RetrogeneDB ID: | retro_cpor_1313 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_7:3254162..3254526(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCPOG00000011755 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_1313
AAGAAAAAACTTAATGTGACAGCAGAGAAAAAGATGGTAAAAATTACATCAAAGAGGCTACACACTGGGAAAACGCAGAA
GAAGACTGAAAATTTTAATGTACCTATTAGCTTGAAAAGTAAAAACCTGTTCCTCCAGCAGCTAGGCTTGGGATTTCTTC
AGTTAAACAAAAGATGTGTCACCGGACACCAAGCCTATGGATCAGCTAAAGGAAAGCACACAAAGACTTGGTTTGAAAGC
CTCTTCATTCTCTAGAAAGTCTGAAGAGGATGAGAAGGTGAATAAGAAGGAGGAGCAATTTGAGGTTGTCACAAGTTCAG
CTGGAACAAAAACCACAGAGGACACAGAAGCAAATGAGGAAAAG
ORF - retro_cpor_1313 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 58.27 % |
| Parental protein coverage: | 59.33 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | EKTVDVAAEKKVVKITSEMPQTERMQKRAERFNVPVS-LES-KKAARAARFGISSVP-TKGLSSDTKPMV |
| .K...V.AEKK.VKITS....T...QK..E.FNVP.S.LE..K....AAR.GISSV..TK..S.DTKPM. | |
| Retrocopy | KKKLNVTAEKKMVKITSKRLHTGKTQKKTENFNVPIS<LEK*KPVPPAARLGISSVK<TKDVSPDTKPM- |
| Parental | NLDKLKERAQRFGLNVSSISRKSEDDEKLKKRKERFGIVTSSAGIGTTEDTEAKKRK |
| ..D.LKE..QR.GL..SS.SRKSE.DEK..K..E.F..VTSSAG..TTEDTEA...K | |
| Retrocopy | --DQLKESTQRLGLKASSFSRKSEEDEKVNKKEEQFEVVTSSAGTKTTEDTEANEEK |
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 |
|---|---|---|
| SRP017611_brain | 0 .00 RPM | 21 .11 RPM |
| SRP017611_kidney | 0 .00 RPM | 30 .78 RPM |
| SRP017611_liver | 0 .00 RPM | 21 .81 RPM |
| SRP040447_lung | 0 .00 RPM | 23 .13 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 23 .53 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_1313 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1313 was not experimentally validated.