DGIL Porcine Translational Research Database
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As of December 2022, the database has been online for 17 years. It is used by research scientists working with pigs worldwide as well as commercial and public developers of new reagents. This database is the largest manually curated database for any agriculture species and is unique among porcine gene databases by linking gene expression to gene function, identification of related gene pathways, and connectivity with other porcine/human gene databases. It is referenced in more than 100 manuscripts or websites and used as an information resource for several reagent vendors.
| Current Statistics (12/13/22) | ||
| Gene Entries | 24,312 | |
| Genes with full-length RNA transcripts (full 5’ and 3’) | 15,204 | |
| Number of transcripts | 18851 | |
| Splice variants | 3,647 | |
| Number of full-length protein sequences | 12,896 | |
| % of genome (estimated) | 64.40% | |
| MicroRNA Sequences | 1,107 | |
| Real-time PCR Assays | 3,339 | |
| Taqman | 2,231 | |
| SYBR Green | 1108 | |
| Antibodies (reactive and non reactive) | 2,362 | |
| Antibodies (# entries) | 975 | |
| Error Analysis | ||
| Protein coding Genes | ||
| Ensembl Build 11.1 | Number | Percent |
| Correct | 4329 | 49.1% |
| Error in assembly or annotation | 4000 | 45.4% |
| Not an annotated gene | 408 | 4.6% |
| Split into multiple loci | 62 | 0.7% |
| Multiple genes into 1 locus | 623 | 7.1% |
| Sequence not present | 21 | 0.2% |
| Total number of genes compared | 8820 | |
| NCBI Build 11.1 | Number | Percent |
| Correct | 3847 | 59.0% |
| Error in assembly or annotation | 1976 | 30.3% |
| Not an annotated gene | 664 | 10.2% |
| Split into multiple loci | 14 | 0.2% |
| Multiple genes into 1 locus | 24 | 0.4% |
| Sequence not present | 15 | 0.2% |
| Total number of genes compared | 6516 | |
| MARC Build 1.0 | Number | Percent |
| Correct | 2956 | 46.4% |
| Error in assembly or annotation | 2798 | 43.9% |
| Not an annotated gene | 346 | 5.4% |
| Split into multiple loci | 31 | 0.5% |
| Multiple genes into 1 locus | 327 | 5.1% |
| Sequence not present | 236 | 3.7% |
| Total number of genes compared | 6367 |
The sequences in this database (and associated informatics) are available (in bulk) to extramural laboratories, via MTA, that are looking to supplement their analysis of the porcine genome. Please contact us if you are interested in this.
Disclaimer
This database is currently in a beta version, there are some incomplete annotations. We cannot guarantee the performance of the antibodies or PCR assays that have not been tested in our lab under conditions not specified in the published literature.
