RetrogeneDB ID: | retro_sscr_601 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 18:46914225..46914509(+) | ||
| 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: | ENSSSCG00000014873 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_sscr_601
AGAGGACTGGATTAAACATCTTTGGGTATATTTTTATTGGGATTTTTATTATGGAACATAGATAACATCTTTTGTGATTC
ATTGAGGAACTTTTCAAAGAAGGTGTCACCTATCATAGGTGTTACCCACAGTTTCACGCATGGTGGCATACTTTAACTGG
CCTTGGTTCTTCTCTTCACATCCTTTTCAGCTTATATACAACACTTTACCTGAGATACAGGCCAAAAGTAAAGTTTCTCT
TTAGAATCTGGCCAGTGATCTTGTTTGAGCCTCTCAGGAAGCAC
ORF - retro_sscr_601 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.66 % |
| Parental protein coverage: | 54.24 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | RGLGYTSLGIFLMGFLLWNIDNIFCDSLRNFRKKVPPIIGVT-TQFHAWWHILTGLGSYLHILFSLYTRT |
| RGL..TSLGIFL.GFLLWNIDNIFCDSLRNF.KKV.PIIGVT..QFHAWWH.LTGLGS.LHILFSLYT.T | |
| Retrocopy | RGLD*TSLGIFLLGFLLWNIDNIFCDSLRNFSKKVSPIIGVT<PQFHAWWHTLTGLGSSLHILFSLYT-T |
| Parental | LYLRYRPKVKFLFGIWPVILFEPLRKH |
| LYLRYRPKVKFLF.IWPVILFEPLRKH | |
| Retrocopy | LYLRYRPKVKFLFRIWPVILFEPLRKH |
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 |
|---|---|---|
| SRP014902_placenta | 0 .00 RPM | 2 .39 RPM |
| SRP014902_testis | 0 .00 RPM | 0 .99 RPM |
| SRP018288_heart | 0 .00 RPM | 7 .81 RPM |
| SRP018288_kidney | 0 .00 RPM | 7 .39 RPM |
| SRP018288_liver | 0 .00 RPM | 1 .60 RPM |
| SRP018288_lung | 0 .00 RPM | 8 .25 RPM |
| SRP018856_adipose | 0 .00 RPM | 7 .94 RPM |
| SRP035408_brain | 0 .00 RPM | 1 .24 RPM |
| SRP035408_liver | 0 .00 RPM | 0 .68 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_601 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_601 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_601 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000026842 | 1 retrocopy | |
| Sus scrofa | ENSSSCG00000014873 | 1 retrocopy |
retro_sscr_601 ,
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