Affymetrix Probes and Multiple Alignments

Question

[JourneyToAbyss]

I am looking at annotation information for the HG-U133A 2.0 human microarray. Probe information can be found here. According to the site, _at probes have "all probes hit one transcript". Yet, in the annotation, there are multiple alignments on different chromosomes.

Is this a case of an ortholog being present on multiple chromosomes and the probe technically hitting "one" transcript? Or am I misunderstanding the annotations completely.

Example:
Probe: 200679_x_at
Alignment: chr13:31034583-31040069 (-) // 88.72 // q12.3 /// chr15:71456199-71457851 (-) // 83.92 // q23

Thank you!

Answer 1

[Kevin Blighe]

A large proportion of microarray probes undoubtedly bind to other cDNA sequences, or other regions of the genome. I suppose that these effects are mostly mitigated by the fact that these other sequences may not even be expressed at a level that rises above the background signal, or, indeed, they only bind to DNA that is not transcribed, meaning that it would not even be a problem when cDNA is generated.

In this case, the main target gene on chr13, HMGB1, has a pseudogene, HMGBP6, on chr15, a region that also comprises othologous (?) HMGB1 sequence in other species:

source: UCSC link

Kevin