2.4 UCSC genome browser

What does the human reference genome actually look like? We can view it in the UC Santa Cruz (UCSC) genome browser, an interactive website for viewing genomes – both the human reference and reference genomes for several other species.

The browser also displays genome annotations, such as the locations of genes and clinically relevant genetic variants.

Go to the UCSC genome browser.

2.4.1 Homepage

There are a few key areas of this page:

Browse/Select Species – choose the species
Human Assembly – choose the version of the human reference genome
Position/Search Term – type in a specific position (ex: chr2:25160915), region (ex: chr1:100000-200000), or gene name (ex: HLA-A)

Fig. 5. UCSC genome browser homepage.

In Position/Search Term, type in a gene you’re interested in and hit enter.

Why are there different versions of the reference genome?

You may have noticed that the name of the reference genome we’re using is GRCh38 or hg38, which stands for Genome Reference Consortium Human Build 38 – version 38 of the reference genome.

Over time, the Genome Reference Consortium makes improvements to the reference genome by closing gaps, fixing problems, and resolving repetitive regions. hg38, the most recent version, was released in 2013.