The pTandem1 vector from Novagen has a CMV promoter, exon1, exon2 (consisting of a bunch of tags followed by and IRES sequence and sprinkled with restriction sites for subcloning GOI). Exon1 and Exon2 are separated by a short intron. Exon 1 appears to have a start and stop codon that are in frame with each other. What exactly is exon1 and why is it there?
From the map it seem that exon1 will be untranslated, I didn't look to closely but I assume the ATG doesn't have a KOZAK sequence around it. In general you need an intron since RNA export from the nucleus is coupled to splicing so unless you have a specific mechanism, like retroviruses Rev protein, unspliced transcripts will not be exported and as a result won't get translated. Hope that answer your question.
The first exon and first intron contain often binding sites for the binding of transcrition factors acting as enhancers as those located before promoter. This maintains chromatin in and open configuration around the transcription start site.
The introns favor mRNA transfer from nucleus to cytoplasm.
The ATG codon in the first exon cannot be used as an initiation codon s it is too close to the transcription start site. At least 80 nucleotides are needed before ATG.
The ATG is not after the Kozak consensus sequence GCCA/GCCATG , thus it cannot be recognized as an initiation codon.
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