Here is the BRCA2 promoter sequence aligned to BRAC2 gene. If it matches, the sequence is very likely the right one. Zoom out a bit, you will be able to determine whether the promoter sequence matches UCSC annotation. the query sequence is now aligned with UCSC genome sequence. On the result page, click browse of the first hit, this will bring you to the genome browser Page. Go to UCSC BLAT search at …t?command=start and choose the right genome (eg, human), paste the sequence there.To make sure the first exon given by ensembl is right, copy the promoter sequence Sometimes there are discrepancies between Ensembl and UCSC annotation regarding TSS.You can put for example “1000” and then save the configuration. If you want to get more, click “Configure this page” in the lower left column, a popup window opens allowing to input the size of 5′ Flanking sequence (upstream). By default, 600 bp 5′-flanking sequence (promoter) is displayed.The exons are high lighted in pink background and red text, the sequence in front of the first exon is the promoter sequence.On the left, under “Gene Summary”, click “Sequence”, the sequence of the gene including 5′ flanking, exons, introns and flanking region will be displayed.For example the link to BRCA2 gene is …ns idx= q=brca2 Click the right hit on the search result page and it will bring you to the gene summary page.Search your gene such as BRCA2 …ns idx= q=brca2.choose an organism such as human …iens/Info/Index.For our purpose, Ensembl provides the most convenient interface. There are three major genome browsers: NCBI, Ensembl and UCSC. Thus promoter sequence retrieval is an easy task. For many organisms, such as as human, mouse, the genome is well annotated and TSS well defined. If we know the TSS of a gene, we will know with confidence where the promoter is even without experimental characterization. Promoter sequences are usually the sequence immediately upstream the transcription start site (TSS) or first exon.
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How to find and retrieve promoter sequences from genome databases. Here I provide ways how I do these things. Don’t forget to try the latest casino games at DaisySlots to help alleviate the stress you’re experiencing. Many people have problem identifying or predicting the promoter sequence of a gene, or don’t know how to get the actual sequence for analysis such as primer design, transcription factor binding site search, etc.
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