RetrogeneDB ID: | retro_mmus_1856 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 19:16059742..16060028(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rpl31 | ||
| Ensembl ID: | ENSMUSG00000073702 | ||
| Aliases: | None | ||
| Description: | ribosomal protein L31 [Source:MGI Symbol;Acc:MGI:2149632] |
Retrocopy-Parental alignment summary:
>retro_mmus_1856
ATGGCTCCCGGAAAGAAGGGTGGCAAGAAGAAGGGCCATTCTACCATCAATAAAGTGGTAACCCAAAAGGCACACCATCA
GTATTCACAAGCACATCCATGGAATGGGTTTCAAGAAGTGTGCCCCTTGTGCACTCAAAGAAATCTAGCGAGTTGCCATG
AAGGAGATGGGGACTTCAGATATTCACATTGACAGCAGCCTCAATAAAGCCATCTGAGCCAAGGGAATAAGGGATGCTCT
ACACGGCATTTGTCTAGTCCAAATATGCTTGTCCAGAAAACATAAT
ORF - retro_mmus_1856 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 62.89 % |
| Parental protein coverage: | 74.4 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MAPAKKGGEKKKGRSAINEVVTRE-YTINIHKRIHGVGFKKRAPRALKEIRKFAMKEMGTPDVRIDTRLN |
| MAP.KKGG.KKKG.S.IN.VVT....TI.IHK.IHG.GFKK.AP.ALKEI...AMKEMGT.D..ID..LN | |
| Retrocopy | MAPGKKGG-KKKGHSTINKVVTQK>HTISIHKHIHGMGFKKCAPCALKEI*RVAMKEMGTSDIHIDSSLN |
| Parental | KAVWAKGIRNVPYRI---RVRLSRKRN |
| KA..AKGIR.....I......LSRK.N | |
| Retrocopy | KAI*AKGIRDALHGICLVQICLSRKHN |
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 | 69 .15 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 44 .55 RPM |
| SRP007412_heart | 0 .00 RPM | 65 .62 RPM |
| SRP007412_kidney | 0 .00 RPM | 77 .00 RPM |
| SRP007412_liver | 0 .00 RPM | 55 .14 RPM |
| SRP007412_testis | 0 .00 RPM | 58 .23 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1856 was not detected
No EST(s) were mapped for retro_mmus_1856 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_62770 | 1020 libraries | 29 libraries | 12 libraries | 3 libraries | 8 libraries |
The graphical summary, for retro_mmus_1856 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_1856 was not experimentally validated.