V. Gene Record Page

The Gene Record Page is the central navigation portal for accessing information relating to each database gene.

Database Sequences:

The database contains two types of sequences, genomic- and transcript-based. Genomic-based sequences are limited to plant genomes or to genomes which are annotated by the ChromDB staff for the DOE Joint Genome Institute (http://www.jgi.doe.gov/). Although genomic sequences are available for other genomes, i.e. Homo sapiens and Drosophila melanogaster, these are important model organisms are available as transcript-based only at ChromDB. ChromDB staff members do not curate non-plant sequences; we depend on sequences from the NCBI Reference Sequence (RefSeq) collection (http://www.ncbi.nlm.nih.gov/RefSeq/). ChromDB users are cautioned that these RefSeq entries have varying levels of curation.

ChromDB does not display whole chromosome sequences for genomic-based organisms, i.e. Arabidopsis thaliana. Genomic sequences are limited to the span of nucleotides which is sufficient to contain the predicted transcript splice model and 5’ and 3’ untranslated sequences as defined by cDNAs.

Gene Record Page Contents:

Formal Name and ChromDB ID:
 
All sequences entered into the database are given a ChromDB ID (identifier). The same ID is use to denote both a transcript and a protein. An explanation of our nomenclature system for IDs can be viewed in the help section for ChromDB Nomenclature. In cases where ChromDB genes have a pre-assigned or formal gene symbol, these are listed in as Formal Names. The Formal Name precedes the ChromDB ID on the gene record page.
Aliases:
 
Additional assigned gene names, other than the formal or published gene symbol, are listed as Aliases on the Gene Record Page.
Entrez GeneID:
 
The NCBI Entrez Gene ID is displayed on each Gene Record Page, if it is available. The ID is a link that takes users out of the ChromDB database to the NCBI Enrez Gene page. Please visit this resource as ChromDB does not try to duplicate data and information when users can be directed to another database.
Taxonomy Link:
 
This entry shows the formal name of the organism; the name is a link to the appropriate NCBI taxonomy page. Common names for organisms are shown in parentheses.
ChromDB Taxon:
 
Organisms are group into convenient taxon groups to facilitate comparative analyses among the different organisms in the database. Database users can see the overall classification scheme by using the “Advanced Search” feature. The first page of this search shows the groups and subgroups, each of which is a link to display the organisms within each group.
Protein Group:
 
ChromDB proteins are placed into protein groups which are unified by similarity and/or homology. Each protein group is designated by a three to five letter abbreviation. This protein classification scheme can be viewed with this link: protein classification
Description:
 
A short description of the protein group is provided here.
ChromDB Model Type:
ChromDB genes are either genomic-based or transcript-based; this entry shows which category the organism fits into. More information on this subject is included in the Database Sequences help section.
Transcript View:
 
A thumbnail view of the transcript is shown here as a GBrowse view. For genomic-based organisms, this thumbnail shows the transcript splice model and the placement of Pfam domains with reference to the translation of each exon. The thumbnail of a transcript-based sequence shows a transcript with introns removed.
Splice Model Status:
 
This entry pertains to genomic-based sequences only and shows the amount of biological proof (cDNA sequences) that are available to support a predicted transcript splice model. The categories are:
  • Confirmed by cDNAs (including ESTs)
  • Partially confirmed by cDNAs (including ESTs)
  • No biological support available
Expression:
 
Arabidopsis thaliana and japonica rice have links to the MPSS website.

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