RetrogeneDB ID: | retro_cpor_1250 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_6:24334953..24335462(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCPOG00000019890 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCPOG00000012081 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_1250
GCCTCTAATTTTAAAAAAGCAAACATGGCATCAAGTGCCCAGAGAAAAAGGATTGAATCCTAAGCCAGAGCTGACTGAAG
AGCAGAAACAGGAAATCCGGGAAGCTTTTGATCTCTTTGATGCAGATGGGACAGGGACCATCGATGTAAAGGAACTAAAG
GTGGCAACGAGAGTCGTGGGCTTGGAGCCCAAGAAAGAAGAAATCAAGAAAATGATAAGTGAAATTGATAAGGAAGGGAC
AGGCAAAATGAACTTCAGTGACTTTCTGACTGTCATGACTCAGAAGATGTCTGAGAAAGACACCAAGGAAGAAATCCGGA
AAGCTTTCAAGCTCTTCGATGATGATGAAACCGGGAAAGTATCGTTTAAAAATCTGAAGTGTGTGGCCAAGGAGCTGGAC
GAGAACCTGACGGATGGGGAGCTGCAGGAGATGACTGACGAAGCCCATCCCTGATGGAGATGATGGAGTTCCTGCAGGAG
TCCTGCGCATCATGAAGAAGACTAGATTA
ORF - retro_cpor_1250 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.05 % |
| Parental protein coverage: | 98.84 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | ASNFKKANMASSAQRKR-MSPKPELTEEQKQEIREAFDLFDADGTGTIDVKELKVAMRALGFEPKKEEIK |
| ASNFKKANMASSAQRKR...PKPELTEEQKQEIREAFDLFDADGTGTIDVKELKVA.R..G.EPKKEEIK | |
| Retrocopy | ASNFKKANMASSAQRKR>LNPKPELTEEQKQEIREAFDLFDADGTGTIDVKELKVATRVVGLEPKKEEIK |
| Parental | KMISEIDKEGTGKMNFSDFLTVMTQKMSEKDTKEEILKAFKLFDDDETGKISFKNLKRVAKELGENLTDE |
| KMISEIDKEGTGKMNFSDFLTVMTQKMSEKDTKEEI.KAFKLFDDDETGK.SFKNLK.VAKEL.ENLTD. | |
| Retrocopy | KMISEIDKEGTGKMNFSDFLTVMTQKMSEKDTKEEIRKAFKLFDDDETGKVSFKNLKCVAKELDENLTDG |
| Parental | ELQEMIDEAD-RDGDGEVNEQEFLRIMKKTSL |
| ELQEM.DEA...DGD..V.....LRIMKKT.L | |
| Retrocopy | ELQEMTDEAH>PDGDDGV-PAGVLRIMKKTRL |
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 .06 RPM | 22 .09 RPM |
| SRP017611_kidney | 0 .00 RPM | 26 .90 RPM |
| SRP017611_liver | 0 .00 RPM | 7 .83 RPM |
| SRP040447_lung | 0 .03 RPM | 14 .15 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 4 .80 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_1250 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1250 was not experimentally validated.