RetrogeneDB ID: | retro_mmus_3255 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 9:25450710..25452057(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Clpb | ||
| Ensembl ID: | ENSMUSG00000001829 | ||
| Aliases: | Clpb, AL118244, Skd3 | ||
| Description: | ClpB caseinolytic peptidase B [Source:MGI Symbol;Acc:MGI:1100517] |
Retrocopy-Parental alignment summary:
>retro_mmus_3255
TGGGTCTGGGCCAAGGTGCTGGTGGTTCAGTGCTACAAGAATCCATCTAACAAGGATGCAGCTCTAATGGAAGCTGCTCT
GGCCAATAACGTGCAGGAAGTCAGAAGGCTGTTGTCAGAAGGTGCAGATGTCAATGCAAGGTACAAACTTGGCTAGACAG
CATTGATGGTGGCAGCCATCAGCCACAATGAGAGTGTGGTGCAGGTCCTGCTTGCTGCTGAAGCTGACTCAAACCTTGGG
GATGGCTTCAGCAGTGTCTACAAAACTGCCAATGAACAGGGAGTCCATTCTTTGGAAGTCCTAGTCATTCAAGAGGATGA
CTTCAACAACCGATTAAACTACCTGGCTAGCTTCAAAAGCTGCACAGCCCTGCACTATGCTGTCCAGGCCCACAACTACA
GCATCGTCAAGGAGCTGCTGGATGGAGAAGCCAACCCCCTTCAGAGGAATATGATGGGACACACAACCCTGGATTATGCC
CAGGAAGAGGAGGTTATAAAACTTCTGAAAACTTCTGAGACCAAGTATATGGAGAAGCAGAGGAAGCGTGAGGCAGAGGA
GAGGCACCGCTTCCTACTGAGCAGCGACTGAAGGAGCACATCATTGACCAAGAGAGTGCCATCGCCACTATTAGTGCTGA
GATCCAGAGGAAGGAGAATGGCTGGTAGGATGAGGAGCACCCTCTAGTCGTCCTCTTCTTGGGATCATCTGGAATAGGGA
AAAGCGAGCTGGCCAAGCAGACAGCCAAGTATATGCACAAAGATGACAAGAAAGGGCTTCATCTTGCTCAACATATCTGA
GTTCCAGGAGTGACATGATGTAGCAAATTTATCGGCTCTTCAGTAGGCTATATCGGCCATGAAGAGGGTGGCCAGCTGAC
CAAGAAACTGAAACAGTGCCCAAATGCAGTAGTCCTGTTTGATGAGATAGACAAGGCCCATCCAGATGTGCTCACCATCA
TGCTGCAGCTGTTTGATGAGGGCTACCTGACAGATGGCAAAGGGAAGACCATTGACTGCAAGGATGCCATCTTCATCATG
ACTCCCATTGTAGCCAGTGCTGAGATTGCCCAGCATGCATTGCAGCTCAGACAGGAAGCTTTGGAGATGAGCCGAAATTG
AATCGCCGAAAACCTTAGGGATGTCCAGATTAGTGACAAGATCACTATCTTGAAGAACTTTAACGAGAATGTGATCTGAC
CCATCCTGAAAGTTCACTTCCAGAGAGATGAGTTTTTTGGGAGGGATCAAAGAGATCATCTACTTCTTCCCTTTCTGCCA
TTCAGAGCTCCTCCAGCTGGTCAACAAGGAACTTCAGGACCAAGAGAGCCAAACAGAGGCACATCAC
ORF - retro_mmus_3255 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.04 % |
| Parental protein coverage: | 66.47 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | WALAMALVVQCYSKNPSNKDAALMEAARANNVQEVRRLLSEGADVNARHKLGWTALMVASISHNESVVQV |
| W..A..LVVQCY.KNPSNKDAALMEAA.ANNVQEVRRLLSEGADVNAR.KLG.TALMVA.ISHNESVVQV | |
| Retrocopy | WVWAKVLVVQCY-KNPSNKDAALMEAALANNVQEVRRLLSEGADVNARYKLG*TALMVAAISHNESVVQV |
