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.
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. (2004) GenBank: update. Nucleic Acids Res. 32 Database issue:D23-6.