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United States Department of Agriculture

Agricultural Research Service

About the database

DGIL Porcine Translational Research Database

PINdb

 

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Current Statistics (07/22/2016)
Gene entries    11,650
Genes with full-length RNA transcripts (full 5’ and 3’)        7,903
% of genome (estimated)  34.7%
Full-length protein sequences    7,113
% of genome (estimated)  37.5%
  MicroRNA Sequences 1045
Error notations (# of entries)    4,908
  Artifactually duplicated genes    1244
  Missing genes (from Ensembl 10.2)   1221
  Truncated proteins   1,934
  Elongated proteins   131
Real-time PCR Assays   2,772
  Taqman   2,243
  SYBR Green     529
Antibodies (reactive and non reactive)   1,263
Antibodies (# entries)    589

 

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.

                                                                       

What’s new?

 

1.   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.

 

2.   Assembly of the Collagen Superfamily.

 

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

 

3. Complete representation of the "Transportome" (Solute Carrier and the ATP binding Cassette 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. 

 

4. Annotation of 356 genes that compose porcine CD markers to conform to human HLDA 10.

 

5. 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

07/22/2016


Last Modified: 7/22/2016
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