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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.