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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 (05/22/2017)      
               
Gene entries              12,981
               
Genes with full-length RNA transcripts (full 5’ and 3’)        9,139
  % of genome (estimated)     41.5%
               
Full-length protein sequences        8,082
  % of genome (estimated)     42.5%
               
  MicroRNA Sequences         1,045
               
Total Number of Errors       8,304
 Number of Entries with Errors       5,354
  Number of Genes not identified in Ensembl Build 10.2. 1,341
  Artifactually Duplicated Loci       1,354
  Elongated proteins         201
  Truncated proteins         2,292
               
Biologically duplicated genes/paralogs     104
               
Real-time PCR Assays          2,864
  Taqman             2,236
  SYBR Green               628
               
Antibodies (reactive and non reactive)    1,342
Antibodies (# entries)          627

 

 

What's new?

  1. Genes involved in Neurological Functioning

 

The database contains full-length sequences for 121 neurotransmitter receptors, 35 neuropeptide receptors, 8 neuropeptides, 10 trace amine associated receptors (TAARs), 37 neurotrophic mediators and 25 taste receptor genes. Thirty of these genes are missing from Ensembl build 10.2 and 69 of these genes encode truncated proteins. A preliminary analysis indicates there are important species differences in these genes. For example there are 15 TAARs in mouse, 6 in human and 10 in pigs. There are 15 serotonin receptors in pigs and human and 12 in mice.

 

  1.   Genes involved in Development

The database 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). These include 46 genes missing from Ensembl build 10.2.

 

  1.   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.

    

  1.   Collagen Superfamily.

The porcine Collagen Superfamily contains 49 members including 3 that are missing from Ensembl build 10.2.

 

  1.   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.

 

     6. Annotation of 356 genes that compose porcine CD markers

 

 

 

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

05/22/2017


Last Modified: 5/23/2017
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