RetrogeneDB ID: | retro_cpor_21 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_14:41664275..41664794(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCPOG00000022066 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCPOG00000012081 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_21
ATGGCGTCTGGCTTCAAGAAGCCCAACGTGGCCTCCAGCAGCCAAAAGAAAAAGGTGGGCCCTAAGCCTGAACTCACTGA
AGAGCAGAAGCAGGAAGTGCGGGAAGCATTTGACCTCTTCGATGCTGACGGCAGTGGGACCATCGACGTGAAGGAGCTGA
AAGTGGCCATGCGGGCCCTGGGCTTTGAGCCCAGGAAGGAGGAAATGAAGAAAATGATCGCGGAGGTGGACAAGGAGGGC
ACGGGCAAGATCAGCTTCAACGACTTCCTGGCTGTGATGACCCAGAAGATGGCTGAGAAGGACACCAAAGAAGAAATCAT
GAAAGCTTTCAGACTCTTCGATGACGACGAGACTGGGAAGATATCTTTCAAAAACCTCAAGCGCGTGGCCAACGAGCTGG
GGGAGAACCTCACCGACGAGGAGCTGCAGGAGATGATCGACGAGGCGGACCGCGACGGCGACGGCGAGGTGAGCGAGGAG
GAGTTCCTCCGGGTCATGAAGAAGACCAACCTGTACTGA
ORF - retro_cpor_21 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 84.8 % |
| Parental protein coverage: | 99.42 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | ASNFKKANMASSAQRKRMSPKPELTEEQKQEIREAFDLFDADGTGTIDVKELKVAMRALGFEPKKEEIKK |
| AS.FKK.N.ASS.Q.K...PKPELTEEQKQE.REAFDLFDADG.GTIDVKELKVAMRALGFEP.KEE.KK | |
| Retrocopy | ASGFKKPNVASSSQKKKVGPKPELTEEQKQEVREAFDLFDADGSGTIDVKELKVAMRALGFEPRKEEMKK |
| Parental | MISEIDKEGTGKMNFSDFLTVMTQKMSEKDTKEEILKAFKLFDDDETGKISFKNLKRVAKELGENLTDEE |
| MI.E.DKEGTGK..F.DFL.VMTQKM.EKDTKEEI.KAF.LFDDDETGKISFKNLKRVA.ELGENLTDEE | |
| Retrocopy | MIAEVDKEGTGKISFNDFLAVMTQKMAEKDTKEEIMKAFRLFDDDETGKISFKNLKRVANELGENLTDEE |
| Parental | LQEMIDEADRDGDGEVNEQEFLRIMKKTSLY |
| LQEMIDEADRDGDGEV.E.EFLR.MKKT.LY | |
| Retrocopy | LQEMIDEADRDGDGEVSEEEFLRVMKKTNLY |
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 | 22 .09 RPM |
| SRP017611_kidney | 0 .00 RPM | 26 .90 RPM |
| SRP017611_liver | 0 .00 RPM | 7 .83 RPM |
| SRP040447_lung | 0 .00 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_21 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_21 was not experimentally validated.