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These simplistic descriptors have been successfully applied to human gene regulatory sequence prediction, enhancer identification, etc.
Thus, it likely represents a previously unidentified essential regulatory sequence.
For instance, a given letter x may occur in the regulatory sequence of gene i.
Further, some of these transcripts appear to have a common upstream regulatory sequence.
The PHO5 promoter contains three regulatory sequence elements, two upstream activation sequences, UASp1 and UASp2, and a TATA box.
These "alternative exons" maintain conserved sequences for human-mouse orthology and conserved regulatory sequence elements for conserved alternative splicing.
The distribution of GCAG sites in 26695 genome has been determined by regulatory sequence analysis tools (RSAT-http://rsat.ulb.ac.be/rsat/).ulb.ac.be/rsat/
How binding sites are arranged in a regulatory sequence is an important, but poorly understood aspect of combinatorial gene regulation.
Thus, the Roc1b regulatory sequence appears to confer expression in the testes that cannot be duplicated by the Roc1a promoter.
Transcription rate data, which is free from interference by mRNA degradation, should be a better input in regulatory sequence analysis.
Our method leverages sequence motifs within a known regulatory sequence to identify co-regulated sequences without explicitly defining binding sites.
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