PlantPromoterDB promoter information of AT3G18860.2

Summary of Gene (AT3G18860.2)

Organism	Arabidopsis thaliana
Chromosome	3
Locus	AT3G18860 TAIR NCBI
Gene model	AT3G18860.2
Description	transducin family protein / WD-40 repeat family protein; FUNCTIONS IN: nucleotide binding; INVOLVED IN: biological_process unknown; LOCATED IN: cellular_component unknown; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: PFU (PLAA family ubiquitin binding) (InterPro:IPR015155), WD40 repeat-like (InterPro:IPR011046), WD40 repeat, region (InterPro:IPR017986), WD40/YVTN repeat-like (InterPro:IPR015943), WD40 repeat (InterPro:IPR001680), PUL (InterPro:IPR013535); BEST Arabidopsis thaliana protein match is: RACK1B_AT (RECEPTOR FOR ACTIVATED C KINASE 1 B); nucleotide binding (TAIR:AT1G48630.1); Has 34215 Blast hits to 17060 proteins in 561 species: Archae - 40; Bacteria - 4260; Metazoa - 15055; Fungi - 7264; Plants - 3193; Viruses - 0; Other Eukaryotes - 4403 (source: NCBI BLink).

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Overview

Focused view (chromosome 3: 6500774-6501973)

`Genome position from initiation codon` `AT3G18860.1 TSS from cDNA TSS information AT3G18860.2 5'->3' (+) Promoter sequence AT3G18850.1 AT3G18850.2 AT3G18850.3 AT3G18850.4 AT3G18850.5 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 AT3G18860.2

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 18 + 6501686 -88

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	18	+	6501686	-88

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone T clone + 6501680 -94

TSS clone C clone + 6501685 -89

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`T`	clone	+	6501680	-94
TSS clone	`C`	clone	+	6501685	-89

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 CCTTATATAAAAG + 6501642 6501654 -132 -120

Y Patch TCTCCTTCCTC + 6501694 6501704 -80 -70

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	`CCTTATATAAAAG`	+	6501642	6501654	-132	-120
Y Patch	`TCTCCTTCCTC`	+	6501694	6501704	-80	-70
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 TAATTACG + 6501435 6501442 -339 -332

AtREG646 TAATTACG ABA PPDB Motif PLACE Motif

REG CGACACGTCATC + 6501532 6501543 -242 -231

AtREG478 CGACACGT     ABA, DREB1Aox, Drought PPDB Motif ACGT PLACE Motif ACGT, ACGTG, ACGTGKC, ACGTGTC

AtREG481 GACACGTC    ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, ACGTGKC, ACGTGTC

AtREG517   ACACGTCA   ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG

AtREG483    CACGTCAT PPDB Motif ACGT PLACE Motif ACGT, ACGTG

AtREG578     ACGTCATC ABA PPDB Motif ACGT PLACE Motif ACGT

REG CAATTGGGCCGGGCTTTGAAAGCCCAC + 6501591 6501617 -183 -157

AtREG647 CAATTGGG                    PPDB Motif PLACE Motif

AtREG418 AATTGGGC                   PPDB Motif GCCCA PLACE Motif

AtREG352   ATTGGGCC                  PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG414    TTGGGCCG                 PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG457     TGGGCCGG                CK PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG404      GGGCCGGG               CK PPDB Motif GCCCA PLACE Motif GGGCC

AtREG559           GGGCTTTG          PPDB Motif GCCCA PLACE Motif

AtREG376                   AAAGCCCA PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG518                    AAGCCCAC PPDB Motif GCCCA PLACE Motif TGGGCY

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`TAATTACG`		+	6501435	6501442	-339	-332
	AtREG646	`TAATTACG`	ABA	PPDB Motif		PLACE Motif
REG	`CGACACGTCATC`		+	6501532	6501543	-242	-231
	AtREG478	`CGACACGT`	ABA, DREB1Aox, Drought	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, ACGTGKC, ACGTGTC`
	AtREG481	`GACACGTC`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, ACGTGKC, ACGTGTC`
	AtREG517	`ACACGTCA`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG`
	AtREG483	`CACGTCAT`		PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG`
	AtREG578	`ACGTCATC`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT`
REG	`CAATTGGGCCGGGCTTTGAAAGCCCAC`		+	6501591	6501617	-183	-157
	AtREG647	`CAATTGGG`		PPDB Motif		PLACE Motif
	AtREG418	`AATTGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG352	`ATTGGGCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG414	`TTGGGCCG`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG457	`TGGGCCGG`	CK	PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG404	`GGGCCGGG`	CK	PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG559	`GGGCTTTG`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG376	`AAAGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG518	`AAGCCCAC`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`

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 - 6501338 AT3G18850.1, AT3G18850.2, AT3G18850.3, AT3G18850.4, AT3G18850.5

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone peak	`T`	clone	-	6501338	AT3G18850.1, AT3G18850.2, AT3G18850.3, AT3G18850.4, AT3G18850.5

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 TTCTTCTTCTTCT - 6501353 6501365 AT3G18850.1, AT3G18850.2, AT3G18850.3, AT3G18850.4, AT3G18850.5

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	`TTCTTCTTCTTCT`	-	6501353	6501365	AT3G18850.1, AT3G18850.2, AT3G18850.3, AT3G18850.4, AT3G18850.5
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG CGTAATTA - 6501435 6501442 AT3G18850.1, AT3G18850.2, AT3G18850.3, AT3G18850.4, AT3G18850.5

AtREG646 CGTAATTA ABA PPDB Motif PLACE Motif

REG GATGACGTGTCG - 6501532 6501543 AT3G18850.1, AT3G18850.2, AT3G18850.3, AT3G18850.4, AT3G18850.5

AtREG578 GATGACGT     ABA PPDB Motif ACGT PLACE Motif ACGT

AtREG483 ATGACGTG    PPDB Motif ACGT PLACE Motif ACGT, ACGTG

AtREG517   TGACGTGT   ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG

AtREG481    GACGTGTC ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, ACGTGKC, ACGTGTC

AtREG478     ACGTGTCG ABA, DREB1Aox, Drought PPDB Motif ACGT PLACE Motif ACGT, ACGTG, ACGTGKC, ACGTGTC

REG GTGGGCTTTCAAAGCCCGGCCCAATTG - 6501591 6501617 AT3G18850.1, AT3G18850.2, AT3G18850.3, AT3G18850.4, AT3G18850.5

AtREG518 GTGGGCTT                    PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG376 TGGGCTTT                   PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG559          CAAAGCCC           PPDB Motif GCCCA PLACE Motif

AtREG404               CCCGGCCC      CK PPDB Motif GCCCA PLACE Motif GGGCC

AtREG457                CCGGCCCA     CK PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG414                 CGGCCCAA    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG352                  GGCCCAAT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG418                   GCCCAATT PPDB Motif GCCCA PLACE Motif

AtREG647                    CCCAATTG PPDB Motif PLACE Motif