RetrogeneDB ID: | retro_mmus_3558 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:162697636..162698047(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000082571 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Sec22b | ||
| Ensembl ID: | ENSMUSG00000027879 | ||
| Aliases: | None | ||
| Description: | SEC22 vesicle trafficking protein homolog B (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1338759] |
Retrocopy-Parental alignment summary:
>retro_mmus_3558
GCCTGTGTGGCTGACGGGCTTCCGCTGGCCACCTCGATGCAGGAGGACAAGCAGTCAGGCCGGGACCTTCAACAGTATCA
GAGTCAGGCTAAGCAACTCTTTTGAAAGCTGAATGAGCAGTCTCCTACCAGATATACCTTGGAAACAGGAGCCATGACTT
TTCACTACAATAATGAGCAGGAGGTGTGTTACTTGGTTTTGTGTGAAGCCGCCTTCCCTAAGAAGTTGGCCTTTGCCTAC
CTAGAAGACTTGCACTCAGAATCTGATGAATAACATGGGAAGAAGGTGCCCACTGTGTCTAGGCCCTATTCCTTCATTGA
GTTTGATACCTTCATTCAGAAAACCAAGAAACTCTACATTGATAGCTGTGCTCAGAGAAATCTAGGCTCCATCAACACCG
AATTGCAAGAT
ORF - retro_mmus_3558 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.51 % |
| Parental protein coverage: | 82.53 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | ARVADGLPLAASMQEDEQSGRDLQQYQSQAKQLFRKLNEQSPTRCTLEAGAMTFHYIIEQGVCYLVLCEA |
| A.VADGLPLA.SMQED.QSGRDLQQYQSQAKQLF.KLNEQSPTR.TLE.GAMTFHY..EQ.VCYLVLCEA | |
| Retrocopy | ACVADGLPLATSMQEDKQSGRDLQQYQSQAKQLF*KLNEQSPTRYTLETGAMTFHYNNEQEVCYLVLCEA |
| Parental | AFPKKLAFAYLEDLHSEFDEQHGKKVPTVSRPYSFIEFDTFIQKTKKLYIDSRARRNLGSINTELQD |
| AFPKKLAFAYLEDLHSE.DE.HGKKVPTVSRPYSFIEFDTFIQKTKKLYIDS.A.RNLGSINTELQD | |
| Retrocopy | AFPKKLAFAYLEDLHSESDE*HGKKVPTVSRPYSFIEFDTFIQKTKKLYIDSCAQRNLGSINTELQD |
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 .02 RPM | 52 .64 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 46 .37 RPM |
| SRP007412_heart | 0 .00 RPM | 28 .48 RPM |
| SRP007412_kidney | 0 .00 RPM | 38 .75 RPM |
| SRP007412_liver | 0 .03 RPM | 38 .37 RPM |
| SRP007412_testis | 0 .00 RPM | 25 .48 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3558 was not detected
No EST(s) were mapped for retro_mmus_3558 retrocopy.
No TSS is located nearby retro_mmus_3558 retrocopy 5' end.
retro_mmus_3558 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3558 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000027879 | 1 retrocopy |
retro_mmus_3558 ,
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