| Parental | LLAAGADPNLGDEFSSVYKTANEQGVHSLEVLVTREDDFNNRLNHRASFKGCTALHYAVLADDYSIVKEL |
| LLAA.AD.NLGD.FSSVYKTANEQGVHSLEVLV..EDDFNNRLN..ASFK.CTALHYAV.A..YSIVKEL | |
| Retrocopy | LLAAEADSNLGDGFSSVYKTANEQGVHSLEVLVIQEDDFNNRLNYLASFKSCTALHYAVQAHNYSIVKEL |
| Parental | LDRGANPLQRNEMGHTPLDYAREGEVMKLLKTSETKYMEKQRKREAEERRRF-PLEQRLKEHIIGQESAI |
| LD..ANPLQRN.MGHT.LDYA.E.EV.KLLKTSETKYMEKQRKREAEER.RF.P.EQRLKEHII.QESAI | |
| Retrocopy | LDGEANPLQRNMMGHTTLDYAQEEEVIKLLKTSETKYMEKQRKREAEERHRF<PTEQRLKEHIIDQESAI |
| Parental | ATVGAAIRRKENGWYDEEHPLVFLFLGSSGIGKTELAKQTAKYMHKDAK-KGFIRLDMSEFQERHEVA-K |
| AT..A.I.RKENGW.DEEHPLV.LFLGSSGIGK.ELAKQTAKYMHKD.K.KGFI.L..SEFQE.H.VA.K | |
| Retrocopy | ATISAEIQRKENGW*DEEHPLVVLFLGSSGIGKSELAKQTAKYMHKDDK>KGFILLNISEFQE*HDVA<K |
| Parental | FIGSPPGYIGHEEGGQLTKKLKQCPNAVVLFDEVDKAHPDVLTIMLQLFDEGRLTDGKGKTIDCKDAIFI |
| FIGS..GYIGHEEGGQLTKKLKQCPNAVVLFDE.DKAHPDVLTIMLQLFDEG.LTDGKGKTIDCKDAIFI | |
| Retrocopy | FIGSSVGYIGHEEGGQLTKKLKQCPNAVVLFDEIDKAHPDVLTIMLQLFDEGYLTDGKGKTIDCKDAIFI |
| Parental | MTSNVASDEIAQHALQLRQEALEMSRNRIAENLGDVQMSDKITISKNFKENVIRPILKAHFRRDEFLGR- |
| MT..VAS.EIAQHALQLRQEALEMSRN.IAENL.DVQ.SDKITI.KNF.ENVI.PILK.HF.RDEF.GR. | |
| Retrocopy | MTPIVASAEIAQHALQLRQEALEMSRN*IAENLRDVQISDKITILKNFNENVI*PILKVHFQRDEFFGR> |
| Parental | INEIVYFLPFCHSELIQLVNKELNFWAKRAKQRH |
| I.EI.YF.PFCHSEL.QLVNKEL..........H | |
| Retrocopy | IKEIIYFFPFCHSELLQLVNKELQDQESQTEAHH |
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 .00 RPM | 39 .46 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 38 .47 RPM |
| SRP007412_heart | 0 .03 RPM | 75 .46 RPM |
| SRP007412_kidney | 0 .02 RPM | 62 .29 RPM |
| SRP007412_liver | 0 .00 RPM | 39 .71 RPM |
| SRP007412_testis | 0 .09 RPM | 701 .82 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3255 was not detected
No EST(s) were mapped for retro_mmus_3255 retrocopy.
No TSS is located nearby retro_mmus_3255 retrocopy 5' end.
retro_mmus_3255 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3255 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000015121 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000001829 | 1 retrocopy |
retro_mmus_3255 ,
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