When I input the word titin in UCSC genome I get multiple relevant hits as shown here. Specifically if I click on
I get a DNA template strand that goes from chr2:178,525,989-178,807,423 . My presumption is that this is the mRNA strand. Please correct me if this is the cDNA.
Now my confusion comes when I refer to titin gene from NCBI RefSeq. The sequence is 178525989..178807423, complement. And when I look at the exact NCBI's FASTA sequence, it is the reverse complement of that from UCSC Genome. So is NCBI's FASTA sequence just the template (non-coding) DNA?
As an extension to this confusion, when we're trying to analyze protein-DNA binding sites, do we usually look at the mRNA/cDNA or the non-coding template DNA?
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NCBI - Sample GenBank Record:
https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
UCSC-manual for gene fishing:
http://hgw2.cse.ucsc.edu/training/ucscGeneFishing.pdf
a Biostars - post:
In RNA-seq data, how to find whether the mRNA is on the forward strand or reverse strand?
Quantification of Gene Expression and more...
http://gene-quantification.de/mrna.html#cdna