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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 (08/30/2018)    
     
Gene Entries    15,306  
     
Genes with full-length RNA transcripts (full 5’ and 3’)        10,008  
% of genome (estimated) 46.1%  
     
Nunber of transcripts 10859  
   Splice variants 1038  
     
Full-length protein sequences    8,784  
% of genome (estimated) 46.2%  
     
  1,045  
MicroRNA Sequences    
  380  
Biologically duplicated genes/paralogs    
  3,234  
Real-time PCR Assays  2,256  
Taqman  978  
SYBR Green       
     
Antibodies (reactive and non reactive)  1,866  
Antibodies (# entries)    848  
     
     
Ensembl Build 11.1.  
Parameter Number Percent
Loci Screened 2823 100.0%
Correct 1292 45.8%
Correct but no annotation or misannotated 244 8.6%
Correct but missing an identified isoform 90 3.2%
Truncated 639 22.6%
Elongated 206 7.3%
Merged Loci 101 3.6%
Present but no locus assigned 81 2.9%
Split Loci 76 2.7%
Missing 15 0.5%
Protein-coding gene annotated as a pseudogene 10 0.4%
Pseudogene annotated as a protein-coding gene 32 1.1%
Artifactually duplicated Loci 14 0.5%
Miscellaneous error 36 1.3%

 

 

 

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.