RetrogeneDB ID: | retro_sscr_314 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 13:23916875..23917199(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSSSCG00000011240 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PLTP | ||
| Ensembl ID: | ENSSSCG00000007435 | ||
| Aliases: | None | ||
| Description: | Sus scrofa phospholipid transfer protein (PLTP), mRNA. [Source:RefSeq mRNA;Acc:NM_214283] |
Retrocopy-Parental alignment summary:
>retro_sscr_314
ATAGCCCTCTTAGGGGCCCTCTTCCTAGTGCTGCTGGCAGGTGCTCACGGGGGGCTCCCTGGCTGCAAAATTTGCATCAC
CTGCAAGGTGCTGGAGCTGGTGAAGCAGGAGGGGCTGCGCTTTCTGGAGCAAGAGCTGGAGACCATTACCATTCCGGATC
TGCAGGGCAGGGAGGGCCACTTCTACTACAACATCTCTGAAGTGAAGGTCACGGAGCTGCAGCTGACATCCTCTGAGCTC
CATTTCCAGCCAGAGCAGGACCTGATGCTACAAATCAACAATGGCTCCTTGGGGCTGCGCTTCCGGAGACAGCTTCTCTA
CTGG
ORF - retro_sscr_314 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.59 % |
| Parental protein coverage: | 66.67 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MALLGALFLVLLAGAHAELPGCKIRITSKALELVKQEGLRFLEQELETITIPDLRGREGHFYYNISEVKV |
| .ALLGALFLVLLAGAH..LPGCKI.IT.K.LELVKQEGLRFLEQELETITIPDL.GREGHFYYNISEVKV | |
| Retrocopy | IALLGALFLVLLAGAHGGLPGCKICITCKVLELVKQEGLRFLEQELETITIPDLQGREGHFYYNISEVKV |
| Parental | TELQLTSSELHFQPEQELMLQINNGSLGLRFRRQLLYW |
| TELQLTSSELHFQPEQ.LMLQINNGSLGLRFRRQLLYW | |
| Retrocopy | TELQLTSSELHFQPEQDLMLQINNGSLGLRFRRQLLYW |
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 .30 RPM |
| SRP014902_testis | 0 .42 RPM | 205 .52 RPM |
| SRP018288_heart | 0 .05 RPM | 0 .79 RPM |
| SRP018288_kidney | 0 .10 RPM | 3 .35 RPM |
| SRP018288_liver | 0 .00 RPM | 4 .48 RPM |
| SRP018288_lung | 0 .00 RPM | 8 .25 RPM |
| SRP018856_adipose | 0 .20 RPM | 10 .36 RPM |
| SRP035408_brain | 0 .00 RPM | 13 .02 RPM |
| SRP035408_liver | 0 .00 RPM | 1 .56 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_314 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_314 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_314 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Sus scrofa | ENSSSCG00000007435 | 1 retrocopy |
retro_sscr_314 ,
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