RetrogeneDB ID: | retro_mmus_3275 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 9:55949985..55952420(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rnf19a | ||
| Ensembl ID: | ENSMUSG00000022280 | ||
| Aliases: | Rnf19a, AA032313, Dorfin, Rnf19, UIP117, Ubce7ip2, XYbp | ||
| Description: | ring finger protein 19A [Source:MGI Symbol;Acc:MGI:1353623] |
Retrocopy-Parental alignment summary:
>retro_mmus_3275
GACTCTGACTCAGTTCTGATAAGCATTTTAGACATGAGTCTACATCAGCAAGTGGGTTCAGAGGGAGATCGTCAACTTTC
TGCTTCCTCTGTGAGCTTGCCTTCTGTCAAAAAGGCACCCAAACAGAGAAGATTTTCAATAGGCTCTCGTTTTCAGGGGA
AGATGGACAGCAAACGAAAATCAAGGGAGCTCAATGGTGGAGTGGAAGCAATTGCAAGGATTGAGAGTATACATTCTGAA
ATGTTTGCTGATAAGAACTCCATTTTCTCAGCAAATACCTCTTCTGACAATAGATTGACTTCCATCAGCAAACAAACTGG
TGACTTTATGGACTGTCCTTTATGCCTTTTACGACTTTCTCAAGACAGATTTCCTGATAACATGACATGTCATCATAGAT
CTTGTGTGGATTGCTTATGACAATACTTAAGGATAGAAATCTCTGAAAGTAGAGTTAACGTCAGTTGTCCAGAATGCACT
GAACGGTTTAATCCCCATGACATTCGCTTGATATTAAGTGATGATGTCTTAATGGGAAAATATGAAGAATTTATGCTTCG
ACAGTGGCTTGTTGCAGATCCTGACTGTAGGTGGTGTCCGGCTCCAGACTGTGGATACGCTGTGATAGCATTTGGATGTG
CCAGGTGTCCAAAATTAACTTGTGGGCAAAAAGGCTATAGAACAGAGTTTTGCTACCACTGTAAACAGATCTGGCATCCC
AAACAGACCTGTGAGGCTGCTCTATGGGAAAGAGCCCAGTGTTTATGCTTAAGAACTTTACCCTTTTCACCTATTAGTTA
CAAACAGGAATCTAGAGCAGCAGCTGATGACATAAAGCCGTGTCCACGATGTGCTCCTTATATAATCAAGATTGAGGATG
AGAGGTGCAATCATATGACATGTGCTGTCTGTGGTTGTGAGTTTTGTTGGTTGTGCATGAAAGAAATCTCCAATTTCCAT
TATCTAAATCCCTCGGGTTGTAGTTTACGGGGGAAGAAACCCTGGACCCGAAAGAAGAAAATCCTGTGGCAGCTGAGAAC
CCTTGTTGGTGCTCCCATAGGGATTGCTCTCATAGCTGGCATTGCCCTGCCTGCCATGATCATTGGCGTTCCTGTGTATG
TGGGCCTCAAGATTCATGATTGCTATGAAGACAGAGATGTTTCAAAACACAAGTGTAATCTGGTCATAGCAAGTGCTGTT
ACCCTGTCTGTAATCATCTCTCTGGTGGTAGCTACAGTGACTATAGGTACTGGTGTTCCTACCATGCTAGGTTATGTCTA
TGGTGTGTTCCCAATTTCCCTCTGCAGAAACAGGAATTGTGGAGAGTCTGCAGGAAATGGGAAAGGAGTAAGGATTGACT
TTGATGATGAGAATGACATAAGCATAGGTTGGACTAAGGCAGCCACGAATACAACATCAGTAGCAGAAGCAAGGCACAAC
CCTAGCATAGGAGAGGGAAGTGTCAGCGGCCTGACTGGCAGTTTGAGTGCAAGTGGAAGCCACATGGATGGAATAGGCAC
TATTGGCAACAACCTGAGTGAGACAGTCAGTACCATAAGCTTAGCTGGAGCTAGTAGCACAGGCAGTCTGTCAGGAAGTG
CCATGGTAAACAGTTTCAGCAATTTGCAAGTTCAAGCAGACGTACAGAAAGAAATGTGTAATCTCAGTAGAGAATCTGGC
ACAGTGAGTTTGGGAAGAGTTTGTAATAACAGCAGCACCAAAGCAGTGGCAGGATCCATTCTGAACTCCTACATCCCTCT
CGACAGAGAAGGGAACAGTGTGGAAGTGCAAGTGGGTATTGAATCAAAGTCATTCAAGTTCCAACACAGCCGTGGAAGCA
