCCCTAAGCACTGTGCATACAGTCTGCTGGGTGTGGCCCTGACTCTTGGCAGA
CAGAACTGGCATTGCTTGAGGGAGACTAATGAGACCCTAGCGTCAGACATGCAGTAGAAAGTTCGAAGAACTCTAGTCTA
CTCTATCCATGAGCTTGCGGTGATTCTTGGAGACCAGCTGACAGAGGCAGACCTGGTTCCAATTTTCAATGGATTTTTTT
AAAAAGACCTTGATGAAGTCAGGATAGGTCTTCTTAAACACTTGCATGACTTTCTGAAGCTTCTTCACACTGATAAAAGA
AGAGAGTACCTTTATCAGCTCCAGGAGATTTTGGTGACAGACAAACAGTAGAAATTTGGGTTTTGGAGCCGAACTGGCAG
AGCAGCTGATTGTACTTCTAGAGTTATATAGTCCCAGAGATGTTTATGATTACTTCAGTCCCATTGCTCTGAATCTGTGT
GCAGGCAGAGTTTCTTCAATCCGTTGGATTCCCTACAAGTTGGTCAGTGAAATGATGAAGAAACTCCACTACACGGCAAC
ACCACCAACATTCGGAGTAGATCTCATCAATGAGCTGGTAGAGAATTTCGGCAGGTGTCCAAAATGGTCTGGATGACAAG
CCTTTGTCTTTGTCTGCCAGACT

ORF - retro_mmus_3230 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.37 %
Parental protein coverage: 89.29 %
Number of stop codons detected: 7
Number of frameshifts detected 8


Retrocopy - Parental Gene Alignment:

