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” and Gene Prediction” Tracks “Gene FlyBase Genes: pack and Regulation” “Expression TSS (Celniker) (R5): pack Click on the blue modENCODE CAGE TSS” link “Combined Change the display mode” to “Maximum “full” Scroll down to the views” section, and change the display mode to “Select “Peaks” “pack” In the Subtracks” section, uncheck the box for CAGE (Plus)” “List “modENCODE Scroll up to the top of the page, and then click on the button to update the “Submit” display. Note: Although we have set the display mode for the Position” track to we “Base “full”, will need to zoom in further to see the nucleotide sequence and the amino acid translations. Enter into the position or search “chrX:11,086,293-11,086,305” “enter terms” text box, and then click on the button. “go” Note that this exercise requires you to examine the region near exon 1 to determine where transcription begins (Figure The start codon for (where translation 4). sev begins) is in exon 2. Q1. Based on the Genes” track, what is the coordinate of the “FlyBase transcription start site? Q2. Based on the Transcription Start Sites (Celniker) (R5) track, what is the coordinate of the transcription start site?
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 “Gene and Gene Prediction” Tracks FlyBase Genes: pack “Expression and Regulation” TSS (Celniker) (R5): pack Click on the blue “Combined modENCODE CAGE TSS” link Change the “Maximum display mode” to “full” Scroll down to the “Select views” section, and change the “Peaks” display mode to “pack” In the “List Subtracks” section, uncheck the box for “modENCODE CAGE (Plus)” Scroll up to the top of the page, and then click on the “Submit” button to update the display. Note: Although we have set the display mode for the “Base Position” track to “full”, we will need to zoom in further to see the nucleotide sequence and the amino acid translations. Enter “chrX:11,086,293-11,086,305” into the “enter position or search terms” text box, and then click on the “go” button. Note that this exercise requires you to examine the region near exon 1 to determine where transcription begins (Figure 4). The start codon for sev (where translation begins) is in exon 2. Q1. Based on the “FlyBase Genes” track, what is the coordinate of the transcription start site? Q2. Based on the Transcription Start Sites (Celniker) (R5) track, what is the coordinate of the transcription start site?