Posted: January 4th, 2014
Draw a map of this gene locus showing all of the gene segments (including leader peptide exon, V exon, D exon, J exon, C exons)
Go to ensemble, find the mouse TCR beta gene. A good starting point is the following:
Question 1. Draw a map of this gene locus showing all of the gene segments (including leader peptide exon, V exon, D exon, J exon, C exons)
On the map at the bottom of the page, you can click on individual gene segments, a popup will appear, click on the “gene” link. For example for TCRB Vb2-201 this is
Gene ENSMUSG00000076462. Now on the left column entitled “gene based displays“, click “sequence” this will show you the genomic DNA sequence. introns are black letters and exons are red letters with pink shading.
Question 2. Copy and paste these sequences into microsoft word and assemble the full cDNA of your specific TCRb gene, look at the legend below. Use the genetic code table (available on wikipedia) to find out what the amino acid sequence of this cDNA will be. Assume no P or N nucleotide addition. If your sequence has premature stop codons, you will need to add N nucleotides to the vdj junctions, annotate these. Annotate the amino acids encoded by the junctions of V-D, D-J, J-C. Make sure that your protein has the TCRb transmembrane region which is SATILYEILLGKATLYAVLVSTLVVMAM.
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