RetrogeneDB ID: | retro_mmus_3651 | ||
Retrocopylocation | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:80196752..80197082(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | Rps10 | ||
| Ensembl ID: | ENSMUSG00000052146 | ||
| Aliases: | Rps10, 2210402A09Rik | ||
| Description: | ribosomal protein S10 [Source:MGI Symbol;Acc:MGI:1914347] |
Retrocopy-Parental alignment summary:
>retro_mmus_3651
GGCTATGGGAAGGAGCACTTTGCTTGGATATATTTCTACTGCTACCTTACAAATGAGGGCATCCAGTATCTTCGAGATTG
TCTGCACCTACCTCCATAGAACTTGTCTGCCATCCTGCACCGTAGCCATCCTGAAACTGGCAGGCCTCGGCCCAAAGATC
AGGAGGGTGAGCAACCTGCAAGATTCACAAGAGGGGAGGCCAACAGAGACACCTGCAGAAGGAGTGCTGTGCCCTCTGGA
GCTGAAAAGAAAGATGAGGTTGGGGGTGGCTCAGCAATTGAATTCCAGTTTAGAGGCAGCTTTGCTCATGGACATGGTCA
GCCACCTCAG
GGCTATGGGAAGGAGCACTTTGCTTGGATATATTTCTACTGCTACCTTACAAATGAGGGCATCCAGTATCTTCGAGATTG
TCTGCACCTACCTCCATAGAACTTGTCTGCCATCCTGCACCGTAGCCATCCTGAAACTGGCAGGCCTCGGCCCAAAGATC
AGGAGGGTGAGCAACCTGCAAGATTCACAAGAGGGGAGGCCAACAGAGACACCTGCAGAAGGAGTGCTGTGCCCTCTGGA
GCTGAAAAGAAAGATGAGGTTGGGGGTGGCTCAGCAATTGAATTCCAGTTTAGAGGCAGCTTTGCTCATGGACATGGTCA
GCCACCTCAG
ORF - retro_mmus_3651 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 74.55 % |
| Parental protein coverage: | 66.67 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | GYVKEQFAWRHFYWYLTNEGIQYLRDYLHLPPEIVPATLRRSRPETGRPRPKGPEGERPARFTRGEADRD |
| GY.KE.FAW..FY.YLTNEGIQYLRD.LHLPP....A.L.RS.PETGRPRPK..EGE.PARFTRGEA.RD | |
| Retrocopy | GYGKEHFAWIYFYCYLTNEGIQYLRDCLHLPP*NLSAILHRSHPETGRPRPKDQEGEQPARFTRGEANRD |
| Parental | TYRRSAVPPGADKKAEAGAGSATEFQFRGGFGRGRGQPPQ |
| T.RRSAVP.GA.KK.E.G.GSA.EFQFRG.F..G.GQPPQ | |
| Retrocopy | TCRRSAVPSGAEKKDEVGGGSAIEFQFRGSFAHGHGQPPQ |
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 | 28 .50 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 20 .41 RPM |
| SRP007412_heart | 0 .00 RPM | 54 .48 RPM |
| SRP007412_kidney | 0 .00 RPM | 36 .63 RPM |
| SRP007412_liver | 0 .00 RPM | 39 .08 RPM |
| SRP007412_testis | 0 .00 RPM | 18 .20 RPM |
RNA Polymerase II actvity near the 5' end of retro_mmus_3651 was not detected
No EST(s) were mapped for retro_mmus_3651 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_158241 | 462 libraries | 498 libraries | 110 libraries | 1 library | 1 library |
The graphical summary, for retro_mmus_3651 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_3651 was not experimentally validated.