Gene track
TL;DR: Gene and transcript features (GFF3, GTF, BED12, and similar) render as glyphs with their exons, UTRs, and CDS segments. Beyond that the track can translate the CDS in place (reading frame colors, amino-acid lettering, mature peptides), color each transcript from a value carried in the file, and reshape the view around a gene by collapsing its introns.
Choosing which transcripts to show
The Gene glyph option in the track menu controls how a gene's transcripts are drawn:
- Auto (default) - stacks every transcript zoomed in, collapses each gene to one transcript zoomed out, and keeps only as many isoforms per gene as the track's height has rows for
- All transcripts - every transcript on its own row, whatever the zoom or track height. A stack taller than the track scrolls
- Representative transcript - one isoform per gene
The representative isoform is the one the annotation tags: RefSeq Select or
MANE Select (NCBI), MANE_Select or Ensembl_canonical (Ensembl, GENCODE).
It is also drawn first when a gene is stacked. Without a tag, it is the longest
by protein length, or by genomic span for a gene with no coding isoform. The
canonicalTranscriptField and canonicalTranscriptTags config slots name the
attribute and tags.
A gene drawn with fewer transcripts than it has shows +N more beside its name. Clicking it opens that one gene, and the badge then reads show fewer. The Gene glyph submenu grows a row to re-collapse every gene opened this way. The badge appears wherever the gene is wide enough on screen to hold it.
While transcripts are being left out, a chip in the track's bottom-right corner
names the rule: Isoforms trimmed where the track's height is the constraint,
otherwise the tag that picked most genes on screen (RefSeq Select,
MANE Select, or Longest isoform). Its tooltip counts the genes under each
rule. Clicking it opens the same three modes.
Collapsing introns
Collapse introns, from a gene's right-click menu, replaces the view's displayed regions with that gene's exons side by side. A window-size setting keeps some flanking sequence around each splice boundary. Right-clicking a transcript offers that isoform as well as the whole gene (exons unioned), and the dialog's transcript dropdown reaches an isoform that isn't drawn.
With an RNA-seq track, the spliced reads' sashimi arcs then span directly between adjacent exons.
Display density and labels
Track-menu toggles:
- Display mode - Normal, Compact, or Super-compact feature heights
- Show subfeature labels - each transcript's name on its row
- Show chevrons - strand chevrons along the intron lines (on by default)
- Show only genes - hides non-gene features
Color by CDS
Color CDS by reading frame, in the linear genome view's hamburger menu, tints each CDS segment by the frame it is read in, so one colour is one frame across the view. Frame is constant within a segment, so a colour change across a junction is a frame shift. The setting applies to every gene track in the view and is remembered across sessions.
Color transcripts by a value in the file
The color slot takes a jexl expression evaluated against each drawn part, so a
per-transcript number in the GFF3 attribute column can drive the fill:
- Attribute names arrive lowercased, values as strings.
dIF=0.79is read under the keydif, and comparing it numerically needsparseFloat - The expression is evaluated against the box being painted (an exon, CDS,
or UTR), so a transcript's own attribute is
feature.parent.dif. A UTR followscolorunlessutrColorclaims it - Test the significance flag, not the magnitude. The expression in the
tutorial below branches on a
dtuattribute the analysis wrote and only then reads the size
Declare what the colors mean in the legend slot; the key is drawn over the
track and can be dismissed. See the
jexl configuration guide.
The differential transcript usage tutorial has the track configuration behind that figure and the pipeline that writes the attributes.
Peptide lettering
The translated protein is drawn on coding features by default. Zooming in, the amino acids first appear as alternating per-codon shading, then at roughly base-pair resolution as single-letter code over each codon, in register with the reference sequence track. Turn off Show amino acids when zoomed in, in the view menu's Show... submenu, to keep the view from fetching the reference.
The translation follows the transcript's strand and CDS phase, splitting codons
that straddle an exon boundary. A CDS with a transl_table attribute (NCBI
convention, e.g. transl_table=2 for vertebrate mitochondria) translates with
that code. The first codon shows as M when it is a valid start for that table
(including GTG or TTG), and transl_except overrides (e.g. selenocysteine
U) are applied and highlighted.
Mature peptides (polyproteins)
Many viral genomes encode one polyprotein cleaved into mature peptides. When a
CDS has mature_protein_region (or mature_protein_region_of_CDS) subfeatures,
each cleavage product is drawn as its own stacked row in a distinct color,
hoverable and clickable. Its name comes from the product attribute when the
track's labels.name reads it:
{
"type": "FeatureTrack",
"trackId": "enterovirus_d_genes",
"name": "Genes",
"assemblyNames": ["GCF_000861205.1"],
"adapter": {
"type": "Gff3TabixAdapter",
"uri": "https://example.com/GCF_000861205.1.gff.gz"
},
"displayDefaults": {
"labels": {
"name": "jexl:feature.product || feature.name || feature.id"
}
}
}jbrowse add-track https://example.com/GCF_000861205.1.gff.gz \
--trackId enterovirus_d_genes \
--name Genes \
--assemblyNames GCF_000861205.1 \
--displayDefaults '{"labels":{"name":"jexl:feature.product || feature.name || feature.id"}}'In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:
{
"type": "FeatureTrack",
"trackId": "enterovirus_d_genes",
"name": "Genes",
"assemblyNames": ["GCF_000861205.1"],
"adapter": {
"type": "Gff3TabixAdapter",
"uri": "https://example.com/GCF_000861205.1.gff.gz"
},
"displayDefaults": {
"labels": {
"name": "jexl:feature.product || feature.name || feature.id"
}
}
}See the jexl configuration guide for the expression syntax.
Reading a feature's protein sequence
Click the feature and use the Sequence section of the details panel for the protein, CDS, cDNA or genomic sequence. See Feature sequence panel.
Using gene tracks with the Protein3d plugin
The Protein3d plugin uses the same transcript-to-protein mapping. Right click a gene and launch the protein structure viewer for an interactive 3D structure (AlphaFold DB or UniProt) linked to the genome view: hovering a position highlights the residue, and vice versa. See the proteins tutorial for launch routes and installation.
A whole chromosome of genes
Zoomed out far enough, a gene track stops fetching and shows a "region too large" message with a Force load button. A track can carry a sidecar instead: a bigWig of feature counts per kilobase, built once from the file, drawn as a band wherever the features are too many to fetch. The band names its peak in its corner, and hovering reads the count under the cursor.
jbrowse make-density writes the sidecar beside the file, and
jbrowse add-track attaches one it finds there; --density names one
elsewhere. What it writes is the densityAdapter slot on the track's adapter:
jbrowse make-density genes.gff3.gz --chrom-sizes hg38.chrom.sizes
jbrowse add-track genes.gff3.gz --load copyThe track menu's Density band submenu: Automatic swaps where the fetch would be too large, Features only keeps the message, Density only always draws the band. While the band is standing in for a fetch that was too large, the same submenu carries Load features anyway, the banner's force-load. See the gene density tutorial.