SGD Help: Sequence Names

The result of a SGD sequence search displays general information about the sequence as well as a variety of options to retrieve and view the DNA sequence and its features. There are a number of sequences available from SGD; the type and source of a sequence is coded within its name. The sequence information available for each type of sequence will differ in content.

Depending on the type of sequence, the general information retrieved for each sequence may include any or all of the following:

• Contains/Contained_in: Cross-references a subsequence within the context of a larger sequence.
• DB_info: indicates the database (GenBank, EMBL, DDBJ) from which the sequence information was obtained. There are external links to the EMBL and GenBank databases. In addition there is an external link to GenBank that enables the user to obtain information about related sequences. If the sequence is a .cds encoding a protein, then the external links are to protein databases containing biochemical information.
  
• Details: Details includes the source of the DNA (whether derived from a GenBank entry or from the systematic sequencing effort), the source exons determine the complete size of the coding sequence without introns. Details may include additional information such as any associated subsequence(s), and chromosome basepair coordinates. A subsequence file, such as a coding (.cds), tRNA, rRNA, or snRNA sequence is obtained from the larger source file.
  
• DNA: This is the name of the sequence.
  
• Homology: Lists similar DNA, peptide, or motif sequences (if available) with their location relative to the DNA sequence.
  
• Keyword: These are determined by the authors of the sequence. They often describe the gene product.
  
• Origin: Identifies the authors, database or laboratory submitting the sequence data. This also contains the date(s) of the GenBank sequence release(s).
  
• Properties: Descriptive information about the sequence most often includes information about mRNA, tRNA, rRNA, and snRNA transcripts.
  
• Remark: Comments about the sequence supplied by its authors.
  
• Repeats: Lists repeated sequences (inverted, tandem, or direct) within the larger sequence. The information may also give information about the property of the repeat.
• Sequence_feature: Additional descriptive information about a sequence provided by the authors of the sequence is listed here. The list of features may include: TATA_signal, Conflict, misc_feature, misc_binding, mutation, polyA_site, promotor, repeat_region, sig_peptide
  
• Visible: This refers to all the tags that can be viewed as text in the graphic sequence display. These may contain the title of the sequence; a link to an associated locus; the See_also tag with links to other sequences; and references that were associated with the submitted sequence.