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DGIL Porcine Translational Research Database

PINdb

 

 

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As of April 2021, the database has been online for 16 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 (11/16/21)  
   
Gene Entries    22,210
   
Genes with full-length RNA transcripts (full 5’ and 3’)        13,793
   
Number of transcripts 15824
   Splice variants 2031
   
Number of full-length protein sequences    11,478
% of genome (estimated) 57.4%
   
MicroRNA Sequences 1,045
   
Biologically duplicated genes/paralogs 738
   
   
Real-time PCR Assays  3,350
Taqman  2,272
SYBR Green    1078
   
Antibodies (reactive and non reactive)  2,209
Antibodies (# entries)    969

 

Ensembl Build 11.1 Number   Percent
       
Correct 2761   47.3%
Error in annotated Ensembl locus 2332   39.9%
Split into multiple loci 48   0.8%
Multiple genes into 1 locus 268   4.6%
Not an annotated gene 415   7.1%
Sequence is not present 15   0.3%
       
Loci screened 5839    

 

NCBI Build 11.1 Number   Percent
       
Correct 4308   73.8%
Error in annotated NCBI locus 1268   21.7%
Split into multiple loci 8   0.1%
Multiple genes into 1 locus 13   0.2%
Not an annotated gene 237   4.1%
Sequence is not present 5   0.1%
       
Loci screened 5839    

 

MARC Build 1.0 Number   Percent
       
Correct 2749   47.1%
Error in annotated MARC locus 2307   39.5%
Split into multiple loci 27   0.5%
Multiple genes into 1 locus 135   2.3%
Not an annotated gene 389   6.7%
Sequence is not present 232   4.0%
       
Loci screened 5839    

 

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.


Last Modified: 04/21/2021).