Question: Confusion in distinguishing between (+) and (-), cDNA and mRNA using RefSeq and UCSC genome
gravatar for pairwiseseq
16 months ago by
pairwiseseq10 wrote:

When I input the word titin in UCSC genome I get multiple relevant hits as shown here. Specifically if I click on

TTN (uc021vtb.4) at chr2:178525989-178807423 - Homo sapiens titin (TTN), transcript variant N2-B, mRNA. (from RefSeq NM_003319)

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?

sequence genome • 538 views
ADD COMMENTlink written 16 months ago by pairwiseseq10

NCBI - Sample GenBank Record:

UCSC-manual for gene fishing:

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...

ADD REPLYlink modified 16 months ago • written 16 months ago by natasha.sernova3.4k
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