RetrogeneDB ID: | retro_mmus_85 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:126814067..126815480(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000058670 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Dmtf1 | ||
| Ensembl ID: | ENSMUSG00000042508 | ||
| Aliases: | Dmtf1, Dimp, Dmp1 | ||
| Description: | cyclin D binding myb-like transcription factor 1 [Source:MGI Symbol;Acc:MGI:1344415] |
Retrocopy-Parental alignment summary:
>retro_mmus_85
ATGAGCTCTGTCTTACTTAGTGAGGACTCAGACAGGAACCTCATGCTTTGCCTTCAGAATGAAGCTAATGAAATGGAAAA
TCCTACTGAACCTCTGAATAAGAGGCCTTGTTTGTCCTCTGAAGTTGATTCTACTTCGTATATGTCAGCTCTTGAATTCC
CACTACAAGAAATGGAGCAAAGTTTTGGTTTGGTCACAACCACAGCCACAGAGGTGGCTGAGGAAGAGTTTGGTGGGGAA
AATATGATGCAATTCGAGGTTTTAAAAGATGACAAACAATATGAAGTTTTCCCCTTGCCTAACAAGGAAGAGTCAGTAGT
TAGCCAAGCATGGTTCACAAGTAAGGAAGCTAAGGATGCTCTAACTCATCAAGGACAGAAATGGAAGCAGGGGATGTGGT
CCAAGGAAGAAACAGCTATTCTGATGAACAACATTGAAAGGTATATGAAGGACCATGGAGTAGAGAATCCTGCAGAAATC
ATTTTTAAGATGGCAAAAGGTAAAAGAAAAGATTTCTACAGGTCTGTATCATTGGGTCTGAATAGACCTTTGTTTTCAGT
TTATAGAAGAGTGGTCCGAATGTATGATGACAGAAACCATGTGGGTAAGTACAGCCCTGAGGAAATAGAGAAGCTCAAGG
AGCTCTGGCAGAAGCATGGCAATGACTGGATAACAATAGGGGCCGCCATGGGAAGAAGTCCATCTTCGGTCAAAGACCGG
TGCCGACTGATGAAGGATACTTGCAACACGGGGAAATGGACCGAAGAAGAAGAACAGCTTCTTGGCGATGTGGTTCATGA
ATTGACATGCACTGAGGTGGATGAGAAAGTTACCCATGGTGTGTGTTGGGCAACAGTGGCTCAACGAGTGGGTACTCGCT
CAGCAAAGCAGTGTCGTGCTAAATGGCTCAACTACTTGAACTGGAAACAGACTGGTGGTATTGAGTGGACAAGGAAAGAT
GAAGTCACTCTCATCCAAAGGCTAGTAGAGCTTGATGTATCCGATGAAAGTGAAATTCGCTGGGATGAATTAGCTAAAGG
ATGGGAAAGTGTTCGTTCACCACAATGGCTGCGAAATAAATGGTGGATCATCAAAAGGCAAATTACAAATCATAAAGATT
TTGCATTCCCAGTCCTAGTAAGATGTCTTCAACAAGAATATGAAAGCCAAAATGCCAGCCTCAGGTTTTGGGAGAATAAA
TCAGGATCTGAAGTACCAGATAGCAACCCTGATATCATTTTTCAACAAGTCCCCTTTGGAGTCACAAGTATAGAAAATAA
TAATGCATCCATCTGTACTGACCCCATGACAGGATTGCAAATTTCATTCCAGCTCATCCCCAGACCCACAACAGAATTAC
CTGATGCTGTTGTTGACTCTGAAACCATAACCCTGCCCACTGGACCACAGTAG
ORF - retro_mmus_85 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 62.68 % |
| Parental protein coverage: | 55.85 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | DATPCISVVALPLSENDQSFEVTMTATTEVADDELSEGTVTQIQILQNDQLDEISPLGTEEVSAVSQAWF |
| D.T...S....PL.E..QSF....T..TEVA..E.......Q...L..D...E..PL...E.S.VSQAWF | |
| Retrocopy | DSTSYMSALEFPLQEMEQSFGLVTTTATEVAEEEFGGENMMQFEVLKDDKQYEVFPLPNKEESVVSQAWF |
| Parental | TTKEDKDSLTNKGHKWKQGMWSKEEIDILMNNIERYLKARGIKDATEIIFEMSKDERKDFYRTIAWGLNR |
| T.KE.KD.LT..G.KWKQGMWSKEE..ILMNNIERY.K..G.....EIIF.M.K..RKDFYR....GLNR | |
| Retrocopy | TSKEAKDALTHQGQKWKQGMWSKEETAILMNNIERYMKDHGVENPAEIIFKMAKGKRKDFYRSVSLGLNR |
| Parental | PLFAVYRRVLRMYDDRNHVGKYTPEEIEKLKELRIKHGNDWATIGAALGRSASSVKDRCRLMKDTCNTGK |
| PLF.VYRRV.RMYDDRNHVGKY.PEEIEKLKEL..KHGNDW.TIGAA.GRS.SSVKDRCRLMKDTCNTGK | |
| Retrocopy | PLFSVYRRVVRMYDDRNHVGKYSPEEIEKLKELWQKHGNDWITIGAAMGRSPSSVKDRCRLMKDTCNTGK |
| Parental | WTEEEEKRLAEVVHELTSTEPGDIVTQGVSWAAVAERVGTRSEKQCRSKWLNYLNWKQSGGTEWTKEDEI |
| WTEEEE..L..VVHELT.TE....VT.GV.WA.VA.RVGTRS.KQCR.KWLNYLNWKQ.GG.EWT..DE. | |
| Retrocopy | WTEEEEQLLGDVVHELTCTEVDEKVTHGVCWATVAQRVGTRSAKQCRAKWLNYLNWKQTGGIEWTRKDEV |
| Parental | NLILRIAELDVADENDINWDLLAEGWSSVRSPQWLRSKWWTIKRQIANHKDVSFPVLIKGLKQLHENQKN |
| .LI.R..ELDV.DE..I.WD.LA.GW.SVRSPQWLR.KWW.IKRQI.NHKD..FPVL...L.Q..E.Q.. | |
| Retrocopy | TLIQRLVELDVSDESEIRWDELAKGWESVRSPQWLRNKWWIIKRQITNHKDFAFPVLVRCLQQEYESQNA |
| Parental | NPVLLENKSGSGVPNSNCNSSVQHVQIRVARLEDNTA-ISPSPMAALQIPVQITHVSSTDSPAASVDSET |
| .....ENKSGS.VP.SN.....Q.V...V...E.N.A.I...PM..LQI..Q......T..P.A.VDSET | |
| Retrocopy | SLRFWENKSGSEVPDSNPDIIFQQVPFGVTSIENNNASICTDPMTGLQISFQLIPRPTTELPDAVVDSET |
| Parental | ITLNSG |
| ITL..G | |
| Retrocopy | ITLPTG |
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 | 59 .74 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 71 .60 RPM |
| SRP007412_heart | 0 .00 RPM | 17 .87 RPM |
| SRP007412_kidney | 0 .00 RPM | 28 .07 RPM |
| SRP007412_liver | 0 .00 RPM | 19 .80 RPM |
| SRP007412_testis | 5 .53 RPM | 29 .50 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_85 was not detected
No EST(s) were mapped for retro_mmus_85 retrocopy.
No TSS is located nearby retro_mmus_85 retrocopy 5' end.
retro_mmus_85 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_85 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000042508 | 1 retrocopy |
retro_mmus_85 ,
|
| Rattus norvegicus | ENSRNOG00000005908 | 2 retrocopies |