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?