Genewindow is split into two views, at the top, a Locus Overview that varies in size depending on the gene or genomic region being viewed and, below it, a Sequence View displaying a 2000bp region within the overview. The grey bar at the far left is the menu, where users can expand the genomic interval, access lists of features, find a sequence segment within the overview, or view the legend. To display contextual information in both views, mouse over the features.introduction
The locus overview displays alternate translations (light purple), current protein (purple), regions sequenced by the CGF (green), current gene (gold), neighboring genes (brown), and polymorphisms color-coded based on CGF’s assay status.locus overview
The sequence view is similar except only the current protein is displayed. The vertical and diagonal lines connecting the two views indicate their spatial relationship. To switch the sequence view to display different regions within the overview, click along the gene in the overview.sequence view
The protein translation seen in the sequence view represents the current translation selected in the overview with its coding regions connected with "splice lines". To choose an alternative translation, in the overview, click on the line with the coding regions above the current protein translation. Please note for particular translations the amino acid sequence may be missing, which reflects whether the amino acid sequence is available from the current public build.proteins
The green bars covering various regions within or around genes show the regions the CGF has plans to sequence or has sequenced.cgf sequences
The current target gene (gold) is typically centered with neighboring genes (brown) near or underneath the current gene. The exons for both the target and neighboring genes are slightly thicker than the line for the gene itself.genes
- Variations have differences in their opacity depending on their frequency derived from either the public or CGF databases. Low opacity indicates no reported frequency.
- SNPs are represented as rectangles and INDELs are represented as rectangles with triangular tops (insertions) or bottoms (deletions) depending on the type of INDEL. Note that some variations can have incorrect "types" and thus not drawn accordingly.
Current color scheme
- Red - These are public variations that have not been analyzed by the CGF (use caution when considering these).
- Green - These variations are under investigations by the CGF.
Clicking and Mousing over
- To view genomic positions and IDs, move the cursor over nucleotides or variations.
- To view additional information, frequencies, or links to other web sites, click on the polymorphism.
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