Genome Browser
Potential lessons
Potential browser sessions suggested by Robert Kuhn, Genome Browser Co-PI, Training and Outreach. These ideas were presented at a Genome Browser workshop at James Maddison University, July 24th, 2015.
Browser Sessions in Education
Sessions designed to illustrate concepts in Molecular Biology
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| start codon - alt starts start codon rev strand start codon rev zoom |
translation / transcription / 5'- UTR / start codon / 3 reading frames -- opposite strand |
| stop codons out-of-frame stop codon |
transcription / translation / stop codon / 3'-UTR isoforms with different stop codons / out-of-frame protein trainslation |
| wobble base third base varies |
wobble base diverges through evolution even when amino acid is the same (conservation score/graph). conservation of function through evolution: V > I > F amino acids, K > R substitutions |
| split codon | split codon -- click little double-headed arrow on left to see other part of codon. note different AA depending on different splicing upstream. |
| UCSC Genes gene details (direct link) |
learn function of protein, association with disease, links to other places etc. -- click into gene for details |
| SNPs ABO variant details |
nonsense missense frameshift -- color-coded ABO blood group variation -- mouseover variant amino acids to see changes in nucleotide and AA |
| isoforms 1 isoforms 2 |
same region in an exon can have different codon numbering. Use caution when reading codon numbers in the literature. -- zoom out ~300x (or click second link) to see alternate splicing. |
| disease associations zoom view |
mouseover and click into OMIM allelic variants (top track) to access details |
| evolution evolution 2 |
conservation of exons / decay of conservation between genes and in introns -- zoom out |
| chr2 human vs chimp chr2 human vs 3 great apes |
evolution - two chimp chroms fused to make human chr2. Use step-wise, adding one species at a time, to teach reasoning: with only chimp turned on, is it a fusion or a split? |
| centromere heterochromatin chimp chr2B centromere |
evolution - heterochromatin around former chimp centromere on human chr2 still visible -- has not evolved away yet Use "View... In Other Genomes to go to chimp and see that it is still a centromere there |
| pathways - FAS gene pathways 2 - ATP6V01 |
FAS gene - cell death. click on top KEGG link follow KEGG links to outside resources - especially oxidative phophorylation on ATP6V0A1 |
| CAG repeats | HTT - Huntingtin - see CAG repeats - polyglutamine region. |
| restriction sites | hit direction arrow at top left to see palindrome = reverse complement. zoom out to see more selected sites |
| segmental duplications - opsin segmental duplications - Prader |
X-linked colorblindness - segDupe as recombination hotspot in opsin region 15q11 - Prader-Willi region -- same-chrom duplications lead to gain and loss of copies |
| microarrays | compare Affy, Agilent, Illumina -- different tiling densities |
| population distribution of alleles | click into HGDP - Human Genome Diversity Project |
| ... work in progress ... | |
| literature about genes | |
| pseudogenes | |
| reverse complement sequence | |
| heterochromatin | |
| PCR | |
| primer design | |
| Alus and other repeats | |
| differential expression / GNF | |
| 1000 Genomes gene alleles | nonsense missense frameshift |
| encode project | |
| DNase hypersensitivity binding sites | |
| DNA/histone modification | |
| Restriction enzymes | blunt and sticky ends, both directions, 5', 3' overhang |