RetrogeneDB ID: | retro_sscr_1000 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 8:77131436..77131802(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SLC25A16 | ||
| Ensembl ID: | ENSSSCG00000022303 | ||
| Aliases: | None | ||
| Description: | solute carrier family 25 (mitochondrial carrier; Graves disease autoantigen), member 16 [Source:HGNC Symbol;Acc:10986] |
Retrocopy-Parental alignment summary:
>retro_sscr_1000
ACTACATATCTGTGGGTTTCTGGTCTGTGCACAGATTAATCGCTGGATGCATGGTAGGTTTAGCAGCAGTTTATCTTTAC
TTACCTTCTTGACATGGTTAGAGTATACCTATCATTCCAGGTGAAAGAGAAGATACTCATACAGGAGTTATTCATACATT
CAGAACAAATTATGCAAAGGAAGGTGATTTCTTTGCATTTTTTGAGGCCTGAAGCCTCCTGTATTAGGAATGGCTCCACA
TACAGGCGTTTCATTTTTTACTTTTGGTGCTTAAAGAGTGTTGGGCTTCCCCAAGTTCCCACCCTTCCTGGAAGCCCTTC
AGACAATCCTGATATCTGAGTTTTGAAAACTTACTTTGTGGTGGTG
ORF - retro_sscr_1000 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 61.24 % |
| Parental protein coverage: | 53.22 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | TTKLGVSG-HVHRLMAGSLAGMTAV-ICTYPLDMVRVRLAFQVKG-EHTYTGIIHAFKTIYAKEGGFLGF |
| TT.L.VSG..VHRL.AG...G..AV.I.TY.LDMVRV.L.FQVK..E.T.TG.IH.F.T.YAKEG.F..F | |
| Retrocopy | TTYLWVSG<SVHRLIAGCMVGLAAV>IFTYLLDMVRVYLSFQVKE<EDTHTGVIHTFRTNYAKEGDFFAF |
| Parental | YR-GLMPTILGMAPYAGVSFFTFGT-LKSVGLSHAPTLLGRPSSDNPNVLVLKTHINLI |
| ...GL.P..LGMAP..GVSFFTFG..LKSVGL...PTL.G.P.SDNP...VLKT..... | |
| Retrocopy | FE<GLKPPVLGMAPHTGVSFFTFGA<LKSVGLPQVPTLPGSP-SDNPDI*VLKTYFVVV |
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 | 1 .99 RPM |
| SRP014902_testis | 0 .00 RPM | 2 .40 RPM |
| SRP018288_heart | 0 .00 RPM | 3 .27 RPM |
| SRP018288_kidney | 0 .00 RPM | 13 .99 RPM |
| SRP018288_liver | 0 .00 RPM | 20 .15 RPM |
| SRP018288_lung | 0 .00 RPM | 9 .88 RPM |
| SRP018856_adipose | 0 .00 RPM | 7 .31 RPM |
| SRP035408_brain | 0 .00 RPM | 13 .91 RPM |
| SRP035408_liver | 0 .00 RPM | 6 .72 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_1000 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_1000 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_1000 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000017305 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000011191 | 1 retrocopy | |
| Sus scrofa | ENSSSCG00000022303 | 1 retrocopy |
retro_sscr_1000 ,
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