SGD Help: Gene/Sequence Resources

Gene/Sequence Resources (GSR) serves as a central point for accessing much of the information available at SGD for a 1) a named DNA 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. Once you have specified a sequence name or region, GSR will present only those options which are available for obtaining information about your entry.

Whenever possible, selecting one of the available options for your entered sequence name or region takes you directly to the results for your entered sequence. In other cases, it takes you directly to the resource with the sequence already pre-pasted (i.e. BLAST or Restriction Analysis).

Contents

  1. Pick a Sequence Query Option
  2. Choose Result to View
    1. Biology/Literature
    2. Display Maps/Tables
    3. Sequence Analysis
    4. Sequence Retrieval
  3. Finding Chromosomal Coordinates
  4. Accessing Gene/Sequence Resources

Pick a Sequence Query Option

    1. Step 1: Choose retrieval option

      Note: Only ONE of the three options described below may be filled out at a time in order for the submission to be processed.

      If you decide you would like to change your selection, use the "Reset Form" button found at the bottom of the page to erase your entries.

      • Option 1. Enter a name
        • With this input option, you can enter a gene name, a GenBank sequence name or accession number, an ORF name, or an ATCC or WashU clone name. After you've entered the sequence name, click the "Submit form" button. Note that you can also enter the first few characters of a named DNA sequence followed by the wildcard character (*). Submit the query. Queries that match multiple names will return a list of sequences from which you can then select a single sequence.
        • You may also retrieve information about flanking sequences upstream and/or downstream of the entered gene/sequence name. To do this, type the length of the flanking region you would like to retrieve in the boxes (upstream and/or downstream) below where you entered the sequence name. Note: negative numbers are not accepted in these boxes. If you would like to retrieve part of an ORF you should use the chromosomal coordinates in retrieval option 2.
      • Option 2. Pick a chromosome
        • This entry option allows you to specify a region by entering the desired chromosome number and coordinates. To use this option, simply select a chromosome number using the pull-down menu, and then enter the left and right chromosomal basepair coordinates in the boxes provided below. If you do not specify the basepair coordinates, the first 100,000 basepairs will be displayed.
        • If you would like to retrieve or manipulate the reverse complement of the sequence, check the "Use the Reverse Complement" box OR enter the coordinates as the Note suggests.
      • Option 3. Type or Paste a sequence
        • This entry option allows you to specify a raw DNA or protein sequence for which you would like to retrieve information. First, use the pull-down menu to select the type of sequence you would like to enter, DNA or protein. Next, position the cursor in the entry box and either type or paste in a sequence.
        • Note that the sequence entered must be provided in RAW format, without comments (numbers are okay).
      • Optional Step 2: If you would like to retrieve or manipulate the reverse complement of the sequence, check the "Use the Reverse Complement" box.
      • Step 3: Select "Submit form" to bring up the list of options available for viewing and retrieving information about the named sequence you entered.

 

Choose Result to View

After you submit either 1) a named sequence 2) a chromosomal region, or 3) a raw DNA or protein sequence, a page is returned that lists all available information, displays, analyses, and sequence retrieval options available for the sequence. You will choose one of these options. Descriptions for each option are below. Please note that some of them may not be available for your selected entry, depending on the type of sequence you have entered.

If you decide you would like to change your original selection, click [Change Selection or Coordinates]. This will bring back the Gene/Sequence Resources entry page with your information still filled in. You can then modify and re-submit the form.

Biology/Literature

Links for Genes and ORFs

These links provide more information about specific genes of S. cerevisiae and are available when a Standard Gene or Systematic ORF name was entered via Option 1:

Locus info This link takes you to the Locus Summary page corresponding to the gene or ORF whose name you originally entered. This page displays or links to many different types of information about a gene or feature.
Literature Summaries: This link takes you the the Literature Guide for an entered gene or ORF name. The Literature Guide categorizes journal articles relevant to a specific gene or ORF into various biological topics.
Protein Info This link goes to the Protein Information page for an entered gene or ORF name. Protein pages contain information about the gene product, such as length (in aa), predicted molecular weight, codon bias, and links to motif information, protein chemistry, protein structure and homologs.
Global Gene Hunter This link goes to a Global Gene Hunter form which is already filled out with the desired gene or ORF name. Global Gene Hunter allows you to simultaneously search for information on a gene or ORF name in any or all of seven different databases.
All Associated Seq This link goes to the All Associated Sequences page which lists all sequence entries associated with that feature.
3-D Structure This link goes to the PDB Homologs resource for the gene entered on the query page. The PDB Homologs page presents information for the proteins of known structure with sequence similarity to the specified S. cerevisiae protein. The results will display both the yeast protein structure (if it has been solved) and the structure of other related proteins (regardless of sequence source).

Links for other types of names

These links provide more information about other types of named entities, e.g., sequencing clones or database sequence entries. Availability depends on the name entered.