GCAGTGTAAATAGCAGTGGTGCTGCCCGAGGCCACATGGGCAGGTCATACAGTGGCTTGCCTGAAGGTAAATCCAGTGCT
ACCGAGTGGTCCAAGGAAGCAACAGGAGGAAAAAAGTCAAAAAGTGGTAAACTGAGGGAAAAGGGTAACATGAAGATCAA
TGAGGCCAGAGAGGACAAGGATGCACAGTTGTTACAGCCTCAAAGCACAGATTTAGGTGAGTTTGAGGTGCCATCCCTGA
GTGACAACTTGCCATCTGTAGCAGTCTCCCACTACAGTCACTCTTCTTACTTAGAAAGCATGAGAATGTCCTGTAGTCAC
CATTCCAGGGGTTGCCACGCTACTTCCCAGCTGTGAACACCCTTCCTGAGGTAAAAAAGGATGGGCTGAAACATTCACCA
CACCAGGGCAGCAGTGCTCTGCTTTCCAAAACTGCTTTCTGTTCAGAAGTCCCACAGTCCAGCCATGCAGCAGATGAGCA
TGGCACCAACTGACGTTGGGGGAAGCTGATGGTGGATGGTGATGCACTGAGAGAGCCAAATAATAACCACTCGCACCAGA
CAGCCGACTTAAAAGTTGCTGTCCAGACTACAGTG
ORF - retro_mmus_3275 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 78.93 % |
| Parental protein coverage: | 97.62 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | DSDSILMSILDMSLHQQMGSDRDLQSSTSSVSLPSVKKAPKQRRISIGSLFRRKKDSKRKSRELNGGVDG |
| DSDS.L.SILDMSLHQQ.GS..D.Q.S.SSVSLPSVKKAPKQRR.SIGS.F..K.DSKRKSRELNGGV.. | |
| Retrocopy | DSDSVLISILDMSLHQQVGSEGDRQLSASSVSLPSVKKAPKQRRFSIGSRFQGKMDSKRKSRELNGGVEA |
| Parental | IASIESIHSEMCADKNSIFSTNTSSDNGLTSISKQIGDFIECPLCLLRHSKDRFPDIMTCHHRSCVDCLR |
| IA.IESIHSEM.ADKNSIFS.NTSSDN.LTSISKQ.GDF..CPLCLLR.S.DRFPD.MTCHHRSCVDCL. | |
| Retrocopy | IARIESIHSEMFADKNSIFSANTSSDNRLTSISKQTGDFMDCPLCLLRLSQDRFPDNMTCHHRSCVDCL* |
| Parental | QYLRIEISESRVNISCPECTERFNPHDIRLILSDDVLMEKYEEFMLRRWLVADPDCRWCPAPDCGYAVIA |
| QYLRIEISESRVN.SCPECTERFNPHDIRLILSDDVLM.KYEEFMLR.WLVADPDCRWCPAPDCGYAVIA | |
| Retrocopy | QYLRIEISESRVNVSCPECTERFNPHDIRLILSDDVLMGKYEEFMLRQWLVADPDCRWCPAPDCGYAVIA |
| Parental | FGCASCPKLTCGREGCGTEFCYHCKQIWHPNQTCDAARQERAQSLRLRTIRSSSISYSQESGAAADDIKP |
| FGCA.CPKLTCG..G..TEFCYHCKQIWHP.QTC.AA..ERAQ.L.LRT...S.ISY.QES.AAADDIKP | |
| Retrocopy | FGCARCPKLTCGQKGYRTEFCYHCKQIWHPKQTCEAALWERAQCLCLRTLPFSPISYKQESRAAADDIKP |
| Parental | CPRCAAYIIKMNDGSCNHMTCAVCGCEFCWLCMKEISDLHYLSPSGCTFWGKKPWSRKKKILWQLGTLVG |
| CPRCA.YIIK..D..CNHMTCAVCGCEFCWLCMKEIS..HYL.PSGC...GKKPW.RKKKILWQL.TLVG | |
| Retrocopy | CPRCAPYIIKIEDERCNHMTCAVCGCEFCWLCMKEISNFHYLNPSGCSLRGKKPWTRKKKILWQLRTLVG |
| Parental | APVGIALIAGIAIPAMIIGIPVYVGRKIHNRYEGKDVSKHKRNLAIAGGVTLSVIVSPVVAAVTVGIGVP |
| AP.GIALIAGIA.PAMIIG.PVYVG.KIH..YE..DVSKHK.NL.IA..VTLSVI.S.VVA.VT.G.GVP | |
| Retrocopy | APIGIALIAGIALPAMIIGVPVYVGLKIHDCYEDRDVSKHKCNLVIASAVTLSVIISLVVATVTIGTGVP |
