Wow it was so easy to find the beginning of exon 1 in using a blastn alignment. D. eugracilis — Why did that work so well, and will this approach work with all genes? Let’s look at the sequence again, using a new tool in the Genome Browser to D. melanogaster answer this question. 1. Open a new web browser window and go to the GEP UCSC Genome Browser Mirror at . 2. To navigate to the genomic region surrounding the sev gene in Drosophila melanogaster, select melanogaster” under Species”, select “D. “Represented “Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6)” under melanogaster Assembly”, and then “D. enter under the Term” field. Click on the button (Figure 4). “sev” “Position/Search “GO” Figure 4 Change the settings on the Genome Browser Gateway page to navigate to the sev gene in the Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6) assembly. D. melanogaster 3. This region on the X chromosome, denoted contains the “chrX:11,071,441-11,086,299” entire gene. The suffix corresponds to the name of the isoform that is associated sev “-RA” with the gene. Hence sev-RA corresponds to the A isoform of the gene. This gene only sev has one isoform. 4. The direction of the arrows in the intron indicates that the gene is on the minus strand. sev Click on the button below the Genome Browser image to reverse complement the “reverse” chrX sequence (Figure 5). Figure 5 Click on the button to reverse complement the entire chrX sequence “reverse” (red arrow). 5. To reset the display settings, click on the all” button. Then, configure the display “hide modes as follows: Under and Sequencing” Tracks “Mapping Base Position: full Click on the blue Match” link “Short Enter (i.e., the Initiator motif) into the (2-30 base) sequence” text “TCAKTY” “Short box Change the mode” to “Display “pack” Click on the button “Submit” Under and Gene Prediction” Tracks “Gene
Wow — it was so easy to find the beginning of exon 1 in D. eugracilis using a blastn alignment. Why did that work so well, and will this approach work with all genes? Let’s look at the D. melanogaster sequence again, using a new tool in the Genome Browser to answer this question. 1. Open a new web browser window and go to the GEP UCSC Genome Browser Mirror at . 2. To navigate to the genomic region surrounding the sev gene in Drosophila melanogaster, select “D. melanogaster” under “Represented Species”, select “Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6)” under “D. melanogaster Assembly”, and then enter “sev” under the “Position/Search Term” field. Click on the “GO” button (Figure 4). Figure 4 Change the settings on the Genome Browser Gateway page to navigate to the sev gene in the D. melanogaster Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6) assembly. 3. This region on the X chromosome, denoted “chrX:11,071,441-11,086,299” contains the entire sev gene. The suffix “-RA” corresponds to the name of the isoform that is associated with the gene. Hence sev-RA corresponds to the A isoform of the sev gene. This gene only has one isoform. 4. The direction of the arrows in the intron indicates that the sev gene is on the minus strand. Click on the “reverse” button below the Genome Browser image to reverse complement the chrX sequence (Figure 5). Figure 5 Click on the “reverse” button to reverse complement the entire chrX sequence (red arrow). 5. To reset the display settings, click on the “hide all” button. Then, configure the display modes as follows: Under “Mapping and Sequencing” Tracks Base Position: full Click on the blue “Short Match” link Enter “TCAKTY” (i.e., the Initiator motif) into the “Short (2-30 base) sequence” text box Change the “Display mode” to “pack” Click on the “Submit” button Under “Gene and Gene Prediction” Tracks
Module_TSS2_Advanced.docx