What does arrow+box mean in UCSC genome browser?

Question

[Rashedul Islam]

I used BLAT to find the match of query B-cell receptor transcript. What does arrow+box (shown in green box) mean in UCSC genome browser? Can anyone help?

the screenshot is here

Answer 1

[Luis Nassar]

The arrow+box (which we refer to as double horizontal lines) represents an alignment with gaps in both the target genome and the query sequence. There are three ways the alignment can be drawn in BLAT results:

• Solid black bar: The query matches the genome entirely in that region.
• Single line arrows: (as seen in the screenshot as well) These represents alignments with gaps in the genome, but not the query. If you were BLAT'ing mRNA, you would expect to see all the mRNA exons as black bars and the introns as single line arrows. The arrows represent the direction of the match.
• Double horizontal lines: Gaps in both the query and the target genome. These should occur less frequently as they represent a poorer match. There is sequence for both the query and the target genome that differs here. The length of the double horizontal line represents the length of the gap on the target genome, but to find out the query length you would have to click into the alignment itself.

If you zoom into your alignment you should see some solid alignment blocks as well. Usually these alignments are at the edges, with large double gaps in between. However, when you are zoomed out (1.3M bp), it can be hard to see these alignment blocks.

There is also some additional color coded information as part of the BLAT display. If you click on the track and scroll all the way to the bottom you should see it under the Description section.

If you have any further questions, you may reach out to the Genome Browser help desk by emailing [e-mail].

[Rashedul Islam]

@Luis,

Thanks a lot for such a detailed reply. I understand most of it but can you elaborate on this sentence "There is sequence for both the query and the target genome that differs here"?

Did you mean mismatches present in query by "both the query and the target genome that differs"? FYI, The immunoglobulin transcript I showed in the example have genomic rearrangements.