PlantPromoterDB promoter information of AT4G23820

Summary of Gene (AT4G23820)

Organism	Arabidopsis thaliana
Chromosome	4
Locus	AT4G23820 TAIR NCBI
Gene model	AT4G23820
Description	glycoside hydrolase family 28 protein / polygalacturonase (pectinase) family protein; FUNCTIONS IN: polygalacturonase activity; INVOLVED IN: carbohydrate metabolic process; LOCATED IN: endomembrane system; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Pectin lyase fold/virulence factor (InterPro:IPR011050), Glycoside hydrolase, family 28 (InterPro:IPR000743), Pectin lyase fold (InterPro:IPR012334), Parallel beta-helix repeat (InterPro:IPR006626); BEST Arabidopsis thaliana protein match is: glycoside hydrolase family 28 protein / polygalacturonase (pectinase) family protein (TAIR:AT5G41870.1); Has 2405 Blast hits to 2400 proteins in 312 species: Archae - 2; Bacteria - 563; Metazoa - 8; Fungi - 896; Plants - 841; Viruses - 0; Other Eukaryotes - 95 (source: NCBI BLink).

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Overview

Focused view (chromosome 4: 12401050-12399851)

`Genome position from initiation codon` `AT4G23820.1 TSS from cDNA TSS information AT4G23820 5'->3' (-) Promoter sequence AT4G23840.1 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 AT4G23820

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 64 - 12400091 -41

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	64	-	12400091	-41

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone A clone - 12400111 -61

TSS clone A clone - 12400091 -41

TSS clone G clone - 12400090 -40

TSS clone C clone - 12400083 -33

TSS clone T clone - 12400077 -27

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`A`	clone	-	12400111	-61
TSS clone	`A`	clone	-	12400091	-41
TSS clone	`G`	clone	-	12400090	-40
TSS clone	`C`	clone	-	12400083	-33
TSS clone	`T`	clone	-	12400077	-27

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 None None None

Y Patch CCTCTCTTC - 12400058 12400066 -8 -16

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	None	None	None
Y Patch	`CCTCTCTTC`	-	12400058	12400066	-8	-16
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 TCACGTGTA - 12400165 12400173 -115 -123

AtREG628 TCACGTGT DREB1Aox PPDB Motif ACGT PLACE Motif ACGT, ACGTG, CACGTG, ACACNNG

AtREG453 CACGTGTA ABA, DREB1Aox PPDB Motif ACGT PLACE Motif ACGT, ACGTG, ACACNNG

REG TATGGCCCGTT - 12400177 12400187 -127 -137

AtREG479 TATGGCCC    PPDB Motif GCCCA PLACE Motif GGGCC

AtREG401    GGCCCGTT PPDB Motif AAACG(C/G), ACGGGC, CCAACGG PLACE Motif GGGCC

REG CTTATTGGGCCACTAAAGCCCAAAC - 12400200 12400224 -150 -174

AtREG611 CTTATTGG                  PPDB Motif PLACE Motif

AtREG417 TTATTGGG                 PPDB Motif GCCCA PLACE Motif

AtREG355   TATTGGGC                PPDB Motif GCCCA PLACE Motif

AtREG352    ATTGGGCC               PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG420     TTGGGCCA              PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG445      TGGGCCAC             PPDB Motif GCCCA PLACE Motif GCCAC, GGGCC, TGGGCY

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

AtREG474                  GCCCAAAC PPDB Motif GCCCA PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`TCACGTGTA`		-	12400165	12400173	-115	-123
	AtREG628	`TCACGTGT`	DREB1Aox	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, CACGTG, ACACNNG`
	AtREG453	`CACGTGTA`	ABA, DREB1Aox	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, ACACNNG`
REG	`TATGGCCCGTