RetrogeneDB ID: | retro_mmus_1760 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 18:30419685..30420060(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rps25 | ||
| Ensembl ID: | ENSMUSG00000009927 | ||
| Aliases: | Rps25, 2810009D21Rik | ||
| Description: | ribosomal protein S25 [Source:MGI Symbol;Acc:MGI:1922867] |
Retrocopy-Parental alignment summary:
>retro_mmus_1760
ATGCCGCCCAAAGACGACAAGAAGAAGAAAGATGCCGGAAAGTCAGCCAAAAAGGATAAAGATCCAGTAAATAAATCTGG
TGGCAAGGCCAAGAAGAAGAAGTGGTCCAAAGGCAAAGTTCGGGACAAGTTGAACAATCTTGTCCTGTTCGACAAAGCGA
CATAAGACAAGCTCTGTAAAGAGGTTCCGAACTATAAGCTTATTACTCCAGCTGTGGTCTCCGAGAGACTGAAGATTCGC
GGTTCCTTGGCCAGGGCAGCCCTTCAGGAGCTCCTTAGTAAAGGACTTATCAAGCTGGTTTCAAAGCACAGAGCCCAAGT
AATTTACACCAGAAACACAAAGGGTGGAGACGCTCCAGCTGCTGGCGAAGATGCA
ORF - retro_mmus_1760 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.2 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MPPKDDKKKKDAGKSAKKDKDPVNKSGGKAKKKKWSKGKVRDKLNNLVLFDKATYDKLCKEVPNYKLITP |
| MPPKDDKKKKDAGKSAKKDKDPVNKSGGKAKKKKWSKGKVRDKLNNLVLFDKAT.DKLCKEVPNYKLITP | |
| Retrocopy | MPPKDDKKKKDAGKSAKKDKDPVNKSGGKAKKKKWSKGKVRDKLNNLVLFDKAT*DKLCKEVPNYKLITP |
| Parental | AVVSERLKIRGSLARAALQELLSKGLIKLVSKHRAQVIYTRNTKGGDAPAAGEDA |
| AVVSERLKIRGSLARAALQELLSKGLIKLVSKHRAQVIYTRNTKGGDAPAAGEDA | |
| Retrocopy | AVVSERLKIRGSLARAALQELLSKGLIKLVSKHRAQVIYTRNTKGGDAPAAGEDA |
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 | 51 .91 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 34 .65 RPM |
| SRP007412_heart | 0 .06 RPM | 53 .73 RPM |
| SRP007412_kidney | 0 .02 RPM | 63 .54 RPM |
| SRP007412_liver | 0 .00 RPM | 64 .01 RPM |
| SRP007412_testis | 0 .00 RPM | 52 .01 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1760 was not detected
No EST(s) were mapped for retro_mmus_1760 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_58337 | 278 libraries | 587 libraries | 200 libraries | 5 libraries | 2 libraries |
The graphical summary, for retro_mmus_1760 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_1760 was not experimentally validated.