Tag: Track Hubs

Coronavirus host gene regulatory elements now annotated by RefSeq Functional Elements

The COVID-19 pandemic has drawn attention to the human host genes associated with SARS-CoV-2 entry and to the elements that regulate expression of these genes. At NCBI, we have prioritized curation of experimentally validated regulatory elements for these genes in the RefSeq Functional Elements project. Our annotations include several enhancers, promoters, cis-regulatory elements and protein binding sites, among other feature types.  We have annotated 236 regulatory features for 27 distinct biological regions in the latest human Annotation Release (109.20200522) including regulatory elements for the ABOACE2, ANPEPCD209CLEC4GCLEC4MCTSL, DPP4,and TMPRSS2 genes

You can view our regulatory element to target gene linkages in the regulatory interactions track using our new track hub that we recently announced.  You can also see the biological regions and features tracks. These have functional and descriptive metadata, including biological region summaries, experimental evidence types, publication support and more.

The example in Figure 1 shows RefSeq Functional Element feature annotation in NCBI’s Genome Data Viewer (GDV) for the ABO gene region (GRCh38, NW_009646201.1: 73,864-103,789) the determiner of the human ABO blood group. A genome-wide association study recently identified non-coding  ABO variants associated with COVID-19 disease severity (PMID:32558485), which map to some of the RefSeq Functional Elements in this region.ABO region showing biological regions in GDVFigure 1. The human ABO gene region in the NCBI GDV displaying the RefSeq Functional Element features.  The biological regions aggregate track shows underlying feature annotation for an ABO upstream enhancer (LOC112637023),  promoter region (LOC112679202),  +5.8 intron 1 enhancer (LOC112679198),  a 3′ regulatory region (LOC112639999), and a +36.0 downstream enhancer (LOC112637025).  Functional Element features include numerous enhancers, promoters, cis-regulatory elements and protein / transcription factor binding sites.

We have more information about RefSeq Functional Elements on our website, including data download and extraction options. Stay tuned to NCBI Insights and other NCBI social media for future announcements about RefSeq Functional Elements!

dbVar clinical and common structural variants track hub now available

dbVar, NCBI’s database of large-scale genetic variants, has a new track hub for viewing and downloading structural variation (SV) data in popular genome browsers. Initial tracks include Clinical and Common SV datasets. dbVar’s new track hub can be viewed using NCBI’s Genome Data Viewer through the “User Data and Track Hubs” feature (Figure 1) and other genome browsers by selecting “dbVar Hub” from the list of public tracks or by specifying the following URL.



Figure 1. Loading the dbVar track hub in the Genome Data Viewer. The Track Hubs feature on the left-hand column of the browser allow you to add the track by searching for it or by entering the direct URL. You can select the specific tracks —  for example, “NCBI curated common SVs: All populations” — to load from the Configure Track Hubs dialog. Continue reading “dbVar clinical and common structural variants track hub now available”

Bulk track hub settings now in Genome Data Viewer

You now have access to bulk settings options for track hubs  in the Genome Data Viewer (GDV) and Sequence Viewer. These settings allow you to pick the default tracks that load into the viewer from your chosen track hub.  You can access the bulk options menu for by clicking on the collapsed menu  or “hamburger” icon (stack of horizontal bars) at the right end of the track grouping in the Configure Track Hubs dialog (Figure 1).Bulk_SettingsFigure 1. The Configure Track Hubs dialog in GDV. You can activate the bulk settings menu for a connected track hub by clicking on hamburger icon at the right of the track grouping.  Clicking Select Default tracks checks on all of the tracks in that grouping, Smoothed PhyloCSF in this case.  Continue reading “Bulk track hub settings now in Genome Data Viewer”