True sequence type/orientation in a GenBank record?

Philipp Pagel philipp.pagel at gmx.de
Wed Jun 11 16:36:27 EST 2003


Peter Frank <peter_frankde at yahoo.de> wrote:
> Assuming I found a GenBank record with a sequence of interest and the
> definition line designates the sequence as mRNA or some other type of
> RNA, then is the sequence given really the RNA sequence or is it the
> sequence of the complementary cDNA?

cDNA is not complementary to the RNA sequence, it's an exact copy (well,
ideally). The only difference is the use of U instead of T in the RNA.

The first strand is synthesized by reverse transcriptase and is of
course complementary. The second strand (synthesized by DNA polymerase)
is identical to the original RNA. The sequence of the latter is given in
cDNA sequences.

The paragraph you quoted just gives examples of the simple statement
that you should call DNA "DNA" and RNA "RNA" regardeless of how exactly
you got the sequence (directly sequenced or with a copy step in between)

cu
	Philipp


-- 
Dr. Philipp Pagel                                Tel.  +49-89-3187-3675
Institute for Bioinformatics / MIPS              Fax.  +49-89-3187-3585
GSF - National Research Center for Environment and Health
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85764 Neuherberg
Germany




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