PlantPromoterDB promoter information of AT3G16640.1

Summary of Gene (AT3G16640.1)

Organism	Arabidopsis thaliana
Chromosome	3
Locus	AT3G16640 TAIR NCBI
Gene model	AT3G16640.1
Description	Encodes a protein homologous to translationally controlled tumor protein (TCTP) from Drosophila. In flies, TCTP functions guanine nucleotide exchange factor in the TOR signaling pathway. TCTP is expressed throughout the plant with highest levels seen in meristematic regions of the shoot and root. Loss of function alleles are not transmitted through the male gametophyte due to defects in pollen tube growth. Hypomorphs, generated through RNAi, are dwarf and have smaller cells. These plants also have defects in lateral and primary root growth as well as root hair growth. The phenotypes are similar to TOR mutants suggesting that TCTP functions in the is pathway in Arabidopsis as well.

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Overview

Focused view (chromosome 3: 5671729-5670530)

`Genome position from initiation codon` `TSS from cDNA TSS information AT3G16640.1 5'->3' (-) Promoter sequence AT3G16650.1 TSS from cDNA TSS information 3'->5' (+) Promoter sequence TSS tag distribution(+) TSS tag distribution(-)`	Your web browser cannot display this window!

ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC

Promoter Summary of AT3G16640.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak G 102 - 5670809 -80

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`G`	102	-	5670809	-80

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone T clone - 5670816 -87

TSS clone C clone - 5670815 -86

TSS clone C clone - 5670814 -85

TSS clone C clone - 5670813 -84

TSS clone C clone - 5670812 -83

TSS clone T clone - 5670811 -82

TSS clone G clone - 5670809 -80

TSS clone T clone - 5670808 -79

TSS clone C clone - 5670805 -76

TSS clone T clone - 5670804 -75

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`T`	clone	-	5670816	-87
TSS clone	`C`	clone	-	5670815	-86
TSS clone	`C`	clone	-	5670814	-85
TSS clone	`C`	clone	-	5670813	-84
TSS clone	`C`	clone	-	5670812	-83
TSS clone	`T`	clone	-	5670811	-82
TSS clone	`G`	clone	-	5670809	-80
TSS clone	`T`	clone	-	5670808	-79
TSS clone	`C`	clone	-	5670805	-76
TSS clone	`T`	clone	-	5670804	-75

Core promoter information

Type Sequence Genome position Position from initiation codon

Strand Start End Start End

initiator Not Available Not Available Not Available

TATA Box ACTATAAATA - 5670842 5670851 -113 -122

Y Patch CGTCTCTCTCCC - 5670791 5670802 -62 -73

GA None None None

Inr None None None

Type	Sequence	Genome position	Position from initiation codon
		Strand	Start	End	Start	End
initiator	Not Available	Not Available	Not Available
TATA Box	`ACTATAAATA`	-	5670842	5670851	-113	-122
Y Patch	`CGTCTCTCTCCC`	-	5670791	5670802	-62	-73
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Position from initiation codon

Strand Start End Start End

REG TTAAAGCCCAAAA - 5670906 5670918 -177 -189

AtREG545 TTAAAGCC      PPDB Motif PLACE Motif

AtREG365 TAAAGCCC     PPDB Motif GCCCA PLACE Motif

AtREG376   AAAGCCCA    PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG407    AAGCCCAA   PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG469     AGCCCAAA PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG529      GCCCAAAA PPDB Motif GCCCA PLACE Motif

