RetrogeneDB ID: | retro_sscr_1066 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 9:84607431..84607841(-) | ||
| 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: | ENSSSCG00000023560 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_sscr_1066
GCAAAATTTGGTTTCTCTAGTATTACTGGAATTGATTACTTTCCATCTGCAACACAGTTTTCTAGAAGTATTATAAAGAA
GAAGGTTTATCTAACATTAAGCTAAAGGTAGAAGACTTTTTGAATCCTTCCACAAAGCTGCCTGGATTTCATATTTGTAT
TGACAAAGGGACTTTAGATGCCATAACCTTAATCCTGAAAATGCAATTGAGAAGAGGAAGCAATATGTGAAATCTCTCTC
CAGGGTGTTAAAACTGAAAGACTTTTTTCCTAATAATCTCATGTAATTGGACCAAGGAAAAGTTGCTAAATGAATTCAGT
GCAGAATGTGAACTTTTTGAAGAACTGCCAACACCTAAGTTCAGCTTTTGAGGCAGATCTGGAAAGAGTATAGCAGCGTT
AGTTTTCCAA
ORF - retro_sscr_1066 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 77.14 % |
| Parental protein coverage: | 58.3 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | AKSGFSNITGIDYSPSAIRLSGSIIEK-EGLSNIKLKVEDFLNPSTKLSGFHVCIDKGTFDAI-SLHPDS |
| AK.GFS.ITGIDY.PSA...S.SII.K.EGLSNIKLKVEDFLNPSTKL.GFH.CIDKGT.DAI..L.P.. | |
| Retrocopy | AKFGFSSITGIDYFPSATQFSRSIIKK<EGLSNIKLKVEDFLNPSTKLPGFHICIDKGTLDAI<NLNPEN |
| Parental | AVEKRKQYVQSLSRAL-NVKGFFLITSCNWTKEELLNEFSEGFELFEELPTPKFTFGGRSGNSVAALVFQ |
| A.EKRKQYV.SLSR.L.N.K.FFLI.SCNWTKE.LLNEFS...ELFEELPTPKF.F.GRSG.S.AALVFQ | |
| Retrocopy | AIEKRKQYVKSLSRVL>N*KTFFLIISCNWTKEKLLNEFSAECELFEELPTPKFSF*GRSGKSIAALVFQ |
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 | 4 .65 RPM |
| SRP014902_testis | 0 .00 RPM | 11 .32 RPM |
| SRP018288_heart | 0 .00 RPM | 7 .12 RPM |
| SRP018288_kidney | 0 .00 RPM | 16 .55 RPM |
| SRP018288_liver | 0 .00 RPM | 6 .88 RPM |
| SRP018288_lung | 0 .00 RPM | 3 .77 RPM |
| SRP018856_adipose | 0 .00 RPM | 4 .17 RPM |
| SRP035408_brain | 0 .00 RPM | 7 .18 RPM |
| SRP035408_liver | 0 .00 RPM | 12 .59 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_1066 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_1066 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_1066 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 | ENSSSCG00000023560 | 2 retrocopies |
retro_sscr_1066 , retro_sscr_579,
|