RetrogeneDB ID: | retro_mmus_3198 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 8:47632331..47632631(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000062458 | |
| Aliases: | Gm8623, EG667422 | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rps16 | ||
| Ensembl ID: | ENSMUSG00000037563 | ||
| Aliases: | Rps16, AA420385, AI317031 | ||
| Description: | ribosomal protein S16 [Source:MGI Symbol;Acc:MGI:98118] |
Retrocopy-Parental alignment summary:
>retro_mmus_3198
CTGCAGTACAAGTTACTGGAGCCTGTTTTGCTTCTGGGCAAGGAGCGATTTGCTGGTGTGGATATTCGGGTCCGTGTGAA
GGGTGGTGGACATGTGGCCCAAATTTATGCCATCCGACAGTCCATCTCAAAGGCCCTGGTAGCTTATTACCAAAAATATG
TGGATGAAGCCTCTAAGAAGGAGATCAAAGATATCCTCATCCAATACGATCGGACCCTGCTTGTAGCTGACCCCCGTCGC
TGCGAATCCAAAAAGTTTGGAGGTCCTGGTGCCCGTGCCCGATACCAGAAATCCTACCGA
ORF - retro_mmus_3198 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 100.0 % |
| Parental protein coverage: | 68.49 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LQYKLLEPVLLLGKERFAGVDIRVRVKGGGHVAQIYAIRQSISKALVAYYQKYVDEASKKEIKDILIQYD |
| LQYKLLEPVLLLGKERFAGVDIRVRVKGGGHVAQIYAIRQSISKALVAYYQKYVDEASKKEIKDILIQYD | |
| Retrocopy | LQYKLLEPVLLLGKERFAGVDIRVRVKGGGHVAQIYAIRQSISKALVAYYQKYVDEASKKEIKDILIQYD |
| Parental | RTLLVADPRRCESKKFGGPGARARYQKSYR |
| RTLLVADPRRCESKKFGGPGARARYQKSYR | |
| Retrocopy | RTLLVADPRRCESKKFGGPGARARYQKSYR |
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 | 27 .17 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 26 .83 RPM |
| SRP007412_heart | 0 .09 RPM | 63 .01 RPM |
| SRP007412_kidney | 0 .04 RPM | 70 .40 RPM |
| SRP007412_liver | 0 .03 RPM | 66 .99 RPM |
| SRP007412_testis | 0 .05 RPM | 33 .53 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3198 was not detected
No EST(s) were mapped for retro_mmus_3198 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_142650 | 111 libraries | 250 libraries | 614 libraries | 85 libraries | 12 libraries |
The graphical summary, for retro_mmus_3198 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_3198 was not experimentally validated.