RetrogeneDB ID: | retro_mmus_186 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 17:26098990..26099221(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000049124 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Snrpg | ||
| Ensembl ID: | ENSMUSG00000057278 | ||
| Aliases: | Snrpg, 2810024K17Rik, AL022803, SMG, sm-G, snRNP-G | ||
| Description: | small nuclear ribonucleoprotein polypeptide G [Source:MGI Symbol;Acc:MGI:1915261] |
Retrocopy-Parental alignment summary:
>retro_mmus_186
ATGAGCAAAGCCCACCCTCCCGAGCTGAAGAAGTTTATGGACAAGAAGTTATCATTGAAGTTAAACGGTGGCAGGCATGT
CCAAGGAATACTGCGGGGCTTTGATCCCTTTATGAACCTTGTGATTGACGAGTGTGTGGAGATGGCAACCAGTGGGCAAC
AGAACAACATTGGCATGGTGGTCATCCGAGGAAACAGCATCATCATGTTAGAAGCCTTGGAAAGAGTCTGA
ORF - retro_mmus_186 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 100.0 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVVIRGNSIIML |
| MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVVIRGNSIIML | |
| Retrocopy | MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVVIRGNSIIML |
| Parental | EALERV |
| EALERV | |
| Retrocopy | EALERV |
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 .86 RPM | 5 .14 RPM |
| SRP007412_cerebellum | 0 .35 RPM | 4 .65 RPM |
| SRP007412_heart | 0 .90 RPM | 5 .51 RPM |
| SRP007412_kidney | 0 .69 RPM | 6 .53 RPM |
| SRP007412_liver | 0 .63 RPM | 5 .73 RPM |
| SRP007412_testis | 1 .51 RPM | 11 .62 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_186 was not detected
No EST(s) were mapped for retro_mmus_186 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_51369 | 399 libraries | 510 libraries | 157 libraries | 5 libraries | 1 library |
The graphical summary, for retro_mmus_186 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_186 was not experimentally validated.