| Parental | IMLAYVYGVVPISLCRSGGCGVSAGNGKGVRIEFDDENDINVGGTNAAIDTTSVAEARHNPSIGEGSVGG |
| .ML.YVYGV.PISLCR...CG.SAGNGKGVRI.FDDENDI..G.T.AA..TTSVAEARHNPSIGEGSV.G | |
| Retrocopy | TMLGYVYGVFPISLCRNRNCGESAGNGKGVRIDFDDENDISIGWTKAATNTTSVAEARHNPSIGEGSVSG |
| Parental | LTGSLSASGSHMDRIGTIRDNLSETASTMALAGASITGSLSGSAMVNCFNRLEVQADVQKERCSLSGESG |
| LTGSLSASGSHMD.IGTI..NLSET.ST..LAGAS.TGSLSGSAMVN.F..L.VQADVQKE.C.LS.ESG | |
| Retrocopy | LTGSLSASGSHMDGIGTIGNNLSETVSTISLAGASSTGSLSGSAMVNSFSNLQVQADVQKEMCNLSRESG |
| Parental | TVSLGTVSDNASTKAMAGSILNSYIPLDREGNSMEVQVDIESKPFKFRHNSGSSSVDDSGATRGHTGGAS |
| TVSLG.V..N.STKA.AGSILNSYIPLDREGNS.EVQV.IESK.FKF.H..GSSSV..SGA.RGH.G... | |
| Retrocopy | TVSLGRVCNNSSTKAVAGSILNSYIPLDREGNSVEVQVGIESKSFKFQHSRGSSSVNSSGAARGHMGRSY |
| Parental | SGLPEGKSSATKWSKEATGGKKSKSGKLRKKGNMKINETREDMDAQLLEQQSTNSSEFEAPSLSDSMPSV |
| SGLPEGKSSAT.WSKEATGGKKSKSGKLR.KGNMKINE.RED.DAQLL..QST...EFE.PSLSD..PSV | |
| Retrocopy | SGLPEGKSSATEWSKEATGGKKSKSGKLREKGNMKINEAREDKDAQLLQPQSTDLGEFEVPSLSDNLPSV |
| Parental | ADSHSSHFSEFSCSDLESMRTSCSHGSSDCHAR-FTAVNTLPEVENDRLENSPHQCSSALLSKAASCSDV |
| A....SH.S..S...LESMR.SCSH.S..CHA..F.AVNTLPEV..D.L..SPHQ.SSALLSK.A.CS.V | |
| Retrocopy | A---VSHYSHSSY--LESMRMSCSHHSRGCHAT<FPAVNTLPEVKKDGLKHSPHQGSSALLSKTAFCSEV |
| Parental | PQPSHAADEHGTSRSGGKPMVDLCFGDALRETNNNHSHQTADLKVAVQTEI |
| PQ.SHAADEHGT....GK.MVD...GDALRE.NNNHSHQTADLKVAVQT.. | |
| Retrocopy | PQSSHAADEHGTN*RWGKLMVD---GDALREPNNNHSHQTADLKVAVQTTV |
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 .30 RPM | 38 .95 RPM |
| SRP007412_cerebellum | 0 .35 RPM | 36 .82 RPM |
| SRP007412_heart | 0 .59 RPM | 24 .16 RPM |
| SRP007412_kidney | 0 .67 RPM | 51 .78 RPM |
| SRP007412_liver | 0 .08 RPM | 36 .89 RPM |
| SRP007412_testis | 23 .92 RPM | 554 .72 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3275 was not detected
1 EST(s) were mapped to retro_mmus_3275 retrocopy
| EST ID | Start | End | Identity | Match | Mis-match | Score |
|---|---|---|---|---|---|---|
| AW990540 | 55950274 | 55950819 | 100 | 545 | 0 | 545 |
No TSS is located nearby retro_mmus_3275 retrocopy 5' end.
retro_mmus_3275 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3275 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000022280 | 3 retrocopies |
retro_mmus_3267, retro_mmus_3275 , retro_mmus_3277,
|