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UCSC Genome Browser

VERIFIED

## Connections

genomics visualization conservation browser

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

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