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Genome Browser

Where genes live on a chromosome: stacked tracks layer annotations, expression, and conservation along a linear coordinate axis.

A genome browser shows a stretch of DNA with multiple tracks of information at the same coordinates: gene models, regulatory regions, expression, conservation, variants, and more.

The horizontal axis is genomic position in base pairs. In a browser search box, coordinates are usually displayed as 1-based, fully closed intervals, like chr7:55,000,001-55,500,000. Many file formats underneath the browser, especially BED and bedGraph, use 0-based, half-open intervals, where the same 500 kb span is written as chr7 55000000 55500000. That one-base shift at the left edge is small enough to miss and large enough to break an analysis.

Alignment is the point: when an expression peak lines up with a gene, a promoter feature, a conserved segment, and a variant, the evidence begins to converge. The browser does not decide what it means. It gives each piece of evidence the same coordinate ruler.

A simulated locus

gene model RNA signal CpG island conservation variant

Figure 1. Interactive genome browser. Drag to pan, scroll to zoom, or use the buttons. Hover the panel for a crosshair and click any gene, CpG island, or variant for details. The label above uses browser-style 1-based coordinates; the simulated intervals are stored internally as half-open spans.

Genes, regulatory elements, variants, and epigenetic marks all live at specific coordinates. Aligning them on a common axis reveals relationships no single dataset can show alone.

Reading the tracks

Gene models (blue arrows): Thick blocks are exons, thin lines are introns, and paler blocks are untranslated regions. Exons are retained in mature RNA; only the coding part becomes protein.
Expression (area chart): RNA-seq coverage across the locus. A peak over a transcript is evidence that RNA from that transcript is abundant in the sample, not proof of protein abundance.
CpG islands (green): CG-rich regions, often near promoters. Promoter CpG methylation can be associated with lower transcription, but the island itself is not a switch.
Conservation (purple): Similarity across species. High conservation is evidence of constraint, not a direct annotation of function.
Variants (brown ticks): Sample or population differences at precise positions. The browser can show where they land, but interpretation needs allele frequency, predicted effect, and context.

Figure 2. Anatomy of a gene model. Exons (thick) are the parts that become protein. Introns (thin lines) are spliced out. The arrow indicates transcription direction. UTRs (medium) are transcribed but not translated.

Stacked tracks

Each track alone is partial. Stacking them aligns evidence at the same coordinate.

Figure 3. A zoomed-in region where signals converge: expression over the transcript, a CpG island at the promoter, and higher conservation over exons. The highlighted span is clipped to the visible window, as a real browser track would be.

Genome browsers show one chromosome at a time. Inter-chromosomal events (translocations, fusions, long-range contacts) need the circos plot.