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Title 

The H-Invitational database (H-InvDB), a comprehensive annotation resource for human genes and transcripts

Authors 

C YamasakiK MurakamiY FujiiY SatoE HaradaJ TakedaNam-Soon KimHyang Sook YooS KimT ImanishiT Gojobori

Publisher 

Oxford University Press

Issue Date 

2008

Citation 

Nucleic Acids Research, vol. 36, no. D, pp. D793-D799

Keywords 

complementary DNAmessenger RNAtranscriptomeuntranslated RNAalternative RNA splicingamino acid sequencecellular distributionH-Invitational Databasehuman genomegene expression profiling

Abstract 

Here we report the new features and improvements in our latest release of the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/), a comprehensive annotation resource for human genes and transcripts. H-InvDB, originally developed as an integrated database of the human transcriptome based on extensive annotation of large sets of full-length cDNA (FLcDNA) clones, now provides annotation for 120 558 human mRNAs extracted from the International Nucleotide Sequence Databases (INSD), in addition to 54 978 human FLcDNAs, in the latest release H-InvDB_4.6. We mapped those human transcripts onto the human genome sequences (NCBI build 36.1) and determined 34 699 human gene clusters, which could define 34 057 (98.1%) protein-coding and 642 (1.9%) non-protein-coding loci; 858 (2.5%) transcribed loci overlapped with predicted pseudogenes. For all these transcripts and genes, we provide comprehensive annotation including gene structures, gene functions, alternative splicing variants, functional non-protein-coding RNAs, functional domains, predicted sub cellular localizations, metabolic pathways, predictions of protein 3D structure, mapping of SNPs and microsatellite repeat motifs, co-localization with orphan diseases, gene expression profiles, orthologous genes, protein-protein interactions (PPI) and annotation for gene families. The current H-InvDB annotation resources consist of two main views: Transcript view and Locus view and eight sub-databases: the DiseaseInfo Viewer, H-ANGEL, the Clustering Viewer, G-integra, the TOPO Viewer, Evola, the PPI view and the Gene family/group.

ISSN 

0305-1048

Link 

http://dx.doi.org/10.1093/nar/gkm999

Appears in Collections

1. Journal Articles > Journal Articles

Registered Date

2019-05-02


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