Clone details This link goes to the Clone class of information for the entered clone name. Within the SGD database, a Clone is defined as a piece of DNA that has been placed on the physical map by sequence alignment or by nucleotide hybridization experiments.
Sequence details This link goes to an external database page, e.g. NCBI Protein or NCBI Nucleotide, for the entered accession number.

Display Maps/Tables

These options are potentially available when Options 1 or 2 have been used. Both display options are available when a Standard Gene Name or a Systematic ORF name as been entered via Option 1 or when Option 2 is used. When clone names are entered, only the Chromosomal Features Map link is available. When accession IDs are used, this section is not available.

Chromosomal Features Map The Chromosomal Features Map link leads to a graphic representation of the genetic features of a region of chromosomal DNA around the selected gene, ORF, clone, or chromosomal region. These features include ORFs, RNA genes, centromeres and Ty elements.
GBrowse The GBrowse link displays the sequence features of a region of chromosomal DNA around the selected gene, ORF, clone, or chromosomal region, including ORFs, RNA genes, centromeres and Ty elements, and also allows visualization of sequence-based experimental data such as nucleosome positioning, mRNAs, transcription factor binding sites, etc., for that region.

Sequence Analysis

General Options

These links provide access to sequence analysis tools and are generally available for Options 1, 2, and 3. However, when a protein accession ID is entered via Option 1 or when a protein sequence is entered via Option 3, the links for the Genome Restriction Map and Design Primers are not available.

BLAST Search This links to a SGD BLAST form in which the query sequence is already pasted. One can then select the desired dataset and search options, and then submit the search form.
Genome Restriction Map This links to the Yeast Genome Restriction Analysis feature, with the sequence you entered already pasted in. You may then select all or a specified set of restriction enzymes with which to generate the Restriction Map.
Design Primers This links to the Design Primer feature, with the selected DNA sequence already pasted in. Design Primers locates primers for PCR or sequencing of an entered sequence based on specified parameters.

Additional Results for Raw DNA Sequence

These links provide access to additional options that are available when raw DNA sequence is entered via Option 3.

Translated Protein Sequence This link brings back the protein translation of the entered DNA sequence (using the first reading frame).
6-Frame Translation (with Restriction Map) This link brings back a 6-Frame Translation of the selected sequence in GCG format. This translation is accompanied by the DNA sequence with a restriction map and is generated at SGD using a licensed version of the Wisconsin Sequence Analysis Package® from the Genetics Computer Group.

Sequence Retrieval

These sequence retrieval links are generally available for Options 1 and 2. However, when a
nucleotide accession ID is entered via Option 1, the Coding Sequence of selected gene/ORF (without introns or flanking regions) link is not available. When a protein accession ID is entered via Option 1, this entire section is not available.

DNA of Region (with introns) Selecting either GCG, FASTA, or NoHeader brings back the DNA of the selected sequence, including any introns, in whichever of the 3 output formats you select.
Coding Sequence of selected gene/ORF (without introns or flanking regions) Selecting either GCG, FASTA, or NoHeader brings back the DNA of the selected sequence, without introns or flanking regions, in whichever of the 3 output formats you select.
Protein Translation of ORF Selecting either GCG, FASTA, or NoHeader brings back the protein translation of the selected gene or ORF sequence (using the first reading frame) in whichever of the 3 output formats you select.
6-Frame Translation (with Restriction Map) Clicking on GCG brings back a 6-Frame Translation of the selected sequence in GCG format. This translation is accompanied by the DNA sequence with a restriction map and is generated at SGD using a licensed version of the Wisconsin Sequence Analysis Package® from the Genetics Computer Group.
Restriction Fragment Sizes Clicking on GCG gives restriction fragment sizes for the selected sequence. This display is generated at SGD using a licensed version of the Wisconsin Sequence Analysis Package® from the Genetics Computer Group.

 

Finding Chromosomal Coordinates

Chromosomal coordinates for ORFs are found on the Locus pages in the Chomosomal Location section. The boundaries for introns (if present) and exons are listed here.

BLASTn reports at SGD generate DNA alignments between similar S. cerevisiae DNA sequences. If you are interested in retreiving the sequence of the 'subject' gene, the chromosomal coordinates of the subject sequence are given at the top of the alignment. You paste these numbers into the GSR tool. (Remember to note the chromosome!) You can also go to the Locus page of the 'subject' gene and get the coordinates there.

The Chromosomal Features Table contains a list of sequence features (ORFs, Ty Elements, ENs, ARSs, and etc) and their chromosomal coordinates for a region. The chromosomal Feature Table is generated in Gene/Sequence Resources when a gene, ORF, ATCC number, or WashU clone name is queried. Chromosomal coordinates can also be derived from the GBrowse Genome Browser.

 

Accessing Gene/Sequence Resources

Gene/Sequence Resources can be accessed by selecting Gene/Sequence resources from:

  • the Sequence pulldown menu, located in the toolbar at the top of most SGD pages
  • the bottom of any Chromosomal Features Map or Synteny Viewer display page

 

Go to Gene/Sequence Resources