RetrogeneDB ID: | retro_mmus_1952 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 2:87526143..87526401(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000082908 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Srp9 | ||
| Ensembl ID: | ENSMUSG00000026511 | ||
| Aliases: | Srp9, 9kDa | ||
| Description: | signal recognition particle 9 [Source:MGI Symbol;Acc:MGI:1350930] |
Retrocopy-Parental alignment summary:
>retro_mmus_1952
ATGCCTCAGTTCCAGACCTGGGAGGAGTTCAGCCGGGCGGCCGAGAAGCTCTACCTGGCGGACCCCATGAAGGTACGGGT
GGTTCTCAAATACAGGCATGTTGATGGGAATTTGTGTATCAAAGTAACGGATGATCTAGTTTGTTTGGTGTACAGAACAG
ACCAAGCGCAAGACGTAAAGAAGATTGAGAAATTCCACAGTCAGTTAATGCGACTTATGGTGGCCAAGGAATCCCGCAAT
GTCACTATGGAAACAGAA
ORF - retro_mmus_1952 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 | MPQFQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKKIEKFHSQLM |
| MPQFQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKKIEKFHSQLM | |
| Retrocopy | MPQFQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKKIEKFHSQLM |
| Parental | RLMVAKESRNVTMETE |
| RLMVAKESRNVTMETE | |
| Retrocopy | RLMVAKESRNVTMETE |
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 .42 RPM | 29 .81 RPM |
| SRP007412_cerebellum | 2 .30 RPM | 24 .62 RPM |
| SRP007412_heart | 0 .09 RPM | 19 .55 RPM |
| SRP007412_kidney | 2 .08 RPM | 19 .62 RPM |
| SRP007412_liver | 2 .21 RPM | 26 .82 RPM |
| SRP007412_testis | 5 .99 RPM | 29 .09 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1952 was not detected
No EST(s) were mapped for retro_mmus_1952 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_89694 | 530 libraries | 397 libraries | 67 libraries | 30 libraries | 48 libraries |
The graphical summary, for retro_mmus_1952 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_1952 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1952 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Echinops telfairi | ENSETEG00000012291 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000026511 | 1 retrocopy |
retro_mmus_1952 ,
|
| Otolemur garnettii | ENSOGAG00000001752 | 1 retrocopy |