RetrogeneDB ID: | retro_mmus_1483 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 16:90089981..90090496(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Myl12b | ||
| Ensembl ID: | ENSMUSG00000034868 | ||
| Aliases: | None | ||
| Description: | myosin, light chain 12B, regulatory [Source:MGI Symbol;Acc:MGI:107494] |
Retrocopy-Parental alignment summary:
>retro_mmus_1483
ATGTCGAGCAAAAAAGCAAAGACCAAGACCACCAAGAAGCACCCTAAGCGCACAACGTCCAATGTGTTCGCCATGTTTGA
CCAGTCCCAGATCCAGGAGTTCAAAGAGGCCTTTAACATGATTGACCAGAACTGGGATGGCTTCATTGACGAGGAGGACC
TGCACGACATGCTGGCGTCTCTGGGAAGAACCCCACTGATGCCTACCTGGACGCCATGATGAACGAGGCCCCGAGCCCCA
TCAATTTCACCATGTTCCTCGCCATGTTTGGAGAGAAGCTGAACGGAACTGACCCCGAGGACGTCATCAGAAACGCCTTC
GCTTGCTTCCATGAGGAAGCCACAGGCACCATCCAGGAGGATTACCTGAGGGAGCTGCTGACCACCATGGGCGACCGCTT
CACAGACGAGGAGGTGGGTGAGCTGTACAGAGAAGCCCCCATTGACAAAAAGGGGAACTTCAACTACATTGAGTTCACAC
GCATCCTGAAGCACGGCGCGAAAGACTAAGATGAC
ORF - retro_mmus_1483 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.64 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MSSKKAKTKTTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDGFIDKEDLHDMLASLG-KNPTDAY |
| MSSKKAKTKTTKK.P.R.TSNVFAMFDQSQIQEFKEAFNMIDQN.DGFID.EDLHDMLASLG.KNPTDAY | |
| Retrocopy | MSSKKAKTKTTKKHPKRTTSNVFAMFDQSQIQEFKEAFNMIDQNWDGFIDEEDLHDMLASLG<KNPTDAY |
| Parental | LDAMMNEAPGPINFTMFLTMFGEKLNGTDPEDVIRNAFACFDEEATGTIQEDYLRELLTTMGDRFTDEEV |
| LDAMMNEAP.PINFTMFL.MFGEKLNGTDPEDVIRNAFACF.EEATGTIQEDYLRELLTTMGDRFTDEEV | |
| Retrocopy | LDAMMNEAPSPINFTMFLAMFGEKLNGTDPEDVIRNAFACFHEEATGTIQEDYLRELLTTMGDRFTDEEV |
| Parental | DELYREAPIDKKGNFNYIEFTRILKHGAKDKDD |
| .ELYREAPIDKKGNFNYIEFTRILKHGAKD.DD | |
| Retrocopy | GELYREAPIDKKGNFNYIEFTRILKHGAKD*DD |
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 .07 RPM | 109 .92 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 68 .13 RPM |
| SRP007412_heart | 0 .06 RPM | 28 .02 RPM |
| SRP007412_kidney | 0 .08 RPM | 70 .05 RPM |
| SRP007412_liver | 0 .03 RPM | 37 .33 RPM |
| SRP007412_testis | 0 .78 RPM | 16 .51 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1483 was not detected
No EST(s) were mapped for retro_mmus_1483 retrocopy.
| TSS No. | TSS Name | TSS expression level (Expr) in TPM range: | ||||
|---|---|---|---|---|---|---|
| no expression | 0 < Expr ≤ 1 | 1 < Expr ≤ 5 | 5 < Expr ≤ 10 | Expr > 10 | ||
| TSS #1 | TSS_49383 | 97 libraries | 209 libraries | 570 libraries | 122 libraries | 74 libraries |
The graphical summary, for retro_mmus_1483 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)
retro_mmus_1483 was not experimentally validated.