RetrogeneDB ID: | retro_mmus_247 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 7:127286040..127286385(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000090460 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rplp1 | ||
| Ensembl ID: | ENSMUSG00000007892 | ||
| Aliases: | Rplp1, 2410042H16Rik, Arpp1, C430017H15Rik | ||
| Description: | ribosomal protein, large, P1 [Source:MGI Symbol;Acc:MGI:1927099] |
Retrocopy-Parental alignment summary:
>retro_mmus_247
ATGGCTTCTGTCTCCGAGCTTGCCTGCATCTACTCCACCCTCATCCTGCATGATGATGAGGTGACAGTCACGGAGGATAA
GATCAGTGCCCTCATTAAAGCAGCTGGTGTCAGCGTTGAACCTTTCTGGCCTGGCTCGTTTGCCAAGGCTCTGGCCAATG
TCAACATTGGGAGCCTCATCTGCAATGTAGGGGCTGGTGGGCCCGCTCCAGCAGCTGGAGCTGCGCCTGCTGGTGGTCCA
GCTCCATCCACTGCTGCCGCCCCAGCTGAGGAGAAGAAAGTGGAAGCAAAGAAGGAAGAGTCCGAGGAGTCTGAAGATGA
CAGGGGCTTTGGTCTTTTTGACTAA
ORF - retro_mmus_247 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 95.61 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MASVSELACIYSALILHDDEVTVTEDKINALIKAAGVSVEPFWPGLFAKALANVNIGSLICNVGAGGPAP |
| MASVSELACIYS.LILHDDEVTVTEDKI.ALIKAAGVSVEPFWPG.FAKALANVNIGSLICNVGAGGPAP | |
| Retrocopy | MASVSELACIYSTLILHDDEVTVTEDKISALIKAAGVSVEPFWPGSFAKALANVNIGSLICNVGAGGPAP |
| Parental | AAGAAPAGGAAPSTAAAPAEEKKVEAKKEESEESEDDMGFGLFD |
| AAGAAPAGG.APSTAAAPAEEKKVEAKKEESEESEDD.GFGLFD | |
| Retrocopy | AAGAAPAGGPAPSTAAAPAEEKKVEAKKEESEESEDDRGFGLFD |
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 | 145 .11 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 79 .07 RPM |
| SRP007412_heart | 0 .00 RPM | 153 .10 RPM |
| SRP007412_kidney | 0 .00 RPM | 121 .10 RPM |
| SRP007412_liver | 0 .03 RPM | 120 .18 RPM |
| SRP007412_testis | 0 .14 RPM | 71 .95 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_247 was not detected
No EST(s) were mapped for retro_mmus_247 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_129126 | 68 libraries | 63 libraries | 627 libraries | 208 libraries | 106 libraries |
The graphical summary, for retro_mmus_247 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_247 was not experimentally validated.