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Variant sequences are identified and enumerated within the unselected and selected libraries.
Sequences shared between multiple isoforms are retained as unique contigs, and any adjacent variant sequences are split off as their own unique contigs.
Twenty different variant sequences are then created by introducing ten different sets of deletions and ten different sets of tandem duplications at known locations.
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Four double (D4Y+M7K, D4Y+S11K, P5Y+M7K, P5Y+S11K), two triple (D4S+P5Y+M7K, D4S+P5Y+S11K) and one quadruple (D4S+P5Y+M7K+S11K) variant sequences were characterized with SPR.
We found that some early CTL responses could cross-recognize their variants with high magnitudes even before the variant sequences were abundant in the viral population.
Such tags harboring homopolymer stretches frequently carry similar sequences with one or two base changes in the original SuperSAGE data, while such variant sequences were not observed in HT-SuperSAGE (Table S4).
The relative affinity of ERRα for the wild-type and variant sequences was assessed in competition binding studies using increasing amounts of unlabeled G or A dsDNA probe to displace wild-type G probe in the EMSA binding reactions.
Predicted EZH2 splice variant sequences were curated from National Center for Biotechnology Information.
Variant sequences were identified in the invertebrate MACITs (see below).
Those variant sequences were also mainly contained within tandem arrays.
The library of thioredoxin variant sequences was constructed by using gene assembly mutagenesis [ 22].
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