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…

Can be used as part of a lecture or assignments.

UCSC education portal — “Educating with the Genome Browser”: a free library of classroom-ready modules and tutorial videos.

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

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.

Wobble-base module session at GRK4 — 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.

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 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.

Missense module session at BRCA2 — The module’s session at *BRCA2*: codons & amino acids over the sequence, with dbSNP variants coloured red = missense / green = synonymous.

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.

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.

FGFR2 alternative splicing (hg19) — *FGFR2* (hg19): GENCODE isoforms include or skip the highlighted exons, the essence of alternative splicing.

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

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.

GTEx tissue-expression barchart for PLP1 — *PLP1* GTEx expression: each bar is a tissue; the tall yellow bars are brain, where this myelin gene is active.

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

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.

TBXT gene with a highlighted Alu element (hg19) — *TBXT* (hg19): the highlighted **Alu** element (a RepeatMasker SINE) sits inside the gene — tied to tail loss in apes.

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