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:
| Parental | MADLSLLQEDLPE-DADGPLDFVSQDEMLTPLGRLDKYAASENVFNRQMVARSLLDTLREVCDDERDCIA |
| .ADLSLLQEDL.E.D.D..LD.VS.DE.LTPLGRLDKYAA.E.V..RQMVA.SLLDTLREVC.DERDCIA | |
| Retrocopy | LADLSLLQEDLLE>DGDRSLDLVSEDEKLTPLGRLDKYAANEKVLKRQMVAWSLLDTLREVCNDERDCIA |
| Parental | VLERISRLADDSEPTVRAELMEQVPHIALFCQENRPSIPYAFSKYLLPIVVRYLADQ-NNQVRKTSQAAL |
| VLE.ISRLADD.EPTVR..LMEQ...IALFCQEN.PSIPYAFSKY.LP..VR.L..Q.N........A.L | |
| Retrocopy | VLEKISRLADDLEPTVRLALMEQ--NIALFCQENLPSIPYAFSKYILPTLVRDLEGQNNHMRKPSQAALL |
| Parental | LALLEQE-LIERFDVETKVCPVLIDLTAPDSNDDVKTEAVAIMCKM-APMVGKDITERLILPRFCEMCCD |
| ..L.....L....D.ET.VCPVLIDLTAPDSNDDVKTEAVA.MCK......G.........P.F...... | |
| Retrocopy | APLEQDL>LSDLTDMETMVCPVLIDLTAPDSNDDVKTEAVAVMCKV<GAWLGRTLLSISSSPGFARCALT |
| Parental | CRMF-HVRKVCAANFGDICSVVGQQATEEMLLPRFFQLCSDNVWGVRK-ACAECFMAVSCATCQEIRRTK |
| ...F.HV.KVC.ANFGDICS.VGQQATEEM.LPRFFQLCSDNVWG.....C........C...QEIRRTK | |
| Retrocopy | VECF<HVQKVCTANFGDICSDVGQQATEEM*LPRFFQLCSDNVWGILR>ECFMAVSCATC---QEIRRTK |
| Parental | LSALFINLISDPSRWVRQAAFQSLGPFISTFANPSSSGQCFKDESKNSEDSSAEDKDRMRDNDVVEEEHR |
| LSALFIN.ISDPS..V.QAAF.SLGPFISTFANP.S.GQ.FKDESK.SEDSS.E.KD..RDNDVVEE.H. | |
| Retrocopy | LSALFINSISDPSH*VHQAAFHSLGPFISTFANPLSLGQGFKDESKSSEDSSVEYKDGIRDNDVVEELHH |
| Parental | RPEDAPSDLSAPHSSARLES-LEGCAAKTPGHSAGDVPAPVDSSLLCTLSSESPQEAASNDENGRKPDTN |
| RPEDAP.DLS.PHSSARLES.LEG.AAKTPGHSAG.V.APVDSSLLCTLSSESPQEAAS.DENGRKPDTN | |
| Retrocopy | RPEDAPIDLSVPHSSARLESTLEGYAAKTPGHSAGEVHAPVDSSLLCTLSSESPQEAASKDENGRKPDTN |
| Parental | SKSASRPDAGTSSPEATPL-DQDMFNSFHFW-RTPLPKIDLDKELQQDPEERLSPERTGDVPAAPLPGPP |
| SKSASRPD.GTSSPEATPL.DQDMFNS.HFW.R.PLPKIDLDKELQQ.PEERLSPERTGD.PA.P.PG.P | |
| Retrocopy | SKSASRPDTGTSSPEATPL>DQDMFNSLHFW>RAPLPKIDLDKELQQNPEERLSPERTGDEPASPAPGSP |
| Parental | NITMATRKELEEMIENLEPHMDDPDVKAQVDVLSAALRASSLDAHEETGGVEQRSELQDEVCVSELPDCN |
| NI.MATRKELEEMIENLEPHMDDPDVKAQV.VL.AALRA.SL.AH.ET.GVEQ.SELQDEV.V..LP.CN | |
| Retrocopy | NIPMATRKELEEMIENLEPHMDDPDVKAQVEVLLAALRAFSLHAHQETSGVEQQSELQDEVRVRDLPGCN |
| Parental | ISHDTCVPLISAAEENAEATPDYVHGGADVSPGDGFSPDEDRRPKVQDVVPQALLDQYLSMTDPSRAQTV |
| I.HDTCVPLISAA.EN.EATPDYV...AD.SPG.GFS.D.DRRPK.QDVVPQ.LLDQ.LSMTDPS.AQTV | |
| Retrocopy | INHDTCVPLISAA*ENMEATPDYVDRSADLSPGGGFSRDDDRRPKIQDVVPQVLLDQCLSMTDPS*AQTV |
| Parental | DTEIAKHCAYSLPGVALTLGRQNWHCLRETYETLASDMQWKVRRTLAFSIHELAVILGDQLTAADLVPIF |
| DTEI.KHCAYSL.GVALTLGRQNWHCLRET.ETLASDMQ.KVRRTL..SIHELAVILGDQLT.ADLVPIF | |
| Retrocopy | DTEIPKHCAYSLLGVALTLGRQNWHCLRETNETLASDMQ*KVRRTLVYSIHELAVILGDQLTEADLVPIF |
| Parental | NGFL-KDLDEVRIGVLKHLHDFLKLLHIDKRREYLYQLQEFLVTD-NSRNWRFRAELAEQLILLLELYSP |
| NGF..KDLDEVRIG.LKHLHDFLKLLH.DKRREYLYQLQE.LVTD.NSRN..F.AELAEQLI.LLELYSP | |
| Retrocopy | NGFF*KDLDEVRIGLLKHLHDFLKLLHTDKRREYLYQLQEILVTD>NSRNLGFGAELAEQLIVLLELYSP |
| Parental | RDVYDYLRPIALNLCADKVSSVRWISYKLVSEMVKKLH-TATPPTFGVDLINELVENFGRCPKWSGRQAF |
| RDVYDY..PIALNLCA..VSS.RWI.YKLVSEM.KKLH.TATPPTFGVDLINELVENFGRCPKWSG.QAF | |
| Retrocopy | RDVYDYFSPIALNLCAGRVSSIRWIPYKLVSEMMKKLHYTATPPTFGVDLINELVENFGRCPKWSG*QAF |
| Parental | VFVCQT |
| VFVCQT | |
| Retrocopy | VFVCQT |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(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 |
RNA Polymerase II activity near the 5' end of retro_mmus_3230 was not detected
No EST(s) were mapped for retro_mmus_3230 retrocopy.
No TSS is located nearby retro_mmus_3230 retrocopy 5' end.
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 | ENSSSCG00000003679 | 1 retrocopy | |
| Sus scrofa | ENSSSCG00000024561 | 1 retrocopy |