SGD Help: Locus Page

Contents

• Description
• Organization of the Locus page
• Basic Information
• Resources
• Additional Information

Description

Organization of the Locus page

• BASIC INFORMATION

The Basic Information section lists the standard locus name, the systematic name, aliases, retired gene names, and also indicates whether a name is standard or reserved. It addition, it includes the following information:

• Feature Type: indicates what feature type resides on this chromosomal sequence. Feature types currently include: ORF, rRNA, snRNA, snoRNA, tRNA, ncRNA, telomeres and associated subfeatures (telomeric repeat, X element combinatorial repeats, X element core sequence, Y' element), centromere, ARS elements, retrotransposon, LTR, transposable element gene (TyORF), pseudogene, as well as features that are "not in the systematic sequence of S288C" and those that are "not physically mapped". ORF's receive additional designations indicating the degree of certainty that they actually encode proteins. ORF's are classified as "Dubious", "Uncharacterized, or "Verified.


• Description: contains a concise summary or description of the function and biological role of each gene product.


• Gene Ontology (GO) annotations: The Gene Ontology (GO) Annotations (Molecular Function, Biological Process, and Cellular Component), describe a gene's molecular function(s), its broad role in biological processes, and its presence in subcellular locations, structures or macromolecular complexes. Each annotation links to a page showing all yeast genes annotated to that term. The GO annotations use a controlled vocabulary that allows powerful searches within SGD and across other databases. For more information about GO at SGD, please see the SGD help page for GO.


• Pathways: lists all the metabolic pathways in which the gene product functions. These pathway displays were created using the Pathway tools software developed by Peter Karp and his associates at SRI. The Main Query Page offers various options to look at all Yeast Biochemical Pathways and the SGD help page on pathways provides more details on how to use and navigate the information available in the Yeast Biochemical Pathways.


• Name Description: contains the expanded form of the standard name, as described in the literature.


• Gene Product: a description of the protein or RNA product that is coded for by the gene.


• Regulatory Role: lists DNA binding motifs for the encoded protein. Details and associated references for the binding motifs are available via a link from this section. Also provides links to predicted regulatory modules in which the protein may be involved [as predicted by Segal et al. (2003)].


• Mutant Phenotype: lists mutant phenotype(s) for the gene, including those reported by the systematic deletion project consortium. Details and associated references are available via a link located at the top of this section.


• Interactions: provides a link to a list of physical and genetic interactions identified between the encoded protein or gene and other proteins or genes, including those curated at other databases (GRID, BIND and MIPS).


• Physical Interactions: provides a link to a list of physical interactions identified between the encoded protein and others, including those curated at other databases (GRID, BIND and MIPS). Within this section, physical interactions have been organized according to the technique used to identify them.


• Genetic Interactions: provides a link to a list of genetic interactions identified between this gene and other genes, including those curated at other databases (GRID, BIND and MIPS). Within this section genetic interactions have been organized according to the interaction type.


• Sequence Information: lists the chromosomal coordinates of the S288C derived gene, feature or subfeature, as well as its genetic position, when applicable. There are links to two genome browsers: the Chromosomal Features Map, and GBrowse. The dates on which the S288C derived sequence and the coordinates last changed are listed in the Last Update section in the following format: year-month-date. There are two types of dates in the "Last Update" section:
  
  
  1. Coordinates: indicates the date when the chromosomal coordinates of the feature were last changed. In most cases this is likely due to an insertion or deletion to the left of the feature, resulting in a shift of all chromosomal coordinates for features located to the right of the insertion or deletion.
  2. Sequence: indicates the date when the sequence of the feature was last changed. This can be due to a sequence change within the feature, a change in the intron/exon structure of the feature or an extension or deletion of the feature at either the 5' or 3' end. At the present time, the oldest date displayed is 2000-05-19.
  
  The relative coordinates and date of the most recent update for associated subfeatures are listed in the Subfeatures Details section. Finally, this section also provides links to the S288C derived sequence of the Genomic DNA, the Coding Sequence and the ORF Translation.


• External Links: provides links to other information sources for the gene. More information on the databases can be found in SGD's glossary.
  
  The external links were generated using the following methods:
  
  
  • All Associated Sequences: directs you to the All Associated Sequences page which lists sequences (includes the S288C reference sequence and sequences from other strains) found in various external databases, including the GenBank/DDBJ/EMBL nucleotide and protein databases. See the All Associated Sequences help page for more information.
  
  
  • E.C.: the NiceZyme Enzyme Commission (E.C.) number is plugged into the search program at NiceZyme.
  
  
  • Entrez Gene: Gene IDs are first downloaded from NCBI RefSeq. Gene name data are provided to NCBI RefSeq by SGD. The gene names and corresponding Gene IDs are parsed out of the RefSeq chromosome flat files. The links are generated by plugging in the NCBI Gene IDs, downloaded from NCBI RefSeq, into the NCBI Entrez Gene's search program.
  
