RetrogeneDB ID: | retro_cpor_439 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_155:1971570..1971885(+) | ||
| Located in intron of: | ENSCPOG00000003790 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MSMP | ||
| Ensembl ID: | ENSCPOG00000021717 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_439
CCAGGAGCCCACAGCAAGTGCTGCTTCCAAGCTCGAGCTCCCTGTGGGAGGAGAGGACAGAGTTCACCCTGGGGAGTCTG
AGCTCCGATAGGACTTCTCTGCTGCCCATCTTCGTCCTGTCAGCGCTGGCTGCCTGGTGTGGCTCAGCATCCCCATCGAC
TCCCCGCTGGGTGAGGCTGGGGGGGAGGCTGGAGCCTGCCAGTTTTCCTTGGTGCAAAAATCTGATCCTTGGTGGCCCTG
CAGAGGTGGAGGGCCGACCTCGAGTGGGGCTCAGCTAACACCCCTATTCCCGGGGCTTCTGCTCCCCACCCCAGC
ORF - retro_cpor_439 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 60.36 % |
| Parental protein coverage: | 77.7 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | PGVHTKCYFQAQAPCHYEGKY-FTLG-ESWLREDCFHCTCLHPVGVGCCDTSQHPIDFPAECEVRREAGT |
| PG.H.KC.FQA.APC...G...FTLG.ES.LR.D.F....L.PV..GC......PID.P...E...EAG. | |
| Retrocopy | PGAHSKCCFQARAPCGRRGQS<FTLG<ESELR*D-FSAAHLRPVSAGCLVWLSIPIDSPLG-EAGGEAGA |
| Parental | CQFSLVQKSDPRLPCKSRGP-DLEWGSANTPVPGAPAPHSS |
| CQFSLVQKSDP..PC...GP.DLEWGSANTP.PGA.APH.S | |
| Retrocopy | CQFSLVQKSDPWWPCRGGGP<DLEWGSANTPIPGASAPHPS |
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 | 12 .31 RPM |
| SRP017611_kidney | 0 .00 RPM | 11 .41 RPM |
| SRP017611_liver | 0 .13 RPM | 6 .44 RPM |
| SRP040447_lung | 0 .00 RPM | 12 .96 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 4 .14 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_439 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_439 was not experimentally validated.
Retrocopy orthology:
Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000021717 | 1 retrocopy |
retro_cpor_439 ,
|