UCSC Genome Browser

The UCSC Genome Browser is a public, freely available, open-source web-based graphical viewer for the display of genome sequences and their annotations.

[UCSC Genome Browser @GenomeBrowser]

Some mobile elements are still jumping!

New Mobile Element Insertions tracks show polymorphic Alu, L1 and SVA sites on hg38, hg19 and T2T-CHM13, from long reads, short-read cohorts and 32 published studies.

Look at our news for more: https://t.co/IN69U7tGpy

[UCSC Genome Browser @GenomeBrowser]

New public hub: Sci-ModoM RNA modification sites. 7.9M m6A, pseudouridine, m5C and 2'-O-methylation sites on hg38 and mm39, with coverage and percent modified. Thanks to @ItsRMaP1 and the Dieterich Lab.

Explore hub: https://t.co/s1EN5q8fV7
More hubs: https://t.co/bnAvWX6a6F

[UCSC Genome Browser @GenomeBrowser]

New on hg38: @GoogleDeepMind AlphaGenome Variant Impact (AVI) scores, all 8.8 billion possible single-base changes. It scores non-coding DNA too, flagging things like the TERT promoter mutations common in cancer.

See our news for more: https://t.co/lMx2PngE0F

[UCSC Genome Browser @GenomeBrowser]

See how any mouse gene's expression shifts through development! New ENCODE Expression default tracks on mm10/mm39 show bulk RNA-seq across 17 tissues and 8 stages, from embryonic day 10.5 to birth.

See our news for more info: https://t.co/tPP5X2rkaK

[UCSC Genome Browser @GenomeBrowser]

We have a new facet interface for composite tracks! A faceted composite is an alternative display with facets along the left side that filter the collection, while a paginated table on the right lists matching subtracks.

Read more: https://t.co/nAUIxwS1Zh

[UCSC Genome Browser @GenomeBrowser]

We are excited to announce the gnomAD v4.1.1 and MPC tracks on the UCSC Genome Browser. This release updates gnomAD's variant and constraint tracks and adds new MPC tracks predicting missense deleteriousness.

Learn more at: https://t.co/PCunYTABcz

[UCSC Genome Browser @GenomeBrowser]

@ENCODE_NIH GRAMMAR is now on the UCSC Genome Browser! 🧬 Base-resolution deep learning predictions, sequence contribution scores & motif instances (BPNet, ChromBPNet, ProCapNet, ReporterNet) across thousands of ENCODE experiments. Explore on hg38: https://t.co/3Qp6IJUP6Q

[UCSC Genome Browser @GenomeBrowser]

ClinPred pathogenicity score track for hg19 and hg38 is now available!

ClinPred is a machine-learning predictor of pathogenicity for nonsynonymous SNVs, combining existing pathogenicity scores with population allele frequency from gnomAD.

Learn more at: https://t.co/4s7AhHs2SF

[UCSC Genome Browser @GenomeBrowser]

Together, these tracks represent the final ENCODE Phase 4 data release integrated into the browser and cover chromatin accessibility, histone modification and CTCF ChIP-seq, transcription factor binding, and transcription across thousands of individual biosamples.

[UCSC Genome Browser @GenomeBrowser]

We are excited to announce the ENCODE4 data collection on the UCSC Genome Browser for hg38 and mm10. This release consists of two major components: the ENCODE Registry of cCREs and the new ENCODE4 Regulation container. Learn more at: https://t.co/ZbCbQk0uXd

[UCSC Genome Browser @GenomeBrowser]

🧬 New: Long-read Structural Variants tracks for human (hg38 & T2T-CHM13/hs1). SV callsets from 14 long-read studies merged into ~2.3M sites, so you can compare structural variation across populations. See our news to learn more: https://t.co/ynPnbiY2io

[UCSC Genome Browser @GenomeBrowser]

26 years ago today, the first public assembly of the human genome went online at UC Santa Cruz. Today, we release version 500 of the UCSC Genome Browser.

From Jim Kent's first assembly to thousands of genomes, the data is still free and open.

https://t.co/rNzeKjgfhl

[UCSC Genome Browser @GenomeBrowser]

Which variants are common in your ancestry but rare globally?

New on hg38: SNV Frequencies. Over 1.2 billion variants pooled from ~1.5M people across 30+ cohorts, including population references, biobanks, and disease case/control studies.

Learn more: https://t.co/LzJBbu8p7H

[UCSC Genome Browser @GenomeBrowser]

We are happy to announce Release 3 of the Varaico Variants and Varaico Variants (suppl) tracks for hg38/hg19. This release contains a precision improvement and an update of the underlying literature.

Learn more at: https://t.co/0ZyeQ0Op7x

[UCSC Genome Browser @GenomeBrowser]

Associated publication: Riesenberg et al., Nature Communications (2025) — https://t.co/2nuqU5cmHb

[UCSC Genome Browser @GenomeBrowser]

We are pleased to announce our new public hub, EVA score for synthetic gRNA efficiency for hg38, hg19 & mm39. Named after MPI-EVA, it predicts on-target SpCas9 cutting activity using chemically synthesized gRNAs: https://t.co/PQnxFyUg87.

Thanks to Tomislav Maricic at MPI-EVA.

[UCSC Genome Browser @GenomeBrowser]

New on the UCSC Genome Browser: a Non-canonical ORFs track collection for hg38!

Explore 1M+ ORFs outside annotated coding genes — uORFs, sORFs & more — from UTRannotator, GENCODE, 5ULTRA, nuORFdb, MetamORF & OpenProt, all colored by Kozak strength.

https://t.co/G9nHOV4sbo

[UCSC Genome Browser @GenomeBrowser]

New on the UCSC Genome Browser (hg38): MPRA tracks. MPRA Base catalogs 40,938 experimentally tested enhancer elements across 6 cell lines; MPRAVarDB scores 239,028 allelic variant effects from 18 studies. Great for GWAS fine-mapping. Learn more: https://t.co/hoQ2c6FKp5

[UCSC Genome Browser @GenomeBrowser]

Two new variant-impact tracks from Illumina on the UCSC Genome Browser: PrimateAI-3D scores every coding missense variant (hg38/hg19); PromoterAI scores every non-coding substitution near transcription start sites (hg38). See our news for more: https://t.co/FMNe3en9L5

[UCSC Genome Browser @GenomeBrowser]

Check out our new NMD Escape tracks on hg38! They predict where premature stop codons escape nonsense-mediated decay. Useful for interpreting truncating variants under ACMG PVS1. Includes GENCODE+RefSeq rulesets + predictive scores. See our news for more: https://t.co/4i01Pn6x5U