mRNA sequence is submitted to the nucleotide database of NCBI. But can we determine from which sequence of the chromosome or gene the mRNA is coming. Because in some cases when we are trying to align the genomic and mRNA sequence,they are aligning completely but sometimes the reverse complement of the mRNA is aligning completely. So how to determine or describe this strand issue?
The submitted sequence can be in sense stand or its complement for mRNA sequences. Typically this depends on if the submitter has submitted the raw sequence obtained by sequencing a cDNA library, in which case the submission will be a mixture of sense and complementary strands, or if they have done some post processing to determine the appropriate orientation for each sequence. In many cases this is as simple as looking for poly-A tails or poly-T headers and orientating appropriately, alternatively examination of translation products and comparison with known homologs or predicted genes can help deduce the orientation.
The mRNA entries representing EST sequences have the same issues. It may be useful to perform clustering on larger EST submissions in order to derive more complete transcripts from the set of ESTs, rather then dealing with them directly.
The mRNA sequences don't normally contain the strand information. That information will typically be held within an annotation file for the organism (presuming that a given mRNA is in said annotation, of course).