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Questions: 3 points each 1) How many unique diabetes-related map elements on the reference assembly did you find using MapViewer? How many elements of type Gene did you find on the reference assembly? List their gene symbols and chromosome on which they are located. Hint: You can use the Advanced Search button to change which assemblies are searched and displayed. 2) How many RefSeq links were returned for the search term “diabetes” against the human genome browser? Would this be a useful way to search for diabetes related loci using this browser? Why or why not? 3) How many links were returned for the search term “diabetes” when searching the Ensembl human genome assembly? How many of these are genes? List their HUGO designation. 4) Which of the three genome browsers do you think was the most useful or user-friendly for finding genes or loci associated with a disease? Why? 5) What chromosome number and band are shown in the default view? 6) Does the default view that you are looking at show you all the STSs that have been mapped to this region? 7) After narrowing down the view to include just the region between STS markers D21S1869 and D21S1989, what are the chromosomal coordinates, in bp, that you are looking at? 8) The gene you are interested in is likely in this region between the two STS markers. List the gene symbols for ALL the genes annotated by NCBI in this region? 9) One of the genes in this region has been shown to involved in cataract formation in the eye. Use the links from MapViewer to OMIM to find the gene and list it here, along with at least one reference which supports the observation of this gene being responsible for cataract formation. 10) What is the gene symbol and name of the RefSeq gene that has been mapped to this region of the human genome? 11) What is the accession number of the BAC clone that was used in this region to create the genome assembly? 12) What are the accession numbers of the human spliced ESTs that encode the 1st-3rd exons of the gene? 13) What RefSeq Genes are immediately upstream and downstream of this gene in the UCSC genome browser? What is the orientation of each of these relative to the gene from question 10? 14) Looking only at the human mRNAs from the GenBank track (Human mRNAs), you see that one or both of the neighboring genes may have alternately spliced forms. What is the accession number(s) of the GenBank mRNA(s) that is spliced differently from the known gene? Look for an mRNA with a potential alternate coding sequence, not just more or less 5’ or 3’ untranslated sequence. 15) Does the downloaded EST appear to be a mouse or a human gene? On the basis of what evidence did you determine your answer? 16) What gene does this EST represent? On what chromosome is it found? 17) What is the Ensemble accession number for the EGFR gene? 18) How many transcripts has Ensemble predicted for this gene? List their accession numbers. 19) What are the lengths of the predicted transcripts, in bp? How many exons do they have? How long is the corresponding genomic sequence interval, in Kb? 20) Is there any EST evidence for the predicted EGFR transcripts? Do you think that all the predicted transcripts are supported by EST evidence? Why or why not? 21) Is there any EMBL mRNA evidence for the predicted transcripts? Does the mRNA evidence support all of the predicted transcripts? 22) What is the Ensembl accession number of the human gene that is the likely ortholog of EGFR? 23) How many known Tlr genes are they on the mouse genome? On the human genome? On the rat genome? 24) Is there of the mouse Tlr genes not mapped on the human chromosome? If any, which and how would you attempt to place the location of this gene? 25) Which human chromosome contains the most Tlr genes? Do you think the Tlr genes located on this chromosome are in synteny with the homologous genes on the mouse chromosome? 26) For the two Tlr genes located on chromosome X in the mouse and human genomes, were you able to find the rat homologs? Describe how you found them, including which assembly was searched. 27) Which two genes flank the Tlr genes on the X chromosome? 28) Are the four genes on chromosome X that you mapped for human, mouse and rat in the same order or orientation on the chromosome? How are they different? What genetic event could have led to the differences observed? Gene name Ensembl NCBI Species Chromosome Rat homolog