Download 20070313_Questions

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