True sequence type/orientation in a GenBank record?

Peter Frank peter_frankde at yahoo.de
Mon Jun 9 10:27:51 EST 2003


I am unsure about the following issue:
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?


This is a quote from a bioinformatics book:
"The acceptable mol types are DNA, RNA, tRNA, rRNA, mRNA, and uRNA and
are intended to represent the original biological molecule. For
example, a cDNA that is sequenced really represents an mRNA, and mRNA
is the indicated mol type for such a sequence. If the tRNA or rRNA has
been sequenced directly or via some cDNA intermediate, then tRNA or
rRNA is shown as the mol type. If the ribosomal RNA gene sequence was
obtained via the PCR from genomic DNA, then DNA is the mol type, even
if the sequence encodes a structural RNA."

This paragraph confused me quite a bit. If the mol type given in the
definition line is xRNA (x standing for any possible letter or none),
then the sequence given in the GenBank record may actually be the
complementary cDNA sequence. Or it may not if the xRNA has been
sequenced directly? How do I know exactly what sequence I have? 

Peter




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