RetrogeneDB ID: | retro_sscr_1175 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | X:121702004..121702290(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSSSCG00000030802 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CETN2 | ||
| Ensembl ID: | ENSSSCG00000012757 | ||
| Aliases: | None | ||
| Description: | centrin, EF-hand protein, 2 [Source:HGNC Symbol;Acc:1867] |
Retrocopy-Parental alignment summary:
>retro_sscr_1175
AGTGAAATTGATAAGGAAGGGACAGGAAAAATGAACTTTAGTGACTTTTTGACTGTGATATCTCAGAAAATGTCTGAGAA
AGATACCAAATAAGAGGTTCTAAAAGATTTCAAGCTCTTCGATGATGATGAAACTGGGAAGATACCAATCCAAAATCTAA
AACGTGTGGCCAAGTTGGGCAAGAAAGCTCACTGATGAGGAGCTGCAGGAAACGACTGAAGAAGCTGATCAAGATGGAGA
CGGAAAAGTCAATGAGGAAGAGTTCCTGTGCATCATGAAGACCACT
ORF - retro_sscr_1175 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.38 % |
| Parental protein coverage: | 55.81 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | SEIDKEGTGKMNFSDFLTVMTQKMSEKDTKEEILKAFKLFDDDETGKISFKNLKRVAKELGE-NLTDEEL |
| SEIDKEGTGKMNFSDFLTV..QKMSEKDTK.E.LK.FKLFDDDETGKI...NLKRVAK.LG...LTDEEL | |
| Retrocopy | SEIDKEGTGKMNFSDFLTVISQKMSEKDTK*EVLKDFKLFDDDETGKIPIQNLKRVAK-LGK>KLTDEEL |
| Parental | QEMIDEADRDGDGEVNEQEFLRIMKKT |
| QE...EAD.DGDG.VNE.EFL.IMK.T | |
| Retrocopy | QETTEEADQDGDGKVNEEEFLCIMKTT |
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 | 7 .96 RPM |
| SRP014902_testis | 0 .00 RPM | 29 .99 RPM |
| SRP018288_heart | 0 .00 RPM | 33 .71 RPM |
| SRP018288_kidney | 0 .00 RPM | 44 .33 RPM |
| SRP018288_liver | 0 .00 RPM | 35 .50 RPM |
| SRP018288_lung | 0 .00 RPM | 54 .99 RPM |
| SRP018856_adipose | 0 .00 RPM | 50 .47 RPM |
| SRP035408_brain | 0 .00 RPM | 72 .73 RPM |
| SRP035408_liver | 0 .00 RPM | 77 .94 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_1175 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_1175 was not experimentally validated.