Upstream regulatory architecture of rice genes: summarizing the baseline towards genus-wide comparative analysis of regulatory networks and allele mining

Rice

Table 1 List of experimentally or computationally defined upstream regulatory sequences, and their cognate transcriptional regulators that determine basal and constitutive expression of rice genes

Cis-element	Core motif	Transcriptional regulator	Biological function
*TATA-box*	CTATAWAWA	TATA-binding protein (OsTBP2)	Core promoter; Pre-initiation complex
*Y-Patch*	CYTCYYCCYC	Unknown	Core promoter; Pre-initiation complex
(Pyrimidine patch)
*Actin (Act) elements*	CCCAA (tandem octa-repeats)	Unknown	Fine-tuner of constitutive OsAct genes
	CAAT (CCAT-box)	Unknown	Positive regulator of constitutive OsAct genes
	GTGAC (intronic)	Unknown	Positive regulator of constitutive OsAct genes
	CCGCGTTGGC (ABA-responsive)	Unknown	Positive regulator of constitutive OsAct genes
	ATTAAT, CACGTA (light-responsive)	Unknown	Positive regulator of constitutive OsAct genes
	(A/T)GCC (dideca-repeats)	Unknown	Positive regulator of constitutive OsAct genes
*Ubiquitin (Ubi) elements*	GTTGTGGTTTG	Unknown	Positive regulator of constitutive OsUbi genes

List was based on seminal studies published in the literature and annotated in public databases.