RetrogeneDB ID: | retro_mmus_2742 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 6:67205618..67206080(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000047905 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Sod1 | ||
| Ensembl ID: | ENSMUSG00000022982 | ||
| Aliases: | Sod1, B430204E11Rik, Cu/Zn-SOD, CuZnSOD, Ipo-1, Ipo1, SODC, Sod-1 | ||
| Description: | superoxide dismutase 1, soluble [Source:MGI Symbol;Acc:MGI:98351] |
Retrocopy-Parental alignment summary:
>retro_mmus_2742
ATGGCGAGGAAAGCGGTGTGCATGCTGAAGGGCGATGGTCCGGTGCAGGGAACCATCCACTTCGAGCAGAAGGCAAGCGG
TGAACCAGTTGTGTTGTCAGGACAAATTACAGGATTAACTGAAGGCCAGCATGGGTTCCACGTCCATCAGTATGGGGATA
ATACACAAGGCTGTACCAGTGCAGGACCTCATTTTAATCCTCACTCTAAGAAACATGGCGGCCCGGCGGATGAAGAGAGG
CATGTTGGAGACCTGGGCAATGTGACTGCTGGAAAGAACGGTGTGGCCAATGTGTCCATTGATGATCGTGTGATCTCACT
CTCAGGAGAGCACTCCATCATTGGCCGTACAATGGTGGTCCACGAGAAACAAGATGACTTGGGCAAAGGTGGAAATGAAG
AAAGTACAAAGACTGGAAATGCTGGGAGCCGCTTGGCCTGTGGAGTGATTGGGATTGCCCAG
ORF - retro_mmus_2742 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.4 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAMKAVCVLKGDGPVQGTIHFEQKASGEPVVLSGQITGLTEGQHGFHVHQYGDNTQGCTSAGPHFNPHSK |
| MA.KAVC.LKGDGPVQGTIHFEQKASGEPVVLSGQITGLTEGQHGFHVHQYGDNTQGCTSAGPHFNPHSK | |
| Retrocopy | MARKAVCMLKGDGPVQGTIHFEQKASGEPVVLSGQITGLTEGQHGFHVHQYGDNTQGCTSAGPHFNPHSK |
| Parental | KHGGPADEERHVGDLGNVTAGKDGVANVSIEDRVISLSGEHSIIGRTMVVHEKQDDLGKGGNEESTKTGN |
| KHGGPADEERHVGDLGNVTAGK.GVANVSI.DRVISLSGEHSIIGRTMVVHEKQDDLGKGGNEESTKTGN | |
| Retrocopy | KHGGPADEERHVGDLGNVTAGKNGVANVSIDDRVISLSGEHSIIGRTMVVHEKQDDLGKGGNEESTKTGN |
| Parental | AGSRLACGVIGIAQ |
| AGSRLACGVIGIAQ | |
| Retrocopy | AGSRLACGVIGIAQ |
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 .49 RPM | 111 .04 RPM |
| SRP007412_cerebellum | 0 .74 RPM | 139 .34 RPM |
| SRP007412_heart | 0 .72 RPM | 200 .48 RPM |
| SRP007412_kidney | 2 .31 RPM | 426 .50 RPM |
| SRP007412_liver | 2 .62 RPM | 804 .92 RPM |
| SRP007412_testis | 1 .05 RPM | 241 .32 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2742 was not detected
No EST(s) were mapped for retro_mmus_2742 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_124040 | 844 libraries | 214 libraries | 12 libraries | 1 library | 1 library |
The graphical summary, for retro_mmus_2742 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_2742 was not experimentally validated.