extracting the mRNA sequences of the canonical isoforms
Bogdan Tanasa
Luis Nassar
Hello, Bogdan.
Thank you for your continued interest in the Genome Browser.
For both mm10 and hg38 you can use the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables), making the selections
group: Genes and Gene Predictions
group: GENCODE VM23 (mouse) or GENCODE v32 (human)
group: knownCanonical
Then:
output format: Sequence
To extract the mRNA sequences for a canonical isoform for each gene. Note that if you are using RefSeq, you can use the RefSeq Select+Mane track (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&c=chrX&g=refSeqComposite) which are a list of canonical transcripts released by NCBI. You can follow the steps above to extract the sequence, or get the raw files directly from NCBI (https://www.ncbi.nlm.nih.gov/refseq/refseq_select/).
Secondary structure information can be found in the UniProt track (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=uniprot), specifically the Structure subtrack which contains primary and secondary structure annotations. These annotations are available for both hg38 and mm10.
I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.
Lou Nassar
UCSC Genomics Institute
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