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Genomatix GEMS Launcher: Strategies


Full length cDNA

Many biologists regard cDNAs as full length when they contain the complete reading frame, i.e. up to the ATG start codon. However, a real full length cDNA reaches up to the transcriptional initiation point and contains the 5'-untranslated region (5'-UTR).

mRNA


This can make a big difference with regard to the promoter location although this 5'-UTR usually encompasses only 50 to 200 nucleotides of the mRNA. However, if the first exon is untranslated (not too unusual) there is a chance that the genomic sequence contains a huge intron of 10kb or more within this 5'-UTR.

cDNA mapping

In the case shown above any cDNA lacking the first exon is not suitable for promoter mapping.

Note: First introns of > 20kb have been observed!

Note: There may also exist several non-coding exons.
For example, the human RCC1 gene ( D00591) was found to have 14 exons, 8 of which (starting from the seventh one) code the RCC1 protein (Furuno N. et al., 1991, MEDLINE: 92120669). The first 6 exons (about 23.000 base pairs in length including the introns) are non-coding.