RetrogeneDB ID: | retro_sscr_227 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 10:58454770..58454977(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TRIAP1 | ||
| Ensembl ID: | ENSSSCG00000009908 | ||
| Aliases: | None | ||
| Description: | TP53 regulated inhibitor of apoptosis 1 [Source:HGNC Symbol;Acc:26937] |
Retrocopy-Parental alignment summary:
>retro_sscr_227
CTGAACTGCATAGGGGAGGGTTCCACCAACATGAAGCACAAGTACACCGGTGCTTCTAATATTGGTTTGCCAGAGAAGTT
GCTCAAGGGGGAGGGCTCTGGGGACCCATGCACCAGTCTCTTTGAACACCACCTGTGTTCAAAAGCAATAAAGGAGAAGA
TTCCCATTGAAGAACTGGAGTTCATGGGCCATGGCAAAGAAAAACCT
ORF - retro_sscr_227 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 56.58 % |
| Parental protein coverage: | 94.87 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MNSVGEGCTDMKREYD-QCFNRWFA-EKFLKGEGSGDPCTDLFKRYQQCVQKAIKEKEIPIEGLDCWWAG |
| .N..GEG.T.MK..Y...CF..WFA.EK.LKGEGSGDPCT.LF........KAIKEK.IPIE.L.....G | |
| Retrocopy | LNCIGEGSTNMKHKYT<RCF*YWFA>EKLLKGEGSGDPCTSLFEHH--LCSKAIKEK-IPIEELE--FMG |
| Parental | LSKKKP |
| ..K.KP | |
| Retrocopy | HGKEKP |
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 | 5 .04 RPM |
| SRP014902_testis | 0 .00 RPM | 4 .38 RPM |
| SRP018288_heart | 0 .00 RPM | 15 .22 RPM |
| SRP018288_kidney | 0 .00 RPM | 31 .32 RPM |
| SRP018288_liver | 0 .00 RPM | 16 .95 RPM |
| SRP018288_lung | 0 .00 RPM | 5 .50 RPM |
| SRP018856_adipose | 0 .00 RPM | 11 .27 RPM |
| SRP035408_brain | 0 .00 RPM | 1 .81 RPM |
| SRP035408_liver | 0 .00 RPM | 5 .37 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_227 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_227 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_227 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Sus scrofa | ENSSSCG00000009908 | 2 retrocopies |
retro_sscr_140, retro_sscr_227 ,
|