  
  • Entrez RefSeq Protein: RefSeq Protein Version IDs are downloaded from NCBI RefSeq. Gene name data are provided to NCBI RefSeq by SGD. The gene names and corresponding RefSeq Protein Version IDs are parsed out of the RefSeq chromosome flat files. The links are generated by plugging in the RefSeq Protein Version ID into the NCBI Entrez RefSeq search program. The files are located at: ftp://ftp.ncbi.nih.gov/genomes/Saccharomyces_cerevisiae/
  
  
  • MIPS: the ORF name is plugged into the Munich Information Center for Protein Sequences (MIPS) database search program.
  
  
  • SwissProt: SwissProt IDs are linked to SGD ORFs based on scores obtained through a BLASTP search against the SGD ORFP dataset. The results of the BLASTP searches are manipulated in various ways based on the assumption that there exists a 1:1 relationship between SGD and SwissProt's S. cerevisiae entries.

• RESOURCES

The Resources Section provides resources for analysis and additional information retrieval for a particular gene. The Resources section has the following information retrieval options, organized into pull-down menus:

• Graphic Genome Viewers: At the top of the Resources Section are two graphic representations of the genetic features that surround a particular chromosomal location. Clicking on either the SGD ORF map, (also known as the Chromosomal Features Map) or GBrowse will take you to an expanded view of this region of the genome so that the feature of interest can be viewed in the context of its chromosomal surroundings.


• Literature:
• Literature Guide: retrieves SGD's Literature Guide page, which organizes papers about a gene by various topics.


• Community Annotation: retrieves research highlights, as submitted by members of the yeast community. See the Community Annotation form to submit a research highlight.


• GermOnline: retrieves available information from GermOnline, a cross-species community annotation knowledgebase located at the University of Basel, that provides access to basic locus information, expression data, protein/proteomic information and access to various alignment, modelling and cluster analysis tools.


• Search Google Scholar: takes you to the results of a Google Scholar search where the Standard or Systematic Name and "cerevisiae" have been used as keywords.


• Search PubMed Only: searches the abstracts of papers in PubMed for the co-occurrence of locus name(s) (or systematic name) and Saccharomyces cerevisiae.


• Search All NCBI (Entrez): takes you to the results of an NCBI Entrez search where the Standard or Systematic Name and "cerevisiae" have been used as keywords in a search of NCBI databases.
• Retrieve Sequences: retrieves the sequence of the features Genomic DNA (includes introns) with or without 1kb of upstream and downstream sequences, as derived from the S288C reference strain, the Coding Sequence (CDS) and the ORF Translation (as appropriate). In addition, a link to All Associated Sequences provides access to both S288C and non-S288C sequences stored in various external databases. Finally, a Custom Retrieval option allows users to perform custom sequence queries using SGD's Gene/Sequence Resources.


• Sequence Analysis Tools: retrieves both internally processed BLASTP, BLASTN, FASTA aa, FASTA nt searches and the results of an externally processed BLASTP at NCBI. A Restriction Map of the sequence or just the predicted restriction fragment sizes, a Web Primer tool used to design primers for PCR or sequencing, and a Six-Frame Translation overview with restriction sites can also be retrieved.


• Protein Info & Structure: provides links to basic Protein Information, as well as links to mass spec. data at GPM DB, information on predicted protein Motifs generated using eMOTIFs developed at Stanford University, information about proteins of known structure with sequence similarity to the locus of interest using the SGD resource, PDB Homologs and structural assignments to protein sequences at the superfamily level using the SCOP superfamily resource, co-developed at Stanford University and the MRC.


• Localization Resources: provides access to several external databases that contain localization data for many yeast proteins including the: Yeast GFP Localization Database at UCSF, the YGAC Triples Database at Yale, and the Yeast Protein Localization Database at University Graz.


• Interactions: provides access to several external databases containing genetic and physical interaction data including: the Yeast Resource Center Informatics Platform at the University of Washington, the Biomolecular Interaction Database (BIND) at the University of Toronto, the Database of Interacting Proteins (DIP) at UCLA, the General Repository of Genetic and Physical Interations (GRID) at the University of Toronto, and the PortalPath Calling Yeast Interaction Database, at CuraGen Corporation.


• Phenotype Resources: provides access to several external databases containing phenotype data including: the Profiling of Phenotypic Characteristics in Yeast (PROPHECY) at Goteburg University, the Saccharomyces cerevisiae Morphological Database (SCMD) at the University of Tokyo, the Yeast Proteins Functional Assignment Database at UCLA and the the YGAC Triples Database at Yale.


• Maps and Displays: retrieves several locus-centered maps or graphs, including a Map display of Chromosomal Features, a Gbrowse map showing the position of both ATCC and WashU clones, a table of flanking features for viewing and downloading neighboring chromosomal features, Combined Physical & Genetic Map that displays a side-by-side representation of the combined physical and genetic maps, and a graph displaying Physical/Genetic Map Ratios.


• Comparison Resources: contains links to tools for comparing DNA and protein sequences as well as chromosomal arrangements between S. cerevisiae and other species. For more information on the BLAST programs. Please see NCBI's BLAST program selection guide for more details.
  
