Question: Confusion in distinguishing between (+) and (-), cDNA and mRNA using RefSeq and UCSC genome
0
gravatar for pairwiseseq
16 months ago by
pairwiseseq10
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:

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

ADD REPLYlink modified 16 months ago • written 16 months ago by natasha.sernova3.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 681 users visited in the last hour