Locate exon intervals using Exon Interval Finder

 

The Exon Interval Finder tool returns a list of the exonic genomic intervals that are associated with specific genomic targets. You can enter a single search string, and retrieve all exonic intervals whose annotation contains that search string. You can also enter multiple values for specific types of annotations, and retrieve exonic intervals whose annotation exactly matches your search terms. In addition, you can limit returned exons to only those that fall within coding regions.

From the search results, you can select exonic intervals of interest and use them as input intervals for a Bait Tiling job. You can also download the intervals, and view a list of chromosomes that are associated with them.

  1. Click the Workspace tab. (Exon Interval Finder searches are not available in collaborations.)

  1. Set the application type to SureSelect Target Enrichment or SureSelect RNA Enrichment.

  2. Click Baits.

    The Search page appears.

  3. Select Exon Interval Finder.

    The Exon Interval Finder pane appears.

  4. In Search Type, select one of the following options, then enter the desired search terms as described below.

Option

Instructions/Details

All

This type of search returns exonic intervals that have any annotation that matches a single search term that you enter.

  1. In Search Term(s), type the desired term.

  2. By default, eArray returns intervals that contain the search term within any associated annotation. To limit returned intervals to those whose annotation matches the search term exactly, mark Exact Search.

Accessions

In Search Term(s), type an accession number, without its source, or multiple accession numbers separated by pipe "|" characters. The search returns the exonic genomic intervals that correspond with each of the accessions. For the search to return intervals, accessions must match exactly. Use upper case (capital) letters in accessions.

Example: NM_012257|Q0055|NM_012298

You can also upload a file of accessions. Prepare a plain text file with an extension of .txt. Put one accession on each line, and end each line with a new line character (press Enter). To upload the file, click Upload. For details, see Upload data for probe searches.

Cytoband

In Search Term(s), type a cytoband, without its source, or multiple cytobands separated by pipe "|" characters. The search returns the exonic genomic intervals that correspond with each of the cytobands. For the search to return intervals, cytobands must match exactly. Use lower case letters to specify the p or q chromosome arms.

Example: 1p22.2|2q33.3

You can also upload a file of cytobands. Prepare a plain text file with an extension of .txt. Put one cytoband on each line, and end each line with a new line character (press Enter). To upload the file, click Upload. For details, see Upload data for probe searches.

Gene Symbol

In Search Term(s), type a gene symbol, or multiple gene symbols separated by pipe "|" characters. The search returns the exonic genomic intervals that correspond with each of the gene symbols. For the search to return intervals, gene symbols must match exactly. Use upper case (capital) letters in gene symbols.

Example: H3N2|BRMS1|BRCA1

You can also upload a file of gene symbols. Prepare a plain text file with an extension of .txt. List one gene symbol per line, and end each line with a new line character (press Enter). To upload the file, click Upload. For details, see Upload data for probe searches.

  1. Enter these additional search parameters:

Parameter

Instructions/Details

Return Coding Exons Only

(Optional) To limit returned exons to only those within coding regions, mark this option.

Species

(Required) Select the desired species. H. sapiens is selected by default.

  1. Click Search.

    A search results pane displays the annotation(s) that you entered as search terms, and the exonic (or coding exonic) intervals that are associated with them. The results also show whether the exon is found on the + strand or the – strand of the DNA, and a brief description (when available). For annotations that are associated with multiple exons, eArray displays each exon on a separate line.

    After eArray displays the retrieved exonic genomic intervals, you can take action on them.

  1. Use the tasks in the table below to navigate among the returned intervals and select them for further action.

Task

Instructions/Details

Select a single interval

Mark the check box in its row.

Select additional intervals

Mark the check boxes next to the name of each desired interval.
eArray remembers your selections if you navigate to different pages.

Go to another page of Search Results

Click the Pages links. eArray remembers your selections as you go from page to page.

Sort the results

Click the heading of a column.
eArray sorts the results based on the contents of the given column. To reverse the order of the items in the list, click the heading again.

Select all intervals on all pages

Mark Select Entire Result.

Select all intervals on one page

Mark the check box in the column heading row.

  1. Use the tasks in the table below to take action on the intervals that you selected in the previous step.

Task

Instructions/Details

Download the selected intervals as a list

  1. Click Download.
    A progress message appears, and a File Download dialog box opens.

  2. Click Save.
    A Save As dialog box appears.

  3. Select a location for the downloaded file, then click Save.
    eArray downloads the intervals in ZIP format. The ZIP archive contains a single *.tdt file that has one interval on each line.

Download the selected intervals as a BED format file

This task can be useful if you want to use the selected intervals in a genome browser or other software that accepts BED format files.

  1. Click Download in BED Format.
    A progress message appears, and a File Download dialog box opens.

  2. Click Save.
    A Save As dialog box appears.

  3. Select a location for the downloaded file, then click Save.
    eArray downloads the intervals in ZIP format. The ZIP archive contains a single *.tdt file that has one interval on each line. The file contains only the genomic coordinates of the selected intervals.

Start a Bait Tiling job based on the selected intervals

  1. Click Run Bait Tiling.
    The Bait Tiling page appears. The selected intervals appear in pipe-separated format in Genomic Target Intervals.

  2. Set the other Bait Tiling parameters, as needed, then click Submit. See Bait Tiling (SureSelect Target Enrichment) and Bait Tiling (SureSelect RNA Enrichment).

Download a list of the search terms that did not return any intervals

  1. Click Download Unfound Terms.
    A progress message appears, and a File Download dialog box opens.

  2. Click Save.
    A Save As dialog box appears.

  3. Select a location for the downloaded file, then click Save.
    eArray downloads the intervals in ZIP format. The ZIP archive contains a single *.tdt file that has one unfound term on each line.

View a list of the chromosomes associated with the selected intervals

  • Click List Chromosomes.
    A list of the chromosomes represented in the selected intervals appears in a new window.