Go back to the web browser tab with the GEP UCSC Genome Browser to examine the D. sequence further. eugracilis Enter into the position or search terms” text box, “KB465191:113,830-114,429” “enter and then click on the button to navigate to the region surrounding the TSS of Sev “go” Ensure that your browser is still configured as follows: Base Position: full, D. mel Transcripts: pack, modENCODE RNA-Seq Coverage: full, Match: pack Under and Sequencing Tracks”, click on the blue Match” link “Mapping “Short Enter the BREd consensus sequence RTDKKKK in the (2-30 base) “Short sequence” text box Click “Submit” Figure 8 UCSC Genome Browser view of the Short Match search results to the BREd motif consensus sequence The Match” track shows there are multiple matches to the RTDKKKK sequence on both “Short the plus and minus strands in this genomic region (Figure 8). Note that we expect the core promoter motifs to be in the same orientation as the direction of transcription. In addition, given the information in Table 2, we can see that BREd motifs are usually found at position -23 relative to the TSS in The location of the Inr motif and alignment with Drosophila. D. melanogaster sequence allow us to predict the TSS position. Let’s zoom into this region to investigate further. Enter into the position or search terms” text box, “KB465191:114,064-114,196” “enter and then click on the button to zoom in closer to the beginning of exon 1. “go” Q12. Analyze the BREd motif instance on the Short Match track (Figure 9). Is the BREd motif at -23 relative to the start of transcription (+1)? Note that the core promoter motif should be in the same orientation as the direction of transcription. Based on the information about the characteristics of core promoter motifs above, sev? is there a canonical BREd motif for the core promoter of Figure 9 BREd instance on the Short Match track Q13. Perform Short Match searches for the rest of the core promoter motifs in
Go back to the web browser tab with the GEP UCSC Genome Browser to examine the D. eugracilis sequence further. Enter “KB465191:113,830-114,429” into the “enter position or search terms” text box, and then click on the “go” button to navigate to the region surrounding the TSS of Sev Ensure that your browser is still configured as follows: Base Position: full, D. mel Transcripts: pack, modENCODE RNA-Seq Coverage: full, Match: pack Under “Mapping and Sequencing Tracks”, click on the blue “Short Match” link Enter the BREd consensus sequence RTDKKKK in the “Short (2-30 base) sequence” text box Click “Submit” Figure 8 UCSC Genome Browser view of the Short Match search results to the BREd motif consensus sequence The “Short Match” track shows there are multiple matches to the RTDKKKK sequence on both the plus and minus strands in this genomic region (Figure 8). Note that we expect the core promoter motifs to be in the same orientation as the direction of transcription. In addition, given the information in Table 2, we can see that BREd motifs are usually found at position -23 relative to the TSS in Drosophila. The location of the Inr motif and alignment with D. melanogaster sequence allow us to predict the TSS position. Let’s zoom into this region to investigate further. Enter “KB465191:114,064-114,196” into the “enter position or search terms” text box, and then click on the “go” button to zoom in closer to the beginning of exon 1. Q12. Analyze the BREd motif instance on the Short Match track (Figure 9). Is the BREd motif at -23 relative to the start of transcription (+1)? Note that the core promoter motif should be in the same orientation as the direction of transcription. Based on the information about the characteristics of core promoter motifs above, is there a canonical BREd motif for the core promoter of sev? Figure 9 BREd instance on the Short Match track Q13. Perform Short Match searches for the rest of the core promoter motifs in
Module_TSS2_Advanced.docx