Description

This track shows alignments of full-length cDNAs that were used as the basis of the H-Invitational Gene Database (HInv-DB version 7.0). This is the version 7.0 update from March 2010.

HInv-DB entries describe the following entities:

• gene structures
• functions
• novel alternative splicing isoforms
• non-coding functional RNAs
• functional domains
• sub-cellular localizations
• metabolic pathways
• predictions of protein 3D structure
• mapping of SNPs and microsatellite repeat motifs in relation with orphan diseases
• gene expression profiling
• comparative results with mouse full-length cDNAs gene structures

Methods

To cluster redundant cDNAs and alternative splicing variants within the H-Inv cDNAs, a total of 41,118 H-Inv cDNAs were mapped to the human genome using the mapping pipeline developed by the Japan Biological Information Research Center (JBIRC). The mapping yielded 40,140 cDNAs that were aligned against the genome using the stringent criteria of at least 95% identity and 90% length coverage. These 40,140 cDNAs were clustered to 20,190 loci, resulting in an average of 2.0 cDNAs per locus. For the remaining 978 unmapped cDNAs, cDNA-based clustering was applied, yielding 847 clusters. In total, 21,037 clusters (20,190 mapped and 847 unmapped) were identified and integrated into H-InvDB. H-Inv cluster IDs (e.g. HIX0000001) were assigned to these clusters. A representative sequence was selected from each cluster and used for further analyses and annotation.

A full description of the construction of the HInv-DB is contained in the report by the H-Inv Consortium (see References section).

Credits

The H-InvDB is hosted at the Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST) in Japan. The human-curated annotations were produced during invitational annotation meetings held in Japan during the summer of 2002, with a follow-up meeting in November 2004. Participants included 158 scientists representing 67 institutions from 12 countries.

The full-length cDNA clones and sequences were produced by the Chinese National Human Genome Center (CHGC), the Deutsches Krebsforschungszentrum (DKFZ/MIPS), Helix Research Institute, Inc. (HRI), the Institute of Medical Science in the University of Tokyo (IMSUT), the Kazusa DNA Research Institute (KDRI), the Mammalian Gene Collection (MGC/NIH) and the Full-Length Long Japan (FLJ) project.

References

Genome Information Integration Project And H-Invitational 2, Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, Taniya T, Sakate R, Kikugawa S et al. The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res. 2008 Jan;36(Database issue):D793-9. PMID: 18089548; PMC: PMC2238988

Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi- Kabata Y, Tanino M et al. Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol. 2004 Jun;2(6):e162. PMID: 15103394; PMC: PMC393292

Yamasaki C, Murakami K, Takeda J, Sato Y, Noda A, Sakate R, Habara T, Nakaoka H, Todokoro F, Matsuya A et al. H-InvDB in 2009: extended database and data mining resources for human genes and transcripts. Nucleic Acids Res. 2010 Jan;38(Database issue):D626-32. PMID: 19933760; PMC: PMC2808976