RetrogeneDB ID: | retro_mmus_385 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 1:164489014..164489375(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rpl32 | ||
| Ensembl ID: | ENSMUSG00000057841 | ||
| Aliases: | Rpl32, AU020185, rpL32-3A | ||
| Description: | ribosomal protein L32 [Source:MGI Symbol;Acc:MGI:98038] |
Retrocopy-Parental alignment summary:
>retro_mmus_385
CCCTCCTGTCTCTGTCGAAGAGGATCAAGACGATCATCAGGCACCAGTCAAACTTACGTCAAAATTAAGCGACACTGACT
GAACCCCAGAGGTGTAGACGACAAGATGAGGAAAAGATTCCAGGGCCAGATCCTGATGCCCAACATCGGTTACTGGAGCA
AAAAGAAAACCAAGTACATTCTACCCAGCGGCTTCCGGAAGTTTCTGGCCCACAATGTCAAGGAGCTGATGTGCAATCAA
AAGTTACTGTGCCATGATCTCTCATGTTTAGTCCAAAAACCACAAAGCCATCGTAGAAAGAACAGTGCAGCTGGTTACCA
GAGTCACTAATCCCAATGCCAGTCCACGTAGCAAAGAAAAT
ORF - retro_mmus_385 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 62.7 % |
| Parental protein coverage: | 92.59 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | PKIVKKRTKKFIRHQSDRYVKIKRNWRKPRGIDNRVRRRFKGQILMPNIGYGSNKKTKHMLPSGFRKFLV |
| P.....R........S..YVKIKR....PRG.D...R.RF.GQILMPNIGY.S.KKTK..LPSGFRKFL. | |
| Retrocopy | PSCLCRRGSRRSSGTSQTYVKIKRH*LNPRGVDDKMRKRFQGQILMPNIGYWSKKKTKYILPSGFRKFLA |
| Parental | HNVKELEVLLMCN-KSYCAEIAHNVSSKNRKAIVERAAQLAIRVTNPNARLRSEEN |
| HNVKEL....MCN.KSYCA.I.H.V.SKN.KAIVER..QL..RVTNPNA..RS.EN | |
| Retrocopy | HNVKEL----MCN>KSYCAMISH-V*SKNHKAIVERTVQLVTRVTNPNASPRSKEN |
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 | 66 .84 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 42 .08 RPM |
| SRP007412_heart | 0 .00 RPM | 82 .62 RPM |
| SRP007412_kidney | 0 .00 RPM | 85 .24 RPM |
| SRP007412_liver | 0 .00 RPM | 93 .26 RPM |
| SRP007412_testis | 0 .46 RPM | 100 .40 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_385 was not detected
No EST(s) were mapped for retro_mmus_385 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_71315 | 465 libraries | 520 libraries | 86 libraries | 1 library | 0 libraries |
The graphical summary, for retro_mmus_385 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_385 was not experimentally validated.