Related Experiment Video
Updated: Jun 25, 2026

Breeding by Design for Functional Rice with Genome Editing Technologies
Published on: January 3, 2025
Genome-wide analysis of rice (Oryza sativa L. subsp. japonica) TATA box and Y Patch promoter elements
1Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynská dolina B-1, 842 15 Bratislava, Slovakia. civan@fns.uniba.sk
Abstract:
The TATA box is one of the best characterized transcription factor binding sites. However, it is not a ubiquitous element of core promoters, and other sequence motifs such as Y Patches seem to play a major role in plants. Here, we present a first genome-wide computational analysis of the TATA box and Y Patch distribution in rice (Oryza sativa L. subsp. japonica) promoter sequences. Utilizing a probabilistic sequence model, we ascertain that only approximately 19% of rice genes possess the TATA box, but approximately 50% contain one or more Y Patches in their core promoters. By computational processing of identified elements, we generated extended TATA box and Y Patch nucleotide frequency matrices capable of predicting these motifs in plants with a high degree of confidence.
More Related Videos
Related Concept Videos
The Eukaryotic Promoter Region
The Eukaryotic Promoter Region
Genome-wide Association Studies-GWAS
GWAS does not require the identification of the target gene involved in...
Ribosome Profiling
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
DNA Microarrays
Reporter Genes
Commonly used reporter...

