UCSC Genome Browser

Gold-standard genome visualization tool. Shows genes, variants, conservation, regulation, and 100+ annotation tracks aligned to the genome.

What It Does

• Visualize any genomic region with dozens of annotation tracks
• Conservation scores (PhyloP, PhastCons) across 100 vertebrates
• ENCODE regulatory data (DNase, histone marks, TF binding)
• Repeat masker (important for STRC/STRCP1 region)
• Custom track upload

How to Use

Web

1. Go to https://genome.ucsc.edu
2. Search: “STRC” or “chr15:43599563-43618800”
3. Enable tracks: Conservation (100 Vert.), ENCODE Regulation, RepeatMasker
4. Zoom in/out to explore context

Direct Link (STRC Region)

https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr15:43599563-43618800

API (Table Browser)

# Get PhyloP scores for STRC region
curl "https://api.genome.ucsc.edu/getData/track?genome=hg38&track=phyloP100way&chrom=chr15&start=43599563&end=43618800"

bigWig Files (PhyloP, PhastCons)

# Download conservation scores
curl -O https://hgdownload.soe.ucsc.edu/goldenPath/hg38/phyloP100way/hg38.phyloP100way.bw
# Query with UCSC tools
bigWigSummary hg38.phyloP100way.bw chr15 43600000 43601000 10

Verified Status

VERIFIED — STRC region visible. Conservation tracks show high conservation at E1659 position. RepeatMasker confirms segmental duplication (STRC/STRCP1).

STRC Research Usage

• STRC Cross-Species Conservation Analysis — PhyloP/PhastCons scores
• STRC Pseudogene Problem — segmental duplication visualization
• Conservation at E1659: high PhyloP score across 100 vertebrates

Results (April 2026)

• Enhancer mapping DONE via Ensembl: 2 enhancers + 1 promoter in STRC region (see Ensembl REST API)
• STRC vs STRCP1: segmental duplication visible in RepeatMasker track
• Next: custom variant track (upload 427 ClinVar STRC variants as BED), Hi-C contact maps, CpG island analysis

Connections

• Ensembl REST API [see-also] — programmatic equivalent
• AlphaGenome [see-also] — predicts same regulatory features
• STRC Cross-Species Conservation Analysis [used-in] 68|- STRC Pseudogene Problem [used-in]

STRC E1659A Results

Web-based genome visualization. No direct API for variant scoring. Tested: 2026-04-08