ParentalMADLSLLQEDLPE-DADGPLDFVSQDEMLTPLGRLDKYAASENVFNRQMVARSLLDTLREVCDDERDCIA
.ADLSLLQEDL.E.D.D..LD.VS.DE.LTPLGRLDKYAA.E.V..RQMVA.SLLDTLREVC.DERDCIA
RetrocopyLADLSLLQEDLLE>DGDRSLDLVSEDEKLTPLGRLDKYAANEKVLKRQMVAWSLLDTLREVCNDERDCIA
ParentalVLERISRLADDSEPTVRAELMEQVPHIALFCQENRPSIPYAFSKYLLPIVVRYLADQ-NNQVRKTSQAAL
VLE.ISRLADD.EPTVR..LMEQ...IALFCQEN.PSIPYAFSKY.LP..VR.L..Q.N........A.L
RetrocopyVLEKISRLADDLEPTVRLALMEQ--NIALFCQENLPSIPYAFSKYILPTLVRDLEGQNNHMRKPSQAALL
ParentalLALLEQE-LIERFDVETKVCPVLIDLTAPDSNDDVKTEAVAIMCKM-APMVGKDITERLILPRFCEMCCD
..L.....L....D.ET.VCPVLIDLTAPDSNDDVKTEAVA.MCK......G.........P.F......
RetrocopyAPLEQDL>LSDLTDMETMVCPVLIDLTAPDSNDDVKTEAVAVMCKV<GAWLGRTLLSISSSPGFARCALT
ParentalCRMF-HVRKVCAANFGDICSVVGQQATEEMLLPRFFQLCSDNVWGVRK-ACAECFMAVSCATCQEIRRTK
...F.HV.KVC.ANFGDICS.VGQQATEEM.LPRFFQLCSDNVWG.....C........C...QEIRRTK
RetrocopyVECF<HVQKVCTANFGDICSDVGQQATEEM*LPRFFQLCSDNVWGILR>ECFMAVSCATC---QEIRRTK
ParentalLSALFINLISDPSRWVRQAAFQSLGPFISTFANPSSSGQCFKDESKNSEDSSAEDKDRMRDNDVVEEEHR
LSALFIN.ISDPS..V.QAAF.SLGPFISTFANP.S.GQ.FKDESK.SEDSS.E.KD..RDNDVVEE.H.
RetrocopyLSALFINSISDPSH*VHQAAFHSLGPFISTFANPLSLGQGFKDESKSSEDSSVEYKDGIRDNDVVEELHH
ParentalRPEDAPSDLSAPHSSARLES-LEGCAAKTPGHSAGDVPAPVDSSLLCTLSSESPQEAASNDENGRKPDTN
RPEDAP.DLS.PHSSARLES.LEG.AAKTPGHSAG.V.APVDSSLLCTLSSESPQEAAS.DENGRKPDTN
RetrocopyRPEDAPIDLSVPHSSARLESTLEGYAAKTPGHSAGEVHAPVDSSLLCTLSSESPQEAASKDENGRKPDTN
ParentalSKSASRPDAGTSSPEATPL-DQDMFNSFHFW-RTPLPKIDLDKELQQDPEERLSPERTGDVPAAPLPGPP
SKSASRPD.GTSSPEATPL.DQDMFNS.HFW.R.PLPKIDLDKELQQ.PEERLSPERTGD.PA.P.PG.P
RetrocopySKSASRPDTGTSSPEATPL>DQDMFNSLHFW>RAPLPKIDLDKELQQNPEERLSPERTGDEPASPAPGSP
ParentalNITMATRKELEEMIENLEPHMDDPDVKAQVDVLSAALRASSLDAHEETGGVEQRSELQDEVCVSELPDCN
NI.MATRKELEEMIENLEPHMDDPDVKAQV.VL.AALRA.SL.AH.ET.GVEQ.SELQDEV.V..LP.CN
RetrocopyNIPMATRKELEEMIENLEPHMDDPDVKAQVEVLLAALRAFSLHAHQETSGVEQQSELQDEVRVRDLPGCN
ParentalISHDTCVPLISAAEENAEATPDYVHGGADVSPGDGFSPDEDRRPKVQDVVPQALLDQYLSMTDPSRAQTV
I.HDTCVPLISAA.EN.EATPDYV...AD.SPG.GFS.D.DRRPK.QDVVPQ.LLDQ.LSMTDPS.AQTV
RetrocopyINHDTCVPLISAA*ENMEATPDYVDRSADLSPGGGFSRDDDRRPKIQDVVPQVLLDQCLSMTDPS*AQTV
ParentalDTEIAKHCAYSLPGVALTLGRQNWHCLRETYETLASDMQWKVRRTLAFSIHELAVILGDQLTAADLVPIF
DTEI.KHCAYSL.GVALTLGRQNWHCLRET.ETLASDMQ.KVRRTL..SIHELAVILGDQLT.ADLVPIF
RetrocopyDTEIPKHCAYSLLGVALTLGRQNWHCLRETNETLASDMQ*KVRRTLVYSIHELAVILGDQLTEADLVPIF
ParentalNGFL-KDLDEVRIGVLKHLHDFLKLLHIDKRREYLYQLQEFLVTD-NSRNWRFRAELAEQLILLLELYSP
NGF..KDLDEVRIG.LKHLHDFLKLLH.DKRREYLYQLQE.LVTD.NSRN..F.AELAEQLI.LLELYSP
RetrocopyNGFF*KDLDEVRIGLLKHLHDFLKLLHTDKRREYLYQLQEILVTD>NSRNLGFGAELAEQLIVLLELYSP
ParentalRDVYDYLRPIALNLCADKVSSVRWISYKLVSEMVKKLH-TATPPTFGVDLINELVENFGRCPKWSGRQAF
RDVYDY..PIALNLCA..VSS.RWI.YKLVSEM.KKLH.TATPPTFGVDLINELVENFGRCPKWSG.QAF
RetrocopyRDVYDYFSPIALNLCAGRVSSIRWIPYKLVSEMMKKLHYTATPPTFGVDLINELVENFGRCPKWSG*QAF
ParentalVFVCQT
VFVCQT
RetrocopyVFVCQT

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain 0 .12 RPM 41 .26 RPM
SRP007412_cerebellum 0 .35 RPM 46 .72 RPM
SRP007412_heart 0 .03 RPM 44 .70 RPM
SRP007412_kidney 0 .00 RPM 57 .06 RPM
SRP007412_liver 0 .00 RPM 32 .61 RPM
SRP007412_testis 0 .18 RPM 344 .41 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_3230 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_3230 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_3230 retrocopy 5' end.

Lab - click to see more details

retro_mmus_3230 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_3230 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Mus musculus ENSMUSG00000061950 1 retrocopy
retro_mmus_3230 ,
Sus scrofa ENSSSCG000000036791 retrocopy
retro_sscr_694,
Sus scrofa ENSSSCG000000245611 retrocopy
retro_sscr_695,


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