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
Genes with many isoforms can stack into tall, hard-to-read blocks. The Gene glyph option in the track menu controls how a gene's transcripts are drawn:
- Auto (default) - stacks every transcript when you are zoomed in, but collapses each gene to a single transcript when you are zoomed out, so dense regions stay legible. Zoomed in it also keeps only as many isoforms per gene as the track's height has rows for.
- All transcripts - always draws every transcript on its own row.
- Representative transcript - collapses each gene to one isoform.
Which isoform that is comes from the annotation where it says: a transcript
tagged RefSeq Select or MANE Select (NCBI), or MANE_Select /
Ensembl_canonical (Ensembl, GENCODE) is the one kept, and it is also the first
one drawn when a gene is stacked. Failing a tag, it is the longest by protein
length — or, for a gene with no coding isoform at all, the one with the widest
genomic span. The attribute read and the tags that count are the
canonicalTranscriptField and canonicalTranscriptTags config slots.
A gene left short by the track's height says so on its own label: a small +N more beside the gene name, counting the isoforms that gene is missing. Clicking it opens that one gene, and the badge then reads show fewer and closes it again. The count sits on the gene, since one gene in a window can be missing twenty isoforms and its neighbour one. The Gene glyph submenu grows a row to re-collapse every gene opened this way. Representative transcript puts no badge on a gene you have not opened, since that mode is a choice you made and the chip below already names it. A gene you did open keeps its badge in every mode, which is the way back to a collapsed one.
While transcripts are being left out, the track's bottom-right corner says so
with a chip naming the rule that did it: Isoforms trimmed where the track's
height is the constraint, otherwise the tag that picked most of the genes on
screen — RefSeq Select, MANE Select, or Longest isoform for an annotation
that tags nothing. Its tooltip counts the genes under each rule when a window
holds a mix, which is usual: NCBI tags its protein-coding genes and leaves most
non-coding ones alone. Clicking the chip opens the same three modes; once that
menu has been opened the chip shrinks to the small icon that stays in that
corner.
Collapsing introns
Genes often span far more intronic than exonic sequence, so the coding parts are spread thinly across the view.
- Collapse introns, from a gene's right-click menu, replaces the view's displayed regions with just that gene's exons placed side by side.
- A window-size setting controls how many base pairs of flanking sequence to keep around each splice boundary.
- Right-clicking a specific transcript offers that isoform as well as the whole gene, whose exons are unioned; the dialog also has a transcript dropdown, which is how to reach an isoform that isn't drawn.
This pairs especially well with an RNA-seq track: the spliced reads draw sashimi arcs connecting splice donors and acceptors, and with the introns collapsed those arcs span directly between the adjacent exons.
Display density and labels
Several track-menu toggles tune how gene glyphs are drawn:
- Display mode - Normal, Compact, or Super-compact progressively shrink each feature's height to fit more rows in dense regions.
- Show subfeature labels - draws each transcript's name on its row, not just the gene name.
- Show chevrons - directional chevrons along the intron lines indicating the strand (on by default).
- Show only genes - hides non-gene features in the track.
Color by CDS
By default CDS segments use the track's feature color. Turning on Color CDS by reading frame tints each CDS segment by the frame it is read in, so one colour is one frame across the whole view.
Frame is constant within a CDS segment, so the colour changes at a junction rather than inside an exon: two consecutive coding exons in the same colour are in phase, and a change of colour across a junction is a shift. Both need enough of the gene in frame to see two exons at once, which is a wider window than the one below.
Enable it from the linear genome view's hamburger menu → Color CDS by reading frame. The setting applies to every gene track in that 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 carried in the GFF3 attribute column can drive the fill.
Two things to know before writing one:
- Attribute names arrive lowercased, and their values arrive as strings. An
attribute written
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 read with
feature.parent.dif. One expression covers the whole glyph: a UTR followscolorunlessutrColorclaims it. - Test the significance flag, not the magnitude. A large effect on a
transcript the test could not separate is not a result, so the expression
below branches on a
dtuattribute the analysis wrote and only then reads the size. Thresholding on the number alone colors those too.
A jexl: color is a lookup table only its author can read, so declare what it
means in the legend slot; the key is drawn over the track and can be
dismissed. Hovering a transcript names the isoform and the exon under the
cursor; clicking one opens that transcript's own attributes in the details
panel.
See the jexl configuration guide for the expression syntax.
The differential transcript usage tutorial has the track configuration behind that figure, and the pipeline that writes the attributes the expression reads.
Peptide lettering
The translated protein is drawn on coding features by default, independently of the frame coloring above. As you zoom in, the amino acids are first drawn as an alternating per-codon shading over the CDS, and once you are zoomed in far enough (roughly base-pair resolution) the single-letter amino acid code is drawn over each codon, as in the lower frame of the figure above. The letters line up with the codons in the reference sequence track, so you can read the genomic sequence, the codons, and the resulting peptide in register. The translation uses the standard genetic code (NCBI table 1).
Translating needs the reference sequence. Turn off Show amino acids when zoomed in, in the view menu's Show... submenu, to keep the view from fetching it.
The translation follows the transcript's strand and CDS phase, and codons that
straddle an exon boundary are split across the two exons. When a CDS carries a
transl_table attribute in the GFF (the NCBI convention, e.g. transl_table=2
for the vertebrate mitochondrial code), that alternative genetic code is used
for the translation, so a mitochondrial gene translates TGA as tryptophan
rather than a stop. The first codon of the CDS is shown as M when it is a
valid start codon for that table (including alternative initiators such as GTG
or TTG), and transl_except overrides (e.g. selenocysteine U) are applied
and highlighted.
Mature peptides (polyproteins)
Many viral genomes encode a single large polyprotein that is cleaved into
several 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, colored from a distinct palette so adjacent peptides are
easy to tell apart. Each region is individually hoverable and clickable, and its
name comes from the feature's product attribute when the track's labels.name
is configured to read it, e.g.:
{
"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"}}'See the jexl configuration guide for the expression syntax.
Reading a feature's protein sequence
To extract the full protein (or CDS, cDNA, or genomic sequence) for a single transcript, click the feature and use the Sequence section of the feature details panel. See Feature sequence panel for the available options.
Using gene tracks with the Protein3d plugin
The Protein3d plugin builds on the same transcript-to-protein mapping. Right click a gene and launch the protein structure viewer to open an interactive 3D structure (from AlphaFold DB or UniProt) linked to the genome view: hovering a position in the genome highlights the corresponding residue on the structure, and vice versa. Color-by-CDS and the peptide lettering give you the protein in the linear track; Protein3d shows where each residue sits in the folded structure.
See the proteins tutorial for the launch routes, installation and connected-view examples.