  
  • PSI-BLAST Results: retrieves the results of a Sequence Similarity Query using the protein sequence of the ORF as the query for PSI-BLAST analysis against NCBI's non-redundant (nr) protein dataset.
  
  
  • Ashbya Homologs (AGD): provides a direct link between the S. cerevisiae locus page and the Ashbya gosspyii ortholog at the Ashbya Genome database (AGD) located at the University of Basel.
  
  
  • BLASTN vs. fungi: facilitates the comparison of the nucleotide sequence of the gene of interest to fungal nucleotide sequence datasets gathered from GenBank.
  
  
  • BLASTP at NCBI: provides a direct link to BLASTP at NCBI, to facilitate the comparison of the amino acid sequence of the protein of interest to all non-redundant GenBank CDS translations + PDB + SwissProt + PIR + PRF excluding environmental samples.
  
  
  • Candida Homologs (CandidaDB): provides a direct link between the S. cerevisiae gene and the respective gene from the fungal pathogen Candida albicans identified using BLAST.
  
  
  • Fungal Alignment: displays a ClustalW based Fungal Sequence Alignment of the Saccharomyces cerevisiae protein with identified orthologs in other fungal species.
  
  
  • Model Organism BLASTP Best Hits: displays Model Organism Best Hits resulting from an NCBI BLASTP analysis using the S. cerevisiae protein sequence of interest to query predicted protein sequences from several model organisms that currently include: Saccharomyces cerevisiae, Arabidopsis thaliana, Ashbya gossypii, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens.
  
  
  • Synteny Viewer: provides a regional map based view of the synteny that exists between Saccharomyces cerevisiae and the closely related yeast species: Saccharomyces paradoxus, Saccharomyces mikatae, and Saccharomyces bayanus. Please see the SGD Synteny Viewer help page for more details.
  
  
• Functional Analysis: retrieves a summary of expression data for the gene of interest from any of several large-scale microarray experiments using Expression Connection and in addition accesses three external databases:
• GermOnline: provides access to basic locus information, expression data, protein/proteomic information and access to various alignment, modelling and cluster analysis tools.


• YGAC Triples: retrieves gene expression data from transposon insertion experiments, as well as gene descriptions and protein localization data.


• Yeast Microarray Global Viewer: displays a graphical representation of gene expression data from published genome-wide experiments, as well as other useful resources.

• ADDITIONAL INFORMATION

The Additional Information section provides links to pages and features in SGD that provide further information about a locus. In addition, when available this section also contains: Gene Summary Paragraphs, and a list of references for basic locus page information.
• Summary Paragraph: the Gene Summary Paragraph provides a summary of published biological information for a gene and its product that is designed to familiarize both yeast and non-yeast researchers with the general facts and important subtleties regarding a locus.


• References Cited On This Page: lists the references used to curate information displayed in the Standard Name, Alias, Description, Name Description, Gene Product and the Summary Paragraph fields. Note that this section is not a comprehensive listing of publications relevant to this gene. To retrieve a list of all publications annotated to this gene, select the "View Complete Literature Guide for [gene name]" link at the top of this section, or the "Literature" tab at the top of the page.


• Additional Information Links:
  
  
  • Locus History: retrieves notes about the locus, which are used to alert users of: nomenclature conflicts, gene name history, proposed and completed sequence and annotation changes, mapping data, alternative processing information and notes concerning repeated loci. For reserved gene names, the Locus History includes both the reservation and expiration date.
  
  
  • Expression Connection: links to a form that allows you to search gene expression data fron multiple microarray experiments.
  
  
  • Function Junction: links to the Function Junction search form that allows users to simultaneously search a variety of functional analysis project sites for all available functional information for a given gene or ORF (already filled out with the gene (or ORF) name for the locus).
  
  
  • Gene/Sequence Resources: links to a form that allows you to retrieve a list of options for accessing information available for 1) a named gene or sequence, 2) a specified chromosomal region, or 3) a raw DNA or protein sequence. This information includes biological information, table/map displays, and sequence analysis and retrieval options (already filled out with the gene (or ORF) name when accessed via the locus page).
  
  
  • Global Gene Hunter: links to a search form that allows the user to simultaneously search one or more of six different databases for a given gene name. The user selects the set of databases to be queried allowing the rapid retrieval of information contained in specific databases for a given gene.
  
  
  • Mapping Data: retrieves a table summarizing the available two-point genetic mapping data for that gene in SGD.
  
  
  • Motifs: uses the eMOTIF search to query the eMOTIF database to retrieve shared motif information about the query protein.
  
  
  • PDB Homologs: retrieves information about proteins in the PDB database with known structural and sequence similarity to that of the query protein.
  
  
  • Protein Info: retrieves basic information about the gene product including the sequence, predicted cleavage sites, predicted mass and pI, amino acid composition, as well as links to other protein resources.
  
  
  • Researchers: retrieves the Colleague entry for researcher(s) that work on that gene; if there is more than one contact person for a gene, this link retrieves a list of Colleague entries.

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