Register with the Affymetrix support site and log in to their NetAffx portal. Put your probe in the search option and you will be linked to every detail that Affy knows about it, including linkouts to the recognition sequence in the UCSC Genome and Emsembl browsers.   There will also be detailed information of all probes in the probe set, their recognition sequences and genome information. You can also download a FASTA file,with every probes actual sequence if you want to map it to a genome yourself.

We have an option to do this in the Genes & Genomes package of the Genomatix Software Suite. You can enter probe ids there to get a mapping to the genomic location and any overlapping genes (it would be DDR1 for 1007_s_at). Visualization of the exact position is also possible in the GenomeBrowser. You can get a free trial account at the link below. 

Hello Dr. Korbinian,

Thanks Much. But I am looking for a probe to transcript mapping(which of the DDR1's ~5 possible transcripts does this map to?). Any way that could be identified too?

Register with the Affymetrix support site and log in to their NetAffx portal. Put your probe in the search option and you will be linked to every detail that Affy knows about it, including linkouts to the recognition sequence in the UCSC Genome and Emsembl browsers.   There will also be detailed information of all probes in the probe set, their recognition sequences and genome information. You can also download a FASTA file,with every probes actual sequence if you want to map it to a genome yourself.

That would be a lot of transcripts, including ENST00000376569, ENST00000446312, ENST00000376575, ENST00000376568, ENST00000376567 from Ensembl and NM_001954, NM_013993, NM_013994, NM_001202621, NM_001202522 from NCBI RefSeq. 1007_s_at overlaps with a 3' UTR which all of these alternative transcripts share. There are a few other transcripts from Ensembl and NCBI Genbank that are also associated with DDR1 but are shorter and don't share that UTR.

Thanks everybody!

So my takeaway is that probes map to multiple transcripts. And if I want transcript wise details I will have to go to some other technique like RNA-Seq.

True.  Affy probe sets are designed to detect a given sequence or gene (or gene region) so yes a given probe set may map to multiple and different transcripts within that sequence or gene.  The technology inherently was designed to detect annotated (or at least, predicted) features of a genome, not individual transcripts from those annotated features.

Remember when you search with something like your example, 1007_s_at, that is NOT a probe, but a probe set composed of multiple discrete probes (see http://www.affymetrix.com/support/help/faqs/mouse_430/faq_8.jsp for affy's explanation).  Collectively, the probes in a probe set are designed to give a signal for a sequence or sequence region (i.e. a gene by virtue of detection of one or more of that gene's transcripts in the mRNA pool that was sampled).

If you want high quality individual transcript information, you would be best to use paired end RNA-seq (or if you know the specific transcripts, deep targeted sequencing for those specific transcripts).

With Affy data, you could see if there are already available best match, transcript specific qPCR assays available.  For example, LifeTechnologies' TaqMan assays can be linked to Affy probe set best match assays and they often will have assays already designed that are transcript specific.  So you could use qPCR to see if your specific transcript(s) of interest for a given probe set were present in your original sample.

Thanks Micheal, Much Appreciated. I have got a much clearer picture now. Let me go back and try.