RetrogeneDB ID: | retro_mmus_1062 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 13:112937583..112937924(+) | ||
| Located in intron of: | ENSMUSG00000042426 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rps13 | ||
| Ensembl ID: | ENSMUSG00000090862 | ||
| Aliases: | Rps13, 2700063M04Rik | ||
| Description: | ribosomal protein S13 [Source:MGI Symbol;Acc:MGI:1915302] |
Retrocopy-Parental alignment summary:
>retro_mmus_1062
ATGGGTCGCATGCACGCTCCCAGGAAAGGCCTGTCCCAGTCCTTGCTACCCTACCGCCATAGCGTCCCCATGTGGCTGAA
GTTGACATCTGACGACTTGAAGGATCAGATTTACAAACTGGCCAAGAAAGGCCTGACTCCCTCCCAGATAGGTGTGATCC
TGAGGACTCACGTGCTGTGGCCCAGGCCTGTTTTGTGACTGGAAATAAAATCTTGAGAATCCTTAAGTCCAAACACCTTG
CCCTGATCTCCCTGGGGATCTCTCCCATTTGGTTGCTGTCCGAAAGCACCTTGAGAGGAACGAACGGAAAGGATAAGGGT
GCTAAATTCCGCCTGATTCTG
ORF - retro_mmus_1062 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.99 % |
| Parental protein coverage: | 77.48 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MGRMHAPGKGLSQSALPYRRSVPTWLKLTSDDVKEQIYKLAKKGLTPSQIGVILR-DSHGVAQVRFVTGN |
| MGRMHAP.KGLSQS.LPYR.SVP.WLKLTSDD.K.QIYKLAKKGLTPSQIGVILR.DS..VAQ..FVTGN | |
| Retrocopy | MGRMHAPRKGLSQSLLPYRHSVPMWLKLTSDDLKDQIYKLAKKGLTPSQIGVILR<DSRAVAQACFVTGN |
| Parental | KILRILKSKGLA-PDLPEDLYHLIKKAVAVRKHLERN-RK-DKDAKFRLIL |
| KILRILKSK.LA.PDLP.DL.HL.....AVRKHLERN.RK.DK.AKFRLIL | |
| Retrocopy | KILRILKSKHLA<PDLPGDLSHLV----AVRKHLERNERK>DKGAKFRLIL |
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 .02 RPM | 36 .17 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 19 .84 RPM |
| SRP007412_heart | 0 .00 RPM | 43 .08 RPM |
| SRP007412_kidney | 0 .00 RPM | 34 .61 RPM |
| SRP007412_liver | 0 .00 RPM | 31 .90 RPM |
| SRP007412_testis | 0 .00 RPM | 43 .50 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1062 was not detected
No EST(s) were mapped for retro_mmus_1062 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_26747 | 365 libraries | 424 libraries | 271 libraries | 10 libraries | 2 libraries |
The graphical summary, for retro_mmus_1062 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_1062 was not experimentally validated.