dictyBase Help: Locus Page

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Contents

• Description
• Content of the Locus page
• Left Column
• dictyBaseID
• Right Column
• Additional Information
• Summary Paragraph
• Relevant dictyBase Help Documents
• Relevant dictyBase Glossary Terms

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Description

The locus page provides extensive information about a given locus, including links to additional dictyBase resources such as the Genome Browser, BLAST server, Protein Info, and to external databases. The locus page can also be viewed in an 'Alternative Single Page Format', which is more convenient for printing.

Content of the Locus Page

The dictyBase locus page is divided into two columns with additional links at the bottom. If available, the Locus Notes and the Summary Paragraph will appear below these additional links. If you don't see the complete information for a locus it is because more information is currently not available, or because the locus has not yet been curated.

• Left Column

• This section lists any names and aliases for a particular locus. It also includes the following information:

  • External Links
    This field provides links to other information sources for the gene. More information on the databases can be found in dictyBase's glossary.
  • Gene Product
    The Gene Product field lists the protein or gene product that the gene encodes.
  • Systematic Name
    
  • This name contains systematic information. This is a good example: DD000983W-GE.
    • DD000983W-GE - the first D stands for dictyBase.
    • DD000983W-GE - the second letter indicates the chromosomal localization; A to F corresponds to chromosomes 1 - 6, G is Mitochondrial, H is Ribosomal. The example is located on chromosome 4.
    • DD000983W-GE - the number is at the moment filler only, but will contain the position on the chromosome in the future.
    • DD000983WGE - W stands for localization on the Watson strand, C stands for Crick strand.
    • D000983WGE- this describes the source, GE stands for GenBank.
  • Feature Type
    The feature types are indicative of the source of the sequence presented in and obtained from a given locus page. The different features types are:
    
    
    • Gene Prediction from Sequencing Center: Gene models as provided by the Sequencing Centers.
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    • Curated Model: Gene Predictions from Sequencing Centers are manually upgraded by dictyBase curators if there is evidence that the gene exists. Based on available data this may include upgrading the exon/intron boundaries and/or the total length of the molecule. Currently the chromosomal sequence cannot be edited, only the gene coordinates. This sometimes creates unsolvable situations, in which curators are forced to keep the Sequencing Center's model. The evidence used by the curator to create the Curated Model can be found in Locus Notes
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    • Genomic Fragment: The Genomic Fragment feature type corresponds to gene sequences in DNA GenBank records. Note that it does not necessarily correspond to GenBank coding sequences. For all Genomic Fragments in dictyBase the DNA coding sequence that can be retrieved from the "Retrieve Sequence" function does correspond to the GenBank coding sequence (CDS).
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    • mRNA: The mRNA feature corresponds to the sequence provided on mRNA (cDNA) GenBank records and may contain 5' UTR and 3'UTR sequence.
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    • EST: ESTs are expressed sequence tags, and are identified as such on their GenBank records. These are considered partial cDNA sequences.
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    • Chromosome: Chromosome refers to the structure in the cell composed of a very long molecule of DNA and associated histone proteins. At dictyBase, if a locus has been physically mapped, the chromosomal coordinates will appear under the Sequence Coordinates category with a link to the ORF Map, on the Locus page.
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    • contig: A stretch of genomic DNA assembled from raw sequence data. The contig lengths vary and may span part of a gene or many genes. When enough overlapping contigs become available they are assembled into whole chromosome sequences.
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    • Predicted cDNA: Computationally generated gene models that come from sources other than the Sequencing Centers that have produced the sequence.
      
    
    
  • Description
    The Description field provides additional information about a gene product.
  • Gene Ontology (GO) Annotations: Molecular Function, Biological Process, and Cellular Component
    The GO annotations describe a gene's molecular functions, its role in biological processes, and its presence in cellular components or complexes. Each annotation links to a page showing the term definition and all Dictyostelium genes annotated to the term. The GO annotations use a controlled vocabulary that will allow powerful searches within dictyBase and across other databases. Next to each annotation there is an additional link to AmiGO, the Gene Ontology Browser. For more information about the GO project, see www.geneontology.org.
  • Phenotype
    The Phenotype field lists the mutant phenotypes for the gene if available, along with details about the type of mutation that produces the phenotype. Clicking on 'Phenotype details and references' leads to a detailed list of phenotypes for the locus queried. Clicking on a specific phenotype opens a referenced list of curated loci, whose mutation(s) result in that phenotype.
  • Sequence Coordinates
    The Position field lists the chromosomal coordinates of the gene as well as its genetic position, and positions of individual exons. The chromosomal coordinates link to the Genome Browser.
  • Primary dictyBaseID
    Unique identifier for each feature in dictyBase. Features generally correspond to sequences. Therefore, a given locus can have more than one dictyBaseID: every GenBank record, Curated Model, Sequencing Center Gene Prediction, HMM Gene Prediction and EST has a unique dictyBaseID.
    
    While dictyBaseIDs always point to the same database entry, entries are sometimes deleted or modified in such a way that they require a new dictyBaseID. The following are examples of this:
    -Issues with Sequencing Center Gene Predictions: When gene models from Sequencing Centers change it is possible that new dictyBase IDs are generated and others are deleted.
    -Issues with cloned genes: Some genes have been cloned by different groups and were given different names, creating two different loci. Curators merge the two entries into a single locus, therefore deleting one of the dictyBaseIDs.
    
