RetrogeneDB ID: | retro_mmus_1479 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 16:70665304..70665647(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Med31 | ||
| Ensembl ID: | ENSMUSG00000020801 | ||
| Aliases: | Med31, 3110004H13Rik, CGI-125, l11Jus15 | ||
| Description: | mediator of RNA polymerase II transcription, subunit 31 homolog (yeast) [Source:MGI Symbol;Acc:MGI:1914529] |
Retrocopy-Parental alignment summary:
>retro_mmus_1479
ATGCCAATGGCTGTTGCTATGAAGATAGGTGATGCTAGAAATTGACTTTGGATTTAGTTGGAGTTGAAATTTGTGCAGTG
TTTAGTCAACCCAAATTATCTTAATTTTCCTGTCCAAAGAGGTTACTTCAAAAGCAAAGCTTTTGTTAATTAAGTACTTG
CTTTACTGGAAAGAACCAGAATTTGCTAAATAACTAAAGTGCCCTCAGTGTTTATGTATGTTAGAACTGTTCCAACATTT
TCAAAAGGAGCTGGTGAATGCTCTGCGTGTGAAATTTATTGACAAAGAGAAGATTCTACACTGGTAGCACTATTTGTAGA
AGCAGTTGCATCTTCAGCAAGCC
ORF - retro_mmus_1479 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 60.5 % |
| Parental protein coverage: | 90.08 % |
| Number of stop codons detected: | 5 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MAAAVAMETDDAGNRLRFQLELEFVQCLANPNYLN-FLAQRGYFKDKAFVNYLKYLLYWKEPEYAKYLKY |
| M..AVAM...DA.N.L...LEL.FVQCL.NPNYLN.FL......K.K......KYLLYWKEPE.AK.LK. | |
| Retrocopy | MPMAVAMKIGDARN*LWI*LELKFVQCLVNPNYLN>FLSKEVTSKAKLLL--IKYLLYWKEPEFAK*LKC |
| Parental | PQCLHMLELLQYEHFRKELVNAQCAKFIDEQQILHWQHYSRKRVRLQQA |
| PQCL.MLEL....HF.KELVNA...KFID...ILHW.HY..K...LQQA | |
| Retrocopy | PQCLCMLEL--FQHFQKELVNALRVKFIDKEKILHW*HYL*KQLHLQQA |
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 | 5 .75 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 5 .60 RPM |
| SRP007412_heart | 0 .00 RPM | 4 .20 RPM |
| SRP007412_kidney | 0 .00 RPM | 3 .75 RPM |
| SRP007412_liver | 0 .00 RPM | 1 .83 RPM |
| SRP007412_testis | 0 .00 RPM | 10 .75 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1479 was not detected
No EST(s) were mapped for retro_mmus_1479 retrocopy.
No TSS is located nearby retro_mmus_1479 retrocopy 5' end.
retro_mmus_1479 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1479 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000023445 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000010814 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000020801 | 2 retrocopies |
retro_mmus_1479 , retro_mmus_3201,
|