RetrogeneDB ID: | retro_mmus_516 | ||
Retrocopylocation | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 1:180854284..180854497(-) | ||
| Located in intron of: | ENSMUSG00000038806 | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | Polr2k | ||
| Ensembl ID: | ENSMUSG00000045996 | ||
| Aliases: | Polr2k, ABC10-alpha, MafY, Mt1a, RPABC4, RPB10alpha, RPB12, RPB7.0 | ||
| Description: | polymerase (RNA) II (DNA directed) polypeptide K [Source:MGI Symbol;Acc:MGI:102725] |
Retrocopy-Parental alignment summary:
>retro_mmus_516
AGAGAAGGGGCGCTTCTTCCAGCTGAGGAGGCACTACCAATGGACGCTCAGAAAGATGTTCAACCACCAAAGCAGCAGCC
AATGATAGATATTTGTGGAGAGTGTCACACCGAAAATGAGATAAAGTCCAGGGATCCCATCAGATGCAGAGAATGTGGAT
ACAGAATAATGTACAAGAAAAGGACTAAAAGATTGGTGGTTTTTGATGCTCGA
AGAGAAGGGGCGCTTCTTCCAGCTGAGGAGGCACTACCAATGGACGCTCAGAAAGATGTTCAACCACCAAAGCAGCAGCC
AATGATAGATATTTGTGGAGAGTGTCACACCGAAAATGAGATAAAGTCCAGGGATCCCATCAGATGCAGAGAATGTGGAT
ACAGAATAATGTACAAGAAAAGGACTAAAAGATTGGTGGTTTTTGATGCTCGA
ORF - retro_mmus_516 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.67 % |
| Parental protein coverage: | 75.76 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | RGSTLLPFERLEAEALTMDAQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLV |
| R...LLP.E....EAL.MDAQKDVQPPKQQPMI.ICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLV | |
| Retrocopy | REGALLPAE----EALPMDAQKDVQPPKQQPMIDICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLV |
| Parental | VFDAR |
| VFDAR | |
| Retrocopy | VFDAR |
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 | 3 .69 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 3 .95 RPM |
| SRP007412_heart | 0 .00 RPM | 6 .69 RPM |
| SRP007412_kidney | 0 .00 RPM | 6 .06 RPM |
| SRP007412_liver | 0 .00 RPM | 4 .56 RPM |
| SRP007412_testis | 0 .00 RPM | 3 .98 RPM |
RNA Polymerase II actvity near the 5' end of retro_mmus_516 was not detected
No EST(s) were mapped for retro_mmus_516 retrocopy.
No TSS is located nearby retro_mmus_516 retrocopy 5' end.
retro_mmus_516 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_516 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000045996 | 3 retrocopies |
retro_mmus_3312, retro_mmus_516 , retro_mmus_739,
|