    To help you find these dictyBaseIDs we have implemented a redirect feature: whenever possible, searching for a defunct dictyBaseID will redirect you to the current one. An example is the K4 gene, which was also called ksnD. We merged the two loci under the ksnD name. Going to the K4 dictyBaseID DDB0003768 leads to a page that maps the new dictyBaseID: "DDB0003768 has been replaced by DDB0191404", with a link to the new page.
    

• Right Column

• The right column provides resources for analysis and additional information retrieval for a particular gene. The right column has the following information retrieval options, organized into pop-up menus:
  
  • Literature:
  • • Literature Guide: retrieves dictyBase's Literature Summary page, which organizes papers about a gene by various topics.
    • PubMed Search: searches PubMed for papers that mention a locus (or its aliases) as well as Dictyostelium.
  • Retrieve Sequences: retrieves the gene's Genomic DNA (with introns), the DNA Coding Sequence, and Protein Sequence.
    Note that this is true only for sequences that have been submitted to GenBank as 'genes' (genomic DNA), or for GenBank 'mRNAs' that have been mapped on a chromosome (currently chromosome 1, 2, 4, 5, 6, Mitochondrion). In case of 'floating cDNAs', the Genomic DNA and the DNA Coding Sequence options both retrieve coding sequence only. Also, if there is more than one sequence associated to a locus and one is chromosomal, the chromosomal sequence is being displayed. Among several GenBank records, the sequence to be displayed is at the curator's discretion. See also Sequence Retrieval Help.
  • Sequence Analysis Tools: a link to the dictyBase BLAST server (BLASTN, BLASTX, TBLASTN, TBLASTX, BLASTP), or a direct link to NCBI BLASTP. In all cases the sequence, depending on the BLAST program selected, is pasted directly into the query window. Note that, when using any program with DNA as the input sequence, you can define the kind of sequence ('Genomic DNA' or DNA 'Coding Sequence') by making your selection in 'Sequence Retrieval'.
  • Protein Info & Structure: This page provides protein data such as molecular weight and isoelectric point calculations. The Amino Acid Composition link opens in a pop-up window. The Protein Structure option will be available in the future.

• Additional Information

• The Additional Information section has links to pages and features in dictyBase that provide further information about a locus.
  • Summary Paragraph: retrieves the Gene Summary Paragraph for a particular gene. See below.
  • Global Gene Hunter: links to the Global Gene Hunter search form, already filled out with the gene name (or ORF name, for ORFs that do not have a standard or reserved gene name) for the locus.
  • Colleagues: retrieves the Colleague entry for the researcher working on a gene; if there is more than one contact person for a gene, this link retrieves a list of Colleague entries.
  • Locus Notes: All Curated Models have a note by the curator describing the evidence used for the gene model to be confirmed. The evidence can be "gene sequence", "mRNA", or "ESTs". Whether the sequences from the Sequencing Center and from GenBank are identical or differ is also stated, and in cases of discrepancies these are listed for both the DNA sequences and the predicted proteins. Locus Notes may also alert the user to contradictory information in the literature or to potentially confusing gene names. For reserved gene names, the Locus Note includes the reservation date.

• Summary Paragraph

• The Gene Summary Paragraph is a summary of published biological information for a gene and its product that is designed to familiarize both Dictyostelium and non-Dictyostelium researchers with the general facts and important subtleties regarding a locus. dictyBase curators compose Gene Summary Paragraphs using natural language and a controlled vocabulary based on the Gene Ontology (GO). Gene Summary Paragraphs contain links to references and GO terms that will lead to PubMed or a page showing the term definition and all Dictyostelium genes annotated to the term, respectively. These links are listed below:
  1. Links to references. Each fact presented in a Gene Summary Paragraph is supported by one or more references. Clicking on a reference goes to the appropriate dictyBase "curated paper" page. The references with links to dictyBase "curated paper" and PubMed are also listed just below the citation.
  2. Links to Locus Information for mentioned genes. Any Dictyostelium gene other than the gene which the Gene Summary Paragraph is about is linked to its dictybase Locus Page within the paragraph. Click on the gene name to see its Locus information.
  3. Links to GO annotations. Links to a page describing the GO term itself and a list of genes in dictyBase that are associated with that term. For more information, go to the GO Help Page.

We greatly welcome general input from the community regarding the paragraphs, as well as any specific information we should incorporate into the summary for a particular gene. Please send any suggestions to dictybase@northwestern.edu.

Relevant dictyBase Help Documents

• BLAST
• Literature Guide
• Genome Browser
• Global Gene Hunter
• Gene Ontology (GO)
• Sequence Retrieval

Relevant dictyBase Glossary Terms

• ORF
• Gene Name
• Standard Name
• Gene Ontology (GO)
  • Molecular Function
  • Biological Process
  • Cellular Component
• Description
• Gene Product
• Phenotype
• SwissProt
• Entrez
• Kyoto
• PubMed
• Gene Summary Paragraphs
• BLAST
• FASTA
• Locus history
• Colleagues
• Protein Info