New interaction data, downloads and track hub available for RefSeq Functional Elements 

We’ve added several new enhancements to the RefSeq Functional Elements dataset, which provides genome annotation and richly annotated RefSeq and Gene records for experimentally validated non-genic functional regions in human and mouse. Read on to see what we’ve done!

New interaction data

Non-genic biological regions now link to target genes and other biological regions when there is experimental evidence for interactions. We provide interaction data for regulatory interactions, typically between a gene regulatory element and a target gene, and for recombination partner interactions.

You can download this data in bigInteractbigBed or other formats as detailed othe RefSeq Functional Elements website, or you can visualize it in the regulatory interactions and recombination partner tracks in our new track hub.

New download files for biological regions and features

To make it easier to untangle our non-genic annotations from gene-related annotations, we now provide biological regions and features in standalone bigBed files, which also include key metadata. Find out more about these files on our the RefSeq Functional Elements website, and be sure to check out our Feature and Metadata Extraction Examples.

To make it easier to untangle non-genic annotations from gene-related annotations, we now provide biological regions and features in standalone bigBed files, which also include key metadata. Find out more about these files on our website, and be sure to check out our Feature and Metadata Extraction Examples.

New track hub

We are delighted to announce our new track hub, RefSeqFE Hub, for biological regions, features, regulatory interactions and recombination partners. This one-stop shop greatly expands the range of genome browsers you can view our data in.

For example, the aesthetic UCSC bigInteract track format lets you see how functional elements relate to target genes or how recombination regions pair up with each other, view the hierarchical biological region to underlying feature structure of our dataset, and provides a gateway for downloading our annotations and metadata.

Fig5FETrackHub_7-20
Figure 1. UCSC Genome Browser image displaying tracks from the RefSeqFE Hub at the human alpha-globin locus.

Connect to the track hub on a compatible genome browser by using the following URL: https://ftp.ncbi.nlm.nih.gov/refseq/FunctionalElements/trackhub/hub.txt.

Find out more about RefSeqFE Hub in our track hub overview document or on our website.

New GFF3 file source indicator

You can now easily identify and extract the functional element features from our GFF3 annotation files based on the new ‘RefSeqFE’ source indicator in column 2. Check out the feature extraction examples on our website.

We look forward to providing further data enhancements in the future. Stay tuned to NCBI Insights and other NCBI social media for future announcements about RefSeq Functional Elements.

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