RetrogeneDB ID: | retro_mmus_2294 | ||
Retrocopylocation | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 3:116560934..116561426(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | ENSMUSG00000034437 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | Srsf3 | ||
| Ensembl ID: | ENSMUSG00000071172 | ||
| Aliases: | Srsf3, AL024116, Sfrs3, X16 | ||
| Description: | serine/arginine-rich splicing factor 3 [Source:MGI Symbol;Acc:MGI:98285] |
Retrocopy-Parental alignment summary:
>retro_mmus_2294
ATGCATCGTGATTCCTGTCCCTTGGATTGTAAGGTTTATGTAGGTAATCTTGGAAATAATGGAAACAAGACTGAATTAGA
ACGGGCTTTTGGCTATTATGGACCACTCAGAAGTGTGTGGGTTGCTCGAAACCCTCCTGGCTTTGCTTTCGTCGAATTTG
AGGATCCCCGAGATGCTGCTGATGCTGTCCGGGAACTAGATGGAAGAACACTGTGTGGCTGCCGTGTAAGAGTGGAACTG
TCGAATGATGAAAAGAGAAGTCGGAATCGTGGGCCGCCTCCCTCTTGGGGTCGTCGTCCTCGAGATGATTACCGCAGGAG
GAGTCCTCCACCTCGGCGCAGATCCCCAAGAAGGAGAAGCTTTTCCCGAAGCCGGAGCAGGTCACTTTCTAGAGATAGGA
GAAGAGAAAGGTCTCTGTCTCGTGAGAGAAATCACAAGCCGTCTCGATCCTTCTCTAGGTCTCGTAGCTGATCTAGGTCA
AATGAAAGGAAA
ATGCATCGTGATTCCTGTCCCTTGGATTGTAAGGTTTATGTAGGTAATCTTGGAAATAATGGAAACAAGACTGAATTAGA
ACGGGCTTTTGGCTATTATGGACCACTCAGAAGTGTGTGGGTTGCTCGAAACCCTCCTGGCTTTGCTTTCGTCGAATTTG
AGGATCCCCGAGATGCTGCTGATGCTGTCCGGGAACTAGATGGAAGAACACTGTGTGGCTGCCGTGTAAGAGTGGAACTG
TCGAATGATGAAAAGAGAAGTCGGAATCGTGGGCCGCCTCCCTCTTGGGGTCGTCGTCCTCGAGATGATTACCGCAGGAG
GAGTCCTCCACCTCGGCGCAGATCCCCAAGAAGGAGAAGCTTTTCCCGAAGCCGGAGCAGGTCACTTTCTAGAGATAGGA
GAAGAGAAAGGTCTCTGTCTCGTGAGAGAAATCACAAGCCGTCTCGATCCTTCTCTAGGTCTCGTAGCTGATCTAGGTCA
AATGAAAGGAAA
ORF - retro_mmus_2294 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.78 % |
| Parental protein coverage: | 100. % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRT |
| MHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRT | |
| Retrocopy | MHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRT |
| Parental | LCGCRVRVELSNGEKRSRNRGPPPSWGRRPRDDYRRRSPPPRRRSPRRRSFSRSRSRSLSRDRRRERSLS |
| LCGCRVRVELSN.EKRSRNRGPPPSWGRRPRDDYRRRSPPPRRRSPRRRSFSRSRSRSLSRDRRRERSLS | |
| Retrocopy | LCGCRVRVELSNDEKRSRNRGPPPSWGRRPRDDYRRRSPPPRRRSPRRRSFSRSRSRSLSRDRRRERSLS |
| Parental | RERNHKPSRSFSRSRSRSRSNERK |
| RERNHKPSRSFSRSRS.SRSNERK | |
| Retrocopy | RERNHKPSRSFSRSRS*SRSNERK |
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 .05 RPM | 70 .09 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 64 .83 RPM |
| SRP007412_heart | 0 .12 RPM | 53 .05 RPM |
| SRP007412_kidney | 0 .13 RPM | 57 .23 RPM |
| SRP007412_liver | 0 .08 RPM | 20 .86 RPM |
| SRP007412_testis | 0 .05 RPM | 39 .61 RPM |
RNA Polymerase II actvity near the 5' end of retro_mmus_2294 was not detected
No EST(s) were mapped for retro_mmus_2294 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_91507 | 107 libraries | 151 libraries | 733 libraries | 75 libraries | 6 libraries |
The graphical summary, for retro_mmus_2294 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_2294 was not experimentally validated.