RetrogeneDB ID: | retro_sscr_375 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 13:85853013..85853274(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSSSCG00000011655 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DBI | ||
| Ensembl ID: | ENSSSCG00000023435 | ||
| Aliases: | None | ||
| Description: | Sus scrofa diazepam binding inhibitor (GABA receptor modulator, acyl-CoA binding protein) (DBI), mRNA. [Source:RefSeq mRNA;Acc:NM_214119] |
Retrocopy-Parental alignment summary:
>retro_sscr_375
ATGTCTCAGGCAGAGTTTGAGAAAGCTGCTGAGGAAGCCAAGAATCTTAAGACCAAACCAGCAGATGATGAGATGCTGTT
CATCTCCGGCCACTACAAACAAGCGACTGTGGGTGACATAAATACAAAACAGCCTGGAATTTTGGACCTCAAAGGTAAGG
CCAAGTGGGATGCCTGGAATGGGCTGACATGGACTTCCAAGGAAGATGCCATGAAAGCACATAGCAACAAAGTAGAAGAG
CTAAAGAAAAAATATGGAATA
ORF - retro_sscr_375 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.66 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSQAEFEKAAEEVKNLKTKPADDEMLFIYSHYKQATVGDINTERPGILDLKGKAKWDAWNGLKGTSKEDA |
| MSQAEFEKAAEE.KNLKTKPADDEMLFI..HYKQATVGDINT..PGILDLKGKAKWDAWNGL..TSKEDA | |
| Retrocopy | MSQAEFEKAAEEAKNLKTKPADDEMLFISGHYKQATVGDINTKQPGILDLKGKAKWDAWNGLTWTSKEDA |
| Parental | MKAYINKVEELKKKYGI |
| MKA..NKVEELKKKYGI | |
| Retrocopy | MKAHSNKVEELKKKYGI |
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 | 10 .22 RPM |
| SRP014902_testis | 0 .00 RPM | 29 .28 RPM |
| SRP018288_heart | 0 .00 RPM | 54 .88 RPM |
| SRP018288_kidney | 0 .00 RPM | 147 .56 RPM |
| SRP018288_liver | 0 .00 RPM | 177 .50 RPM |
| SRP018288_lung | 0 .00 RPM | 41 .95 RPM |
| SRP018856_adipose | 0 .00 RPM | 552 .16 RPM |
| SRP035408_brain | 0 .00 RPM | 379 .82 RPM |
| SRP035408_liver | 0 .00 RPM | 680 .73 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_375 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_375 was not experimentally validated.