SelenoDB
Release 1.0

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How is the data for each biological feature organized and displayed?

The structure of the Feature Reports is the following:

  1. Identity section. It provides information about the gene name and its accepted synonyms, family and subfamily names and their accepted synonyms, species and its taxonomical classification. In addition, internal and external Feature IDs are given. Internal Feature IDs are composed of:

    1. a three letter code, SPG, SPT, SPR, SPE, SPI, SPP, SPS and SEQ for gene, transcript, promoter, exon, intron, protein, SECIS and sequence respectively.

    2. an eight digit number.

    3. a version number to track changes in the annotation of sequence features. Version numbers will increase as the result of improved annotations due to higher quality sequences to replace the older annotated sequences or annotation errors reported by SelenoDB annotators or users. In any case, older annotated versions will remain available through the web interface.

  2. Annotation section. In all Feature Reports, it provides the annotation method, orientation of the annotated Feature and a structural plot of the fully annotated gene. In Gene Reports, a list of links to the corresponding Transcript, Promoter, Exon, Intron, Protein and SECIS Report is given. In all other Feature Reports, the Annotation section provides the sequence of the Feature of interest, for example, the sequence of a particular exon in an Exon Report, the SECIS sequence in a SECIS Report or the transcript sequence in a Transcript Report. Both the gene structure plot and the displayed sequence in each Feature Report is color coded by feature type:

    1. Promoters in gray.

    2. Coding and noncoding exon regions (UTRs) in dark and light blue respectively.

    3. Introns in black.

    4. SECIS in brown.

    5. Sec, Cys and other homologous residues in red, green and yellow respectively.

  3. Sequence section. In Gene Reports, it provides information about the original source of the sequence used to annotate sequence features in the database and a link to the corresponding Sequence Report.

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