RetrogeneDB ID: | retro_mmus_3298 | ||
Retrocopylocation | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 9:94139461..94140046(+) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | 3110082I17Rik | ||
| Ensembl ID: | ENSMUSG00000053553 | ||
| Aliases: | 3110082I17Rik, AW411904 | ||
| Description: | RIKEN cDNA 3110082I17 gene [Source:MGI Symbol;Acc:MGI:1920462] |
Retrocopy-Parental alignment summary:
>retro_mmus_3298
ATGGCAAAACATAAGAGAAAATGTCTCAGTGGGACAGGGAAGGAGAGGAAAAAGCAGAAGATGACACTGGCAGAGGAGAT
GCCACCGAGGGCATTTGAAGCTAGACCAGACAAGGAGATGGCCGGTCCCATTGTGCAGGAGGCCAGCCCAGAGTTGTCCC
CAGAGGAGAGAAGGGTCTTGGAGAGGAAACTAAAGAAGGAACAGAAGAAGAAAATGAAAAAGCAGCTGCGGGAGGCGGGC
ATTGCCGCAGTACAGACTGCCAAGGTTCAGACCCTGCCAGCCAAACCCTCAGCTACCGTCTTGTCCCTACAGTAACTCGA
AGGGTGGGTTCAGAAGCAAGAGAGCTGGAGATTCCAGAAGATAAAGCAGACGTGGCTCTTGCACGTGTACGATGAGGACA
AGATTTCGGGTGAGCACTTTTCTACCCTGCTGGACTACCTCGAAGGATTGAAGGGCAGTACCCAATTGCTGACAGTACAG
AAGGCCAAGGCCCTGATGCAAAAGCAAGATGAGGCTGACCCCAAGACCAGAGACGGGTCTCTGGGGAAGGTTCATTGCCT
CCGGCAGGTGCTACAGCTACTCTCC
ATGGCAAAACATAAGAGAAAATGTCTCAGTGGGACAGGGAAGGAGAGGAAAAAGCAGAAGATGACACTGGCAGAGGAGAT
GCCACCGAGGGCATTTGAAGCTAGACCAGACAAGGAGATGGCCGGTCCCATTGTGCAGGAGGCCAGCCCAGAGTTGTCCC
CAGAGGAGAGAAGGGTCTTGGAGAGGAAACTAAAGAAGGAACAGAAGAAGAAAATGAAAAAGCAGCTGCGGGAGGCGGGC
ATTGCCGCAGTACAGACTGCCAAGGTTCAGACCCTGCCAGCCAAACCCTCAGCTACCGTCTTGTCCCTACAGTAACTCGA
AGGGTGGGTTCAGAAGCAAGAGAGCTGGAGATTCCAGAAGATAAAGCAGACGTGGCTCTTGCACGTGTACGATGAGGACA
AGATTTCGGGTGAGCACTTTTCTACCCTGCTGGACTACCTCGAAGGATTGAAGGGCAGTACCCAATTGCTGACAGTACAG
AAGGCCAAGGCCCTGATGCAAAAGCAAGATGAGGCTGACCCCAAGACCAGAGACGGGTCTCTGGGGAAGGTTCATTGCCT
CCGGCAGGTGCTACAGCTACTCTCC
ORF - retro_mmus_3298 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 74.49 % |
| Parental protein coverage: | 100. % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAKHKRKGLEGTGKESKRQKITPAEETP-RTSEAGPDKETASTLVQEASPELSPEERRVLERKLKKERKK |
| MAKHKRK.L.GTGKE.K.QK.T.AEE.P.R..EA.PDKE.A...VQEASPELSPEERRVLERKLKKE.KK | |
| Retrocopy | MAKHKRKCLSGTGKERKKQKMTLAEEMPPRAFEARPDKEMAGPIVQEASPELSPEERRVLERKLKKEQKK |
| Parental | EEKKRLREAGIAATQTAKVQTLPAKPSAATLALEYLQGWAQKQESWRFQKTRQTWLLLHMYDEDKVPDEH |
| ..KK.LREAGIAA.QTAKVQTLPAKPSA..L.L..L.GW.QKQESWRFQK..QTW.LLH.YDEDK...EH | |
| Retrocopy | KMKKQLREAGIAAVQTAKVQTLPAKPSATVLSLQ*LEGWVQKQESWRFQKIKQTW-LLHVYDEDKISGEH |
| Parental | FPTLLDYLEGLRGSARELTVRKAEALMQKLDEAEPEDSGGSPGKVQRLRQVLQLLS |
| F.TLLDYLEGL.GS...LTV.KA.ALMQK.DEA.P....GS.GKV..LRQVLQLLS | |
| Retrocopy | FSTLLDYLEGLKGSTQLLTVQKAKALMQKQDEADPKTRDGSLGKVHCLRQVLQLLS |
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 | 4 .18 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 3 .95 RPM |
| SRP007412_heart | 0 .00 RPM | 4 .51 RPM |
| SRP007412_kidney | 0 .00 RPM | 5 .10 RPM |
| SRP007412_liver | 0 .00 RPM | 4 .04 RPM |
| SRP007412_testis | 0 .00 RPM | 17 .47 RPM |
RNA Polymerase II actvity near the 5' end of retro_mmus_3298 was not detected
No EST(s) were mapped for retro_mmus_3298 retrocopy.
No TSS is located nearby retro_mmus_3298 retrocopy 5' end.
retro_mmus_3298 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3298 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000053553 | 1 retrocopy |
retro_mmus_3298 ,
|