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I was wondering if anyone on this forum has experience with the SMARTer RACE Kit from Clontech. I have experienced on some occasions, that I do not get the full SMARTer Oligo adapter sequence from Sanger seq, making it difficult to trust wether the true 5'-end is sequenced.
As an example.
Seq .1 : ctaatacgac tcactatagg gcaagcagtg gtatcaacgc [agag [gtgtcagcttccc]]
Seq. 2 : ctaatacgac tcactatagg gcaagcagtg gtatcaacgc agag tac atggg [gtgtggga]
SMARTer Oligo: ctaatacgac tcactatagg gcaagcagtg gtatcaacgc agag tac-XXXXX
[ ] denote sequence from gene of interest.
Both sequences shown were sequenced from both sides and quality good. Seq. 1. does not contain the full adapter sequence. In the lab we have experienced this in independent experiments.
As an example.
Seq .1 : ctaatacgac tcactatagg gcaagcagtg gtatcaacgc [agag [gtgtcagcttccc]]
Seq. 2 : ctaatacgac tcactatagg gcaagcagtg gtatcaacgc agag tac atggg [gtgtggga]
SMARTer Oligo: ctaatacgac tcactatagg gcaagcagtg gtatcaacgc agag tac-XXXXX
[ ] denote sequence from gene of interest.
Both sequences shown were sequenced from both sides and quality good. Seq. 1. does not contain the full adapter sequence. In the lab we have experienced this in independent experiments.