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+UCSC Genome Browser · Tutorial 5
+Teaching with the Browser
+Ready-made, interactive modules for the classroom
+~20 free modules on the Education portal · genome.ucsc.edu
+The Education portal
+
+ 
+ “Educating with the Genome Browser”: a free library of classroom-ready modules and tutorial videos.
+
+
+
+ -
+
- genome.ucsc.edu/training/education: ~20 interactive modules + videos. +
- Self-contained, undergraduate-level, each built on clickable Browser sessions. +
- Topics: codons & reading frames, the Variants curriculum, splicing, CpG/methylation, CRISPR, Huntington’s, lactase, FOXP2… +
Can be used as part of a lecture or assignments.
+
+ Reading the gene
+the central dogma, made visible
+Reading the gene, base by base
+-
+
- 5′ → 3′ direction — which way a gene is transcribed open +
- Start & stop codons — the signals that begin and end translation open +
- Three reading frames — how one sequence can be read three ways open +
Same recipe Each module is a clickable session + a short page, ready to drop into a lecture or assignment.
+Another module: the “Wobble Base” module
+
+ 
+ The GRK4 kinase domain (hg19): codons + amino acids, PhyloP conservation, and a 100-vertebrate alignment, the protein is conserved while the wobble (3rd) base varies.
+
+
+
+ -
+
- Teaches codon degeneracy: the 3rd base of a codon can change without changing the amino acid (“wobble”). +
- Example: the GRK4 kinase domain (hg19), codons & amino acids drawn over the sequence. +
- Read it down the 100-vertebrate alignment: the amino acid (V, K, A…) is identical across species even where the wobble base differs, and PhyloP shows those residues are conserved. +
Try it, ▶ open s/education/hg19_wobble2
+ Find a column where a base varies between species but the amino acid stays the same.
+ Same recipe
+ Another session + a page: the portal has ~20 like this.
+
+ Variants and their effects
+what a change does to the protein
+Variants and their effects
+-
+
- Synonymous — a base change that leaves the amino acid unchanged open +
- Nonsense — a change that creates a premature stop codon open +
- Frameshift — an insertion or deletion that shifts the reading frame open +
Same recipe Each module is a clickable session + a short page, ready to drop into a lecture or assignment.
+Spotlight: the “Missense Variants” module
+
+ 
+ The module’s session at BRCA2: codons & amino acids over the sequence, with dbSNP variants coloured red = missense / green = synonymous.
+
+
+
+ -
+
- The Missense Variants module teaches a missense variant on the cancer gene BRCA2 (rs135936718, His→Gln). +
- Students click a shared link; dbSNP colours green = synonymous, red = missense. +
- A nice sum-up of the basics: it reuses the gene model, codons & amino acids, and clicking a variant. +
Try it
+ Open s/education/hg19_BRCA2missense; find the red variant.
+ The takeaway
+ A module is just a saved view + a web page. You’ll learn to build your own in the Sessions section of Tutorial 1.
+
+ Splicing & isoforms
+one gene, many mRNAs
+Bonus module: the “Splicing” module if time
+
+ 
+ FGFR2 (hg19): GENCODE isoforms include or skip the highlighted exons, the essence of alternative splicing.
+
+
+
+ -
+
- The Splicing module teaches alternative splicing: different exon combinations make distinct mRNA isoforms. +
- Example: FGFR2 (hg19), with exons included or skipped across its GENCODE isoforms. +
- The Spliced ESTs (expressed sequence tags) and alternative splicing tracks show which exons each transcript version includes or skips. +
Try it, ▶ open the FGFR2 session
+ Compare isoforms across the two highlighted exons.
+ Same recipe
+ Another session + a page, one of ~20 ready-made modules.
+
+ Isoforms and tissues
+-
+
- Isoforms across tissues — tissue-dependent alternative splicing open +
- Tissue-specific expression — where a gene is switched on (the PLP gene) open +
Same recipe Each module is a clickable session + a short page, ready to drop into a lecture or assignment.
+Spotlight: tissue-specific expression
+
+ 
+ PLP1 GTEx expression: each bar is a tissue; the tall yellow bars are brain, where this myelin gene is active.
+
+
+
+ -
+
- The GTEx track shows how strongly a gene is expressed across 54 human tissues — one coloured bar per tissue. +
- Example: PLP1, a myelin gene, is switched on almost only in the brain (the tall yellow bars). +
- A quick, visual way to ask “where is this gene active?” +
Try it, ▶ open PLP1 with GTEx
+ Read which tissues light up for this gene.
+ Same recipe
+ Another session + a page, one of ~20 ready-made modules.
+
+ Regulation & epigenetics
+beyond the coding sequence
+Regulation & epigenetics
+-
+
- CpG islands & methylation — DNA methylation and epigenetic regulation open +
- CRISPR — gene editing, explored in the Browser open +
Same recipe Each module is a clickable session + a short page, ready to drop into a lecture or assignment.
+Disease & evolution case studies
+genetics with a story
+Case studies: disease
+-
+
- Huntington’s & CAG repeats — a trinucleotide-repeat expansion in HTT open +
- Lactase persistence (LCT) — the genetics of digesting milk open +
- Alcohol intolerance — variation in alcohol metabolism in East Asians open +
Same recipe Each module is a clickable session + a short page, ready to drop into a lecture or assignment.
+Case studies: evolution
+-
+
- FOXP2 & the evolution of speech — comparing a speech gene across species open +
- Why apes have no tails — an evolutionary loss, seen in the genome open +
- Ebola & Marburg conservation — conserved regions of viral genomes open +
Same recipe Each module is a clickable session + a short page, ready to drop into a lecture or assignment.
+Spotlight: why apes have no tails
+
+ 
+ TBXT (hg19): the highlighted Alu element (a RepeatMasker SINE) sits inside the gene — tied to tail loss in apes.
+
+
+
+ -
+
- An Alu insertion (a “jumping-gene” element) landed inside the tail-development gene TBXT in the common ancestor of apes. +
- It makes an exon get skipped, altering the protein — linked to the loss of the tail. +
- The RepeatMasker track marks the Alu (highlighted); the GENCODE isoforms show the affected exon. +
Try it, ▶ open s/education/hg19_TBXTalus
+ Find the highlighted Alu element inside the TBXT gene.
+ Same recipe
+ Another session + a page, one of ~20 ready-made modules.
+
+ Bringing it into the classroom
+-
+
- Around 20 self-contained modules, each built on a clickable Browser session. +
- They span the central dogma (reading frames, codons, splicing), variant effects, and real disease & evolution case studies. +
- Use them as lecture demos or student assignments — no install required. +
- Build your own the same way: save a session (see Tutorial 1) and wrap it in a page. +
Try it Browse the full library at genome.ucsc.edu/training/education.
+Thank you!
+Questions? · genome@soe.ucsc.edu
+UCSC Genome Browser · genome.ucsc.edu
+