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UCSC Genome Browser · Tutorial 5: Teaching with the Browser
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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
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…
+ Topics: codons & reading frames, variant effects, splicing, CpG/methylation, CRISPR, Huntington’s disease, lactase, FOXP2…
Can be used as part of a lecture or assignments.
“Educating with the Genome Browser”: a free library of classroom-ready modules and tutorial videos.
Open the portal and scroll the list so they see the breadth. Each module is classroom-ready: built around clickable sessions, no install for students.
Many here teach undergrad genetics/cancer: these are free, vetted teaching assets.
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 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.
+ Same recipe Each module is really just a saved session you can reuse, ready to drop into a lecture or assignment.
Another module: the “Wobble Base” module
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.
Same recipe
- Another session + a page : the portal has ~20 like this.
+ Another saved session; the portal has ~20 like this.
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.
A second education-portal module, paired with the missense one. It makes the synonymous / silent-mutation point concrete: open the GRK4 kinase-domain session, read the amino-acid row, then scan down the Multiz 100-vertebrate alignment, the amino acid (e.g. valine, lysine, alanine) is the same across species even though the third codon base differs. PhyloP conservation (high = functionally critical) reinforces that these residues matter while the wobble position tolerates change. Reinforces codons/reading-frame and conservation from the basics. Source: genome.ucsc.edu/training/education/wobble.html.
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 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.
+ Same recipe Each module is really just a saved session you can reuse, ready to drop into a lecture or assignment.
Spotlight: the “Missense Variants” module
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.
+ Open the shared link ; dbSNP colors green = synonymous, red = missense.
A nice sum-up of the basics : it reuses the gene model, codons & amino acids, and clicking a 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.
+ A module is just a
session . You’ll learn to build your own in the
Sessions section of Tutorial 1.
The module’s session at BRCA2 : codons & amino acids over the sequence, with dbSNP variants coloured red = missense / green = synonymous . The module’s session at BRCA2 : codons & amino acids over the sequence, with dbSNP variants colored red = missense / green = synonymous .
- Walk the module live: open the BRCA2 missense session, point out the dbSNP colour key (green synonymous / red missense), the codon change His→Gln, and the ClinVar call.
- Use this to wrap up the navigation/tracks basics; it reuses the gene model, codons and clicking-a-variant they just practised. Forward pointers (don't dwell): BRAF V600E, coming up in the oncology section, is itself a missense variant; and a module is just a session + a page, so they'll be able to author their own once you save a session in Tutorial 1.
+ Walk the module live: open the BRCA2 missense session, point out the dbSNP color key (green synonymous / red missense), the codon change His→Gln, and the ClinVar call.
+ Use this to wrap up the navigation/tracks basics; it reuses the gene model, codons and clicking-a-variant they just practised. Forward pointers (don't dwell): BRAF V600E, coming up in the oncology section, is itself a missense variant; and a module is really just a saved session, so they'll be able to author their own once you save a session in Tutorial 1.
Splicing & isoforms
one gene, many mRNAs
Bonus module: the “Splicing” module if time
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.
Same recipe
- Another session + a page, one of ~20 ready-made modules.
+ Another saved session, one of ~20 ready-made modules.
FGFR2 (hg19): GENCODE isoforms include or skip the highlighted exons, the essence of alternative splicing.
Optional third education module on alternative splicing (FGFR2, hg19). Cover it only if running ahead; otherwise skip. Open s/education/fgfr2_highlights: the two highlighted exons are alternatively included or skipped across FGFR2's GENCODE isoforms, and the Spliced ESTs / SIB alt-splicing tracks show real transcripts with different exon combinations. Ties back to the gene-model and exon/intron basics. Source: genome.ucsc.edu/training/education/splicing.html.
Isoforms and tissues
- Isoforms across tissues — tissue-dependent alternative splicing open Tissue-specific expression — where a gene is switched on (the PLP gene) open 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.
+ Same recipe Each module is really just a saved session you can reuse, ready to drop into a lecture or assignment.
Spotlight: tissue-specific expression
- The GTEx track shows how strongly a gene is expressed across 54 human tissues — one coloured bar per tissue.
+ The GTEx track shows how strongly a gene is expressed across 54 human tissues : one colored 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?”
Same recipe
- Another session + a page, one of ~20 ready-made modules.
+ Another saved session, one of ~20 ready-made modules.
PLP1 GTEx expression: each bar is a tissue; the tall yellow bars are brain, where this myelin gene is active.
- A tissue-expression spotlight to pair with the isoforms menu. Open PLP1 with the GTEx track: the colour-coded bars show expression per tissue, and PLP1 (a myelin protein) lights up almost only in brain. Makes "tissue-specific expression" concrete and visual. Same module recipe as the others: a saved view plus a short page.
+ A tissue-expression spotlight to pair with the isoforms menu. Open PLP1 with the GTEx track: the color-coded bars show expression per tissue, and PLP1 (a myelin protein) lights up almost only in brain. Makes "tissue-specific expression" concrete and visual. Same module recipe as the others: a saved session.
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 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.
+ Same recipe Each module is really just a saved session you can reuse, 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 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.
+ Same recipe Each module is really just a saved session you can reuse, 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 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.
+ Same recipe Each module is really just a saved session you can reuse, ready to drop into a lecture or assignment.
Spotlight: why apes have no tails
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.
+ It makes an exon get skipped , altering the protein, and this is linked to the loss of the tail.
The RepeatMasker track marks the Alu (highlighted); the GENCODE isoforms show the affected exon.
Same recipe
- Another session + a page, one of ~20 ready-made modules.
+ Another saved session, one of ~20 ready-made modules.
TBXT (hg19): the highlighted Alu element (a RepeatMasker SINE) sits inside the gene — tied to tail loss in apes.TBXT (hg19): the highlighted Alu element (a RepeatMasker SINE) sits inside the gene, tied to tail loss in apes.
An evolution spotlight to pair with the case-studies menu. Based on the 2021 finding that an AluY insertion in TBXT causes exon skipping and is associated with tail loss in apes/humans. Open the session: the highlight marks the Alu (RepeatMasker SINE) within TBXT, and the GENCODE isoforms show the exon it affects. Ties conservation, repeats and gene models together.
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.
+ Use them as lecture demos or student assignments, with no install required.
Build your own the same way: save a session (see Tutorial 1) and wrap it in a page.
Thank you!
Questions? · genome@soe.ucsc.edu
UCSC Genome Browser · genome.ucsc.edu
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