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H-Invitational Genes mRNA Alignments   (All mRNA and EST tracks)

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Data coordinates converted via liftOver from: Mar. 2006 (NCBI36/hg18)
Data last updated: 2010-12-30

 Note: these data have been converted via liftOver from the Mar. 2006 (NCBI36/hg18) version of the track.

Description

This track shows alignments of full-length cDNAs that were used as the basis of the H-Invitational Gene Database (HInv-DB). The HInv-DB is a human gene database containing human-curated annotation of 41,118 full-length cDNA clones representing 21,037 cDNA clusters. The project was initiated in 2002 and the database became publicly available in April 2004.

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 JBIRC. 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

Imanishi, T. et al. Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol. 2:(6), e162 (2004).