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Resource:Disease Genes Conserved Sequence Tags Database

Name: Resource:Disease Genes Conserved Sequence Tags Database
Description:

The DG-CST database is a collection of conserved sequence elements, identified by a systematic genomic sequence comparison between a set of human genes involved in the pathogenesis of genetic disorders and their murine counterparts.
Human and mouse genomic sequences were compared by BLASTZ, an independent implementation of the Gapped BLAST algorithm, specifically designed for aligning two long genomic sequences. Sequences longer than 100 and with identity better than 70 were selected as CSTs and imported into the database. CSTs are extensively annotated with respect to exon/intron structure and other biological parameters. CST counterparts in other species were identified by using BLAST to scan genomes from other species, and selecting on the basis of homology and co-linearity.
The database can be accessed in a variety of ways:

- Gene: CSTs identified on the basis of the analyzed genes and their features such as gene symbol and description according to ENSEMBL or LocusLink gene definition, tissue localization, alternative splicing and others.
- Chromosomal localization: Use this to search CSTs by chromosomal coordinates, distances from analyzed and closest genes and coding regions, etc. You can, for example, identify intergenic CSTs located in the region proximal to the 5' end of disease genes.
- Graphic browser: A tool for graphic visualization of CSTs on the chromosome and within the gene context. CSTs may be color coded on the basis of alternative features such as percent identity, GC content, CPS value, direct and inverted repeats etc.
- DNA features: About 50 of CSTs do not correspond to previously known exon sequences. At least some of them are expected to be transcriptional regulatory regions and elements involved in chromosome structure and functions.
- RNA features: CSTs may be searched for the presence of conserved RNA secondary structures as determined by a prediction program. A CST with a conserved RNA secondary structure is expected to be transcribed and active as RNA.
- Coding regions: About 30 of CSTs contain coding sequences, according to ENSEMBL exon definitions, but a significant fraction of the remaining 70 retains significant coding potential, when analyzed with a prediction software. Among them there are novel exons belonging to known genes or to novel genes.
Sponsors: This work was supported by the Telethon Foundation, the Associazione Italiana per la Ricerca sul Cancro (AIRC), the Federazione Italiana per la Ricerca sul Cancro (FIRC), the Italian Ministry for Research (MURST), the National Council for Research (CNR), Regione Campania, and BioGeM.
Other Name(s): DG CST
Resource Type(s): web accessible database
Keywords: element, exon, function, gene, genetic, 5' end, algorithm, alternative splice, biological, chromosome, coding, conserve, database, disease, disorder, dna, genomic, graphic visualization, human, intron, localization, mouse, murine, pathogenesis, region, regulatory, rna, secondary, sequence, structure, systematic, tag, tissue, transcribe, transcriptional
Resource: Resource
URL: http://dgcst.ceinge.unina.it/
Id: nif-0000-21121
Link to OWL / RDF: Download this content as OWL/RDF

Curation status: Curated

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Contributors

Ccdbuser, Eddy kim, Nifbot2, Zaidaziz



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Facts about Resource:Disease Genes Conserved Sequence Tags DatabaseRDF feed
CurationStatuscurated  +
DefiningCitationhttp://dgcst.ceinge.unina.it/  +
Definition

The DG-CST database is a collectio
The DG-CST database is a collection of conserved sequence elements, identified by a systematic genomic sequence comparison between a set of human genes involved in the pathogenesis of genetic disorders and their murine counterparts.
Human and mouse genomic sequences were compared by BLASTZ, an independent implementation of the Gapped BLAST algorithm, specifically designed for aligning two long genomic sequences. Sequences longer than 100 and with identity better than 70 were selected as CSTs and imported into the database. CSTs are extensively annotated with respect to exon/intron structure and other biological parameters. CST counterparts in other species were identified by using BLAST to scan genomes from other species, and selecting on the basis of homology and co-linearity.
The database can be accessed in a variety of ways:

- Gene: CSTs identified on the basis of the analyzed genes and their features such as gene symbol and description according to ENSEMBL or LocusLink gene definition, tissue localization, alternative splicing and others.
- Chromosomal localization: Use this to search CSTs by chromosomal coordinates, distances from analyzed and closest genes and coding regions, etc. You can, for example, identify intergenic CSTs located in the region proximal to the 5' end of disease genes.
- Graphic browser: A tool for graphic visualization of CSTs on the chromosome and within the gene context. CSTs may be color coded on the basis of alternative features such as percent identity, GC content, CPS value, direct and inverted repeats etc.
- DNA features: About 50 of CSTs do not correspond to previously known exon sequences. At least some of them are expected to be transcriptional regulatory regions and elements involved in chromosome structure and functions.
- RNA features: CSTs may be searched for the presence of conserved RNA secondary structures as determined by a prediction program. A CST with a conserved RNA secondary structure is expected to be transcribed and active as RNA.
- Coding regions: About 30 of CSTs contain coding sequences, according to ENSEMBL exon definitions, but a significant fraction of the remaining 70 retains significant coding potential, when analyzed with a prediction software. Among them there are novel exons belonging to known genes or to novel genes.
Sponsors: This work was supported by the Telethon Foundation, the Associazione Italiana per la Ricerca sul Cancro (AIRC), the Federazione Italiana per la Ricerca sul Cancro (FIRC), the Italian Ministry for Research (MURST), the National Council for Research (CNR), Regione Campania, and BioGeM.
(CNR), Regione Campania, and BioGeM.
Has default formThis property is a special property in this wiki.Resource  +
Has roleWeb accessible database  +
Idnif-0000-21121  +
KeywordsElement  +, Exon  +, Function  +, Gene  +, Genetic  +, 5' end  +, Algorithm  +, Alternative splice  +, Biological  +, Chromosome  +, Coding  +, Conserve  +, Database  +, Disease  +, Disorder  +, Dna  +, Genomic  +, Graphic visualization  +, Human  +, Intron  +, Localization  +, Mouse  +, Murine  +, Pathogenesis  +, Region  +, Regulatory  +, Rna  +, Secondary  +, Sequence  +, Structure  +, Systematic  +, Tag  +, Tissue  +, Transcribe  +, and Transcriptional  +
LabelResource:Disease Genes Conserved Sequence Tags Database  +
ModifiedDate19 October 2010  +
SuperCategoryResource  +
SynonymDG CST  +