Human Herpesvirus 8 (KSHV)
Gene Image Map

 Human Herpesvirus 8 (common name: KSHV) database overview  
Human herpesvirus 8 from the BC-1 cell line was sequenced by the Moore/Chang Laboratory, Columbia University in 1996, except for a 3kb region at the far right end of the genome that was refractory to cloning. The key publication describing this genome is "Nucleotide sequence of the Kaposi sarcoma-associated herpesvirus (HHV8)" by Russo et al. Proc Natl Acad Sci U S A 1996 Dec 10;93(25):14862-7 and is included in a comprehensive set of KSHV References from Medline (12/1994-1/2002). A second genomic sequence of an isolate from a KS lesion was generated by the Neipel laboratory and published a year later (J Virol 1997 Jun;71(6):4187-92). Generally, less than 1% sequence variation is present between the two strains although hotspots of high sequence variability are present.

Kaposi's sarcoma, a vascular tumor seen very rarely except in immuno-suppressed people, was shown in 1994 to be closely associated with a sexually transmitted and newly identified member of the Herpesviridae family of viruses, namely Human herpesvirus 8. General properties of herpesviruses are reviewed here, Herpesviridae Properties.

An overview map of the genome and information summary is available through the Gene Image Map. The newest version of this map clearly depicts coterminal and overlapping genes, genes coding on opposite strands and repeats, all of which are common in the tightly packed genomes of herpesviruses. Expression Patterns illustrate the cellular localization of several important KSHV proteins.

The core information in this database is the table of annotated records, one for each of 87 genes. Each gene record is identified by a gene id, KSHV001-083 (some with extensions to total 87). Five spliced genes have been located, ORF50 (2 exons), K8 (3 exons), K10.5 (2 exons), K15 (8 exons) while K8.1 with 2 exons is known to be alternatively spliced. Simple summaries of specific information are available below in the Predefined Database Searches including 23 identified Cellular Homologs.

The power of a relational database is demonstrated in the ability to search its information. We provide five search tools, each with different characteristics. The Basic Search allows a simple query of many fields for a text term. The Intermediate Search allows the user to search specific tables, to search a range of molecular weights or isoelectric points and to search the protein or nucleotide sequences for simple patterns. The Advanced SQL Search allows those who understand Structured Query Language to construct cross table and more specific queries and the Protein Motif Search allows searching protein sequences for sophisticated amino acid patterns. Repeat Search queries the repeat table for previously located nucleotide repeats.

User Defined Database Searches
Basic Search
Intermediate Search
Advanced SQL Search
Sequence Search
Protein Motif Search
Repeat Search

Predefined Database Searches
Definition Table
Functional Classes Table
EC Table
PDB Table
Cellular Homolog Table
Repeat Tables
           Tandem
           Terminal
           Inverted
           All

Visualization
Gene Image Map
Expression Patterns in Infected Cells
EBV - KSHV Proteome Comparison

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