The $Organism mRNA track shows alignments between $organism mRNAs in GenBank and the genome. Aligning regions (usually exons) are shown as black boxes connected by lines for gaps (spliced out introns usually). In full display, arrows on the introns indicate the direction of transcription.
GenBank $organism mRNAs are aligned against the genome using the blat program. When a single mRNA aligns in multiple places, the alignment having the highest base identity is found. Only alignments that have a base identity level within 1% of the best are kept. Alignments must also have at least 95% base identity to be kept.
The track filter can be used to change the color or include/exclude a subset of individual items within a track. This is helpful when many items are shown in the track display, especially when only some are relevant to the current task. To use the filter:
When you have finished configuring the filter, click the Submit button.
The $Organism mRNA track is produced at UCSC from mRNA sequence data submitted to the international public sequence databases by scientists worldwide.