I wrote a similar post for downloading sequences of yeast genes.
Basically I needed to do some analysis on the upstream promoter region of about 1200 human genes.
I wasn’t gonna download them one-by-one, and I didn’t want to get a database dump of the whole genome.
Luckily, there’s UCSC’s hgTable! (I love you guys)
So it hit up.
Paste in your list of genes.
Note: No commas at the end of lines
Submit to get your sequences!
You can even toggle between many options, like genomic DNA or protein sequence, or a certain number of bases upstream and downstream of the gene.
The output will be in one giant FASTA file so if you’re getting the sequences of a lot of genes, you better download the gzip, ’cause it’ll take forever to load it in your browser (it’s on the order of 100MB).
Another note: you might get more than one sequence per gene, depending on what tables, groups, and tracks you select.