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The gene mutated in chorea-acanthocytosis (CHAC; approved gene symbol VPS13A) encodes chorein, a protein similar to yeast Vps13p. We detected several similar putative human proteins by BLAST analysis of chorein. We characterized the structure of three new genes encoding these CHAC-similar proteins, located on chromosomes 1p36, 8q22, and 15q21. The most similar gene in yeast to all four human genes is Vps13, and therefore the human genes were named VPS13A (CHAC, 9q21), VPS13B (8q22), VPS13C (15q21), and VPS13D (1p36). VPS13B has recently been reported as COH1, altered in Cohen syndrome. For each gene, we describe several alternative splicing variants; at least two transcripts per gene are major forms. The expression pattern of these genes is ubiquitous, with some tissue-specific differences between several transcript variants. Protein sequence comparisons suggest that intramolecular duplications have played an important role in the evolution of this gene family.
Pubmed ID: 15498460 RIS Download
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THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023. Database that provides special browsing capabilities for a subset of organisms in Entrez Genomes. Map Viewer allows users to view and search an organism's complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest. If multiple maps are available for a chromosome, it displays them aligned to each other based on shared marker and gene names, and, for the sequence maps, based on a common sequence coordinate system.
View all literature mentionsTool for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.
View all literature mentionsService providing functional analysis of proteins by classifying them into families and predicting domains and important sites. They combine protein signatures from a number of member databases into a single searchable resource, capitalizing on their individual strengths to produce a powerful integrated database and diagnostic tool. This integrated database of predictive protein signatures is used for the classification and automatic annotation of proteins and genomes. InterPro classifies sequences at superfamily, family and subfamily levels, predicting the occurrence of functional domains, repeats and important sites. InterPro adds in-depth annotation, including GO terms, to the protein signatures. You can access the data programmatically, via Web Services. The member databases use a number of approaches: # ProDom: provider of sequence-clusters built from UniProtKB using PSI-BLAST. # PROSITE patterns: provider of simple regular expressions. # PROSITE and HAMAP profiles: provide sequence matrices. # PRINTS provider of fingerprints, which are groups of aligned, un-weighted Position Specific Sequence Matrices (PSSMs). # PANTHER, PIRSF, Pfam, SMART, TIGRFAMs, Gene3D and SUPERFAMILY: are providers of hidden Markov models (HMMs). Your contributions are welcome. You are encouraged to use the ''''Add your annotation'''' button on InterPro entry pages to suggest updated or improved annotation for individual InterPro entries.
View all literature mentionsPortal to the PSORT family of computer programs for the prediction of protein localization sites in cells, as well as other datasets and resources relevant to localization prediction. The standalone versions are available for download for larger analyses.
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