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Pipeline publication

[…] d Rab39b genes that promote cell proliferation and migration. These enhancers are directly bound by Twist1 in developing heart valves, and conserved E-box consensus sequences were identified that are required for Twist1-responsive gene expression. Unlike other bHLH transcription factors, whose transcriptional activity requires paired E-box consensus sequences, Twist1 appears to only require one E-box consensus site to promote gene expression . With the exception of Cdh11, each of the ECRs identified in this study contains a single E-box consensus sequence. Conversely, Cdh11-Intron1 contains 2 E-box consensus sequences, however, Twist1 binding and gene induction was detected only for E-box1. rVista2.0, oPOSSUM, DiRE, and Trafac analysis for transcription factor binding sequences revealed that each identified enhancer has additional conserved transcription factor binding consensus sequences –. Enhancer sequences identified in these studies are located in upstream genomic regions, proximal to the gene, in 3′UTR, and intronic gene regions, consistent with locations of previously identified enhancers within the genome . Interestingly, regions within close proximity to the E-box consensus site are enriched for A/T sequences, relative to more distal flanking regions. However, no common binding sequences within close proximity to the E-box consensus site of the Twist1 responsive ECRs were identified (, , […]

Pipeline specifications

Software tools rVISTA, oPOSSUM, DiRE