Contents
The AspGD locus page is divided into three sections: BASIC
INFORMATION, RESOURCES, and ADDITIONAL INFORMATION, as described below.
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 CGD (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:
The ortholog mappings between A. nidulans and
S. cerevisiae were generated using the InParanoid
software (version 3.0) developed at the Karolinska Institutet.
To run InParanoid, the A. nidulans proteins from AspGD were compared to
the latest set of S. cerevisiae proteins from SGD; the set of
C. elegans proteins from the Sanger Institute was used as an outgroup.
Stringent cutoffs were set: BLOSUM80 (instead of the default BLOSUM62),
and an InParanoid score of 100%.
Note, that the ortholog pairings were automatically generated, with no
curator intervention. Thus, there will occasionally be pairings that
may not occur with a different scoring matrix. In the interests of
automating the process, we do not intend to hand-curate the ortholog
pairs at this time.
For A. nidulans proteins that did not have an ortholog that meets
these criteria, we used BLASTp, using the same parameters as were used
by InParanoid (-F \"m S\" -M BLOSUM80) with an expectation value (E)
of 1e-5 to identify their best hit in the S. cerevisiae protein
complement. These best hits data are available here
in the same format as the files containing the ortholog data.
Orthologs and Best Hits are displayed on the AspGD Locus Summary pages, and
linked to the corresponding SGD pages. In addition, all of this
information is available in bulk in files that are available from the homology
download directory on the AspGD web site.
Basic Information
The Description field lists general information about the
gene.
This section provides orthologs and best hit mappings of
Aspergillus genes to S. cerevisiae.
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.
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.
The Sequence Information field
indicates the location of the gene in the A. nidulans 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.
This is an identifier that has been assigned to the locus at AspGD. Resources
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 correspond 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.
Retrieves 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.
Allow comparison of the genomic, coding, or ORF translation sequence
to various Aspergillus 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.
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.
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.
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
Basic Information References
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