RetrogeneDB ID: | retro_mmus_2347 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 4:49342247..49342575(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000096476 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Tusc2 | ||
| Ensembl ID: | ENSMUSG00000010054 | ||
| Aliases: | Tusc2, 1190001E22Rik, AA407686, Fus1, Lgcc, PAP, Pdap2 | ||
| Description: | tumor suppressor candidate 2 [Source:MGI Symbol;Acc:MGI:1931086] |
Retrocopy-Parental alignment summary:
>retro_mmus_2347
ATGGGCGCCAGTGGCTCCAAAGCTCGGGGTCTTTGGCCCTTTGCCTCCACTATGAGGGACGGCGGCCCAGAGGCAGCAGG
CTCTGAGCAGTCTTTGGTGTGGCCTCGAGGCCGAGCACTGCCTCCCTTCGTATTCATGCTCAGTGGCTCCATGTTCTATG
ATGAAGATAGAGATCTAGCTCACGAATTCTATGAGGAGACAATCGTCACCAAGAATGGGCAGAAGCGAGCCAAGCTGAGG
CAGGTACATAAGAATTGGATTCCTCAGGGCATCGTGAAGCTGGATCCCCCGAATCCACATGGATTTCCCCATGATCCTCT
ATGAAGTA
ORF - retro_mmus_2347 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.88 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MGASGSKARGLWPFASTPGGGGPEAAGSEQSLVRSRARAVPPFVFTRRGSMFYDEDGDLAHEFYEETIVT |
| MGASGSKARGLWPFAST...GGPEAAGSEQSLV..R.RA.PPFVF...GSMFYDED.DLAHEFYEETIVT | |
| Retrocopy | MGASGSKARGLWPFASTMRDGGPEAAGSEQSLVWPRGRALPPFVFMLSGSMFYDEDRDLAHEFYEETIVT |
| Parental | KNGQKRAKLRRVHKNLIPQGIVKLDPPRIHVDFP-VILYEV |
| KNGQKRAKLR.VHKN.IPQGIVKLDPP..H..FP..ILYEV | |
| Retrocopy | KNGQKRAKLRQVHKNWIPQGIVKLDPPNPH-GFP>MILYEV |
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 | 46 .24 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 45 .51 RPM |
| SRP007412_heart | 0 .00 RPM | 19 .77 RPM |
| SRP007412_kidney | 0 .00 RPM | 31 .80 RPM |
| SRP007412_liver | 0 .00 RPM | 24 .77 RPM |
| SRP007412_testis | 0 .00 RPM | 16 .33 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2347 was not detected
No EST(s) were mapped for retro_mmus_2347 retrocopy.
No TSS is located nearby retro_mmus_2347 retrocopy 5' end.
retro_mmus_2347 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2347 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dipodomys ordii | ENSDORG00000007859 | 2 retrocopies | |
| Mus musculus | ENSMUSG00000010054 | 2 retrocopies |
retro_mmus_2347 , retro_mmus_2349,
|
| Oryctolagus cuniculus | ENSOCUG00000005259 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000021528 | 1 retrocopy |