REG CCGTTGGA - 5671006 5671013 -277 -284

AtREG554 CCGTTGGA PPDB Motif CCAACGG PLACE Motif YAACKG, CNGTTR

REG AGCCCAACA - 5671027 5671035 -298 -306

AtREG574 AGCCCAAC PPDB Motif GCCCA, CCAACGG PLACE Motif TGGGCY

AtREG543 GCCCAACA PPDB Motif GCCCA PLACE Motif CAACA

REG CCGACCCGAA - 5671050 5671059 -321 -330

AtREG375 CCGACCCG   PPDB Motif CCGAC PLACE Motif CCGAC

AtREG383 CGACCCGA PPDB Motif PLACE Motif

AtREG597   GACCCGAA PPDB Motif GGGACCC PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`TTAAAGCCCAAAA`		-	5670906	5670918	-177	-189
	AtREG545	`TTAAAGCC`		PPDB Motif		PLACE Motif
	AtREG365	`TAAAGCCC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG376	`AAAGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG407	`AAGCCCAA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG469	`AGCCCAAA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG529	`GCCCAAAA`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`CCGTTGGA`		-	5671006	5671013	-277	-284
	AtREG554	`CCGTTGGA`		PPDB Motif	`CCAACGG`	PLACE Motif	`YAACKG, CNGTTR`
REG	`AGCCCAACA`		-	5671027	5671035	-298	-306
	AtREG574	`AGCCCAAC`		PPDB Motif	`GCCCA, CCAACGG`	PLACE Motif	`TGGGCY`
	AtREG543	`GCCCAACA`		PPDB Motif	`GCCCA`	PLACE Motif	`CAACA`
REG	`CCGACCCGAA`		-	5671050	5671059	-321	-330
	AtREG375	`CCGACCCG`		PPDB Motif	`CCGAC`	PLACE Motif	`CCGAC`
	AtREG383	`CGACCCGA`		PPDB Motif		PLACE Motif
	AtREG597	`GACCCGAA`		PPDB Motif	`GGGACCC`	PLACE Motif

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

Not Available Not Available Not Available Not Available Not Available

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
Not Available	Not Available	Not Available	Not Available	Not Available

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone peak T clone + 5671081 AT3G16650.1

TSS clone peak T clone + 5671100 AT3G16650.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone peak	`T`	clone	+	5671081	AT3G16650.1
TSS clone peak	`T`	clone	+	5671100	AT3G16650.1

Core promoter information

Type Sequence Genome position Gene model

Strand Start End

initiator Not Available Not Available Not Available

TATA Box None None None

Y Patch TTCCCTCTCTTCTCTTCC + 5671072 5671089 AT3G16650.1

Y Patch TCTTTCTC + 5671091 5671098 AT3G16650.1

GA None None None

Inr None None None

Type	Sequence	Genome position	Gene model
		Strand	Start	End
initiator	Not Available	Not Available	Not Available
TATA Box	None	None	None
Y Patch	`TTCCCTCTCTTCTCTTCC`	+	5671072	5671089	AT3G16650.1
Y Patch	`TCTTTCTC`	+	5671091	5671098	AT3G16650.1
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG TTTTGGGCTTTAA + 5670906 5670918 AT3G16650.1

AtREG529 TTTTGGGC      PPDB Motif GCCCA PLACE Motif

AtREG469 TTTGGGCT     PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG407   TTGGGCTT    PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG376    TGGGCTTT   PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG365     GGGCTTTA PPDB Motif GCCCA PLACE Motif

AtREG545      GGCTTTAA PPDB Motif PLACE Motif

REG TCCAACGG + 5671006 5671013 AT3G16650.1

AtREG554 TCCAACGG PPDB Motif CCAACGG PLACE Motif YAACKG, CNGTTR

REG TGTTGGGCT + 5671027 5671035 AT3G16650.1

AtREG543 TGTTGGGC PPDB Motif GCCCA PLACE Motif CAACA

AtREG574 GTTGGGCT PPDB Motif GCCCA, CCAACGG PLACE Motif TGGGCY

REG TTCGGGTCGG + 5671050 5671059 AT3G16650.1

AtREG597 TTCGGGTC   PPDB Motif GGGACCC PLACE Motif

AtREG383 TCGGGTCG PPDB Motif PLACE Motif

AtREG375   CGGGTCGG PPDB Motif CCGAC PLACE Motif CCGAC