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AspGD Help: Locus Page

Contents

• Organization of the Locus page
• Basic Information
• Resources
• Additional Information
• Locus Summary Notes
• References Cited on this Page

The AspGD locus page is divided into three sections: BASIC INFORMATION, RESOURCES, and ADDITIONAL INFORMATION, as described below.

• Basic Information

The Basic Information section lists any names and aliases (synonyms, including allele names) for a particular locus, and indicates whether a name is standard or reserved. Additional information about gene names in AspGD (including explanation of the standard format, systematic name format, and other gene identifiers used) may be found on the Nomenclature page. The Basic Information Section also includes the following additional information:

• Feature Type: The Feature Type section indicates what sort of gene or other genetic element resides on this chromosomal sequence (e.g., ORF, tRNA, or CEN). Information about the changes to ORFs is displayed in the Locus History. ORFs and noncoding RNA genes are assigned the additional qualifiers, Verified, Uncharacterized, or Dubious. At first these qualifiers were applied to ORFs in AspGD; as of January 2011, noncoding RNA features are also included systematically. Features are labeled as Verified if there is experimental characterization that indicates that a functional gene product is produced (as defined by the ORF having curated Gene Ontology terms with experimental evidence codes, i.e., evidence codes other than IEA, ISS, RCA, ISA, ISM, ISO, NAS). Uncharacterized ORFs or RNA genes do not currently have curated experimental characterization. Upon publication that provides experimental evidence that an Uncharacterized feature produces a product, it will be reclassified as Verified. Dubious genes are unlikely to encode a product and they have no experimental characterization. Only features that are included in the current sequence assembly are assigned one of these ORF qualifiers.


• Description
  A concise summary of the biological role and molecular function of the gene, and any other particularly salient information. Genes without experimental characterization may have descriptions that discuss orthology to genes in other organisms, as described in more detail here.


• Ortholog(s) and Best Hits
  This section provides ortholog and best hit mappings among Aspergillus genes and also with S. cerevisiae.

  Please note, regarding the issue of orthology and shared function:
  We use the standard evolutionary definition of orthology: genes descended from a common ancestral gene sequence. This definition does not require that the genes are functionally equivalent after the speciation event, although it will often be the case.

  A detailed descriuption of the methodology used to generate the ortholog and best hit mappings is posted here



• 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 all genes annotated to the term in AspGD. The GO annotations use a controlled vocabulary that allow powerful searches within AspGD and across other databases. The "Gene Ontology" tab and the "GO evidence and references" link will display a page with more information about the GO assignments, including links to the references that support assignment of each GO term.
  
  As described here, the evidence code "ND", or "Not Determined" is used with annotations to the three root terms "molecular_function unknown", "biological_process unknown", or "cellular_component unknown" and signifies that a curator has examined the literature and that as of the date of the annotation to the unknown term, there were either no publications concerning that gene, or there was no information in any available publications that allowed a curator to make an annotation to a specific term in that ontology.
  
  In cases where a gene has a characterized orthologous gene in the AspergillusGenome Database (AspGD) or in the Saccharomyces Genome Database (SGD), predicted Gene Ontology (GO) annotations based on orthology, as described here


• Mutant Phenotype
  The Phenotype field lists the mutant phenotype for the gene. The "Phenotype" tab and "Phenotype details and references" links display a page with additional information about the phenotypes, including references and additional notes.


• Sequence Information
  The Sequence Information field indicates the location of the gene in the genome. The coordinates of each exon and intron are listed, with the relative position of these regions with respect to the feature, and to the chromosome. Also displayed are the dates on which the most recent updates to the sequence coordinates and to the sequence itself were made. The section can be expanded or collapsed on the page by clicking on the small +/- icon next to the section heading in the blue panel.


• Primary AspGDID
  This is an identifier that has been assigned to the locus at AspGD.

• Resources

The Resources section provides resources for analysis and addtional information retrieval for a particular gene. The Resources section has the following information retrieval options:


• GBrowse Genome Browser:
  Allows you to view and navigate the chromosomes. GBrowse may be accessed using the GBrowse map thumbnail views. See the VeA Locus Summary as an example. The small map on the right-hand side of the page corresponds to the VeA ORF. Clicking on the map will display a region of the chromosome, with the selected ORF at the center and neighboring ORFs visible on either side. GBrowse is described in more detail on the GBrowse Help Documentation page.


• Literature:
• Literature Guide: retrieves AspGD's Literature Guide 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 the species name.
• Search Google Scholar: searches Google Scholar for papers that mention a locus (or its aliases) as well as the species name.
• Search NCBI: searches Entrez at NCBI for papers that mention a locus (or its aliases) as well as the species name.


• Retrieve Sequences:
  Retrieves and displays various DNA and protein sequence queries, as listed on the pull-down mewnu, including the Genomic DNA (with introns), the Exons-only Sequence (Coding Sequence of an ORF, or the sequence with exons removed of any non-translated feature) , the Genomic DNA with 1 kb of flanking sequence upstream and downstream of the gene (also includes any introns), or the ORF translation. For more details about the sequence datasets, please see the Sequence Documentation page.
  Sequences are displayed by default in FASTA format. Several other sequence formats are available as hyperlinks on the page displaying the sequence, or via the Gene/Seq Resources tool. The other formats include, GCG, No header, Decorated FASTA and Numbered sequence.


• Sequence Analysis Tools:
  
  • BLAST options:
    Allow comparison of the genomic, coding, or ORF translation sequence to various sequence datasets. For more detailed instructions for use of the BLAST tool, please see the BLAST Search Help page. For a detailed description of the search output, please see the BLAST Results Help page.
  • Design Primers:
    Recommends primers appropriate for either PCR or sequencing of a given sequence, within configurable parameters. For more information about this tool, please see the Web Primer tool help page.
  • Restriction Fragment Map:
    Generates a restriction map of a specified DNA sequence. The restriction map may include all enzymes, or a subset of enzyme types (3' overhangs, 5' overhangs, blunt ends, or enzymes that cut once or twice). For more information about this tool, please see the Restriction Analysis tool help page.


• Maps and Displays:
  The Flanking Features Table provides a tabular view of the other nearby features (ORFs, etc.) on the chromosome, with brief descriptions of each neighboring feature and links to additional resources and information. By default, the table lists features within 5 kb flanking the locus; use the "Retrieve Features Left" or "Retrieve Features Right" options near the bottom of the page to include additional flanking region. The column labeled "Retrieve" provides links to the Locus Summary and to the nucleotide sequence of each feature listed in the table.

• Additional Information

The Additional Information section has links to pages and features in AspGD that provide further information about a locus.


• Locus History link and the Locus History tab: retrieve notes about the locus, including information about ways in which the sequence or annotation has changed from one genome sequence assembly to the next. The Locus History may also alert the user to contradictory information in the literature or to potentially confusing gene names.


• Gene/Sequence Resources: tools for sequence display and analysis. For more detail, please see the Gene/Sequence Resource help document.



• Locus Summary Notes

Some pages display this section, which contains additional information about the locus. For example, some Aspergillus nidulans pages display notes from the Eurofung annotation effort in this section.

• References Cited on this Page

This section lists the references used to curate information displayed in the Standard Name, Alias, Description, and Name Description 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 "Literature" tab at the top of the page.


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