BLAT search..How to interpret the diagram - (May/16/2007 )

Hi,

Is there anyone in the board who is familiar with Blat search? I am trying to look for exon information for SLC4A8 gene using Blat program. However the Blat result displayed a few SLC4A8 gene with different length (pls find attahcment file) and number of exon. Which one should I pick and WHY?

Thank you.

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The view shows that the SLC4A8 gene can exits as different variants. It's hard to tell which one you should pick if we don't know the experiment you want to do. It is possible that all transcripts give the same protein (you can check where the coding sequence begins by inserting the ALC4A8 protein sequence in the BLAT program). If you provide more information regarding the application, maybe I can help you more.

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Thanks a lot DPO.

Actually I am looking for the transcription start site (TSS) as well as the promoter site of SLC4A8 gene. When I clicked on this gene (UCSC prediction gene) and look for more information in the Ensmbl, there are two SLC4A8 transcript: NP_004849.2 with 22 exons and O94843_HUMAN with 24 exons. How can I determine the TSS and promoter site?

Can you further describe how to search for the possible trasncript by inseting SLC4A8 protein sequence in BLAT program? How to look for the LSC4A8 protein sequence and which part of the sequence sholud put in the Blat program.

Thank you.

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