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United States Department of Agriculture

Agricultural Research Service

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DGIL Porcine Translational Research Database

PINdb

 

 

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This database contains functional information on genes commonly studied in humans, pigs, and rodents, including more than 2,300 sequenced at DGIL. Each entry has been manually-annotated and is linked to other porcine databases as well as Homologene, InnateDb and Gene Ontology Annotations.

 

 

Current Statistics (11/22/2016)      
               
Gene entries              12,125
               
Genes with full-length RNA transcripts (full 5’ and 3’)        8,548
  % of genome (estimated)     38.5%
               
Full-length protein sequences        7,643
  % of genome (estimated)     40.2%
               
  MicroRNA Sequences         1,045
               
Total Number of Errors       7,938
  Number of Entries with Errors       5,154
  Number of Genes not identified in Ensembl Build 10.2. 1,297
  Artifactually Duplicated Loci       1,330
  Elongated proteins         173
  Truncated proteins         2,142
               
Biologically duplicated genes/paralogs     92
               
Real-time PCR Assays          2,796
  Taqman             2,228
  SYBR Green               568
               
Antibodies (reactive and non reactive)    1,358
Antibodies (# entries)          602

 

                                                                       

What's new?

  1. Genes involved in Development: The database now provides comprehensive coverage of porcine genes involved in development including members of the Forkhead (44) and Homeodomain (214), Dishevelled (3); Frizzled (13); Hedgehog; (3); Notch (4); Kruppel-like Factor Transcription Factor (18) and Wnt Superfamiles (19). This includes genes 46 genes missing from Ensembl build 10.2.
  2. Assembly of the Mucin Superfamily: The porcine Mucin Superfamily contains 20 members (17 full length and 3 partial length assemblies) including 7 that are missing from Ensembl build 10.2. 
  3. Assembly of the Collagen Superfamily: The porcine Collagen Superfamily contains 49 members including 3 that are missing from Ensembl build 10.2.
  4.  Complete representation of the "Transportome" (Solute Carrier, ATP binding Cassette, Claudin and Aquaporin, Superfamilies): The porcine Solute Carrier Superfamily contains 398 members, including 42 that are missing from Ensembl build 10.2. About 25% of these transporters are dedicated to amino acid and vitamin transport. Several species-specific gene expansion occurs in subfamilies. The porcine ATP binding Cassette Subfamily contains 57 members including 4 that are missing from Ensembl build 10.2. Comprehensive coverage of genes involved in paracellular permeability including members of the Claudin Superfamily (24), Occludin (1); Tight Junction Protein Superfamily (4) and Aquaporin Superfamily (12), are also provided.
  5.  Annotation of 356 genes that compose porcine CD markers to conform to human HLDA 10.
  6.  Resolution of the Tetraspanin (32 porcine members) and Protocadherin beta Superfamilies (12 porcine members)

 

The sequences in this database (and associated informantics) 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.

Updated

11/22/2016


Last Modified: 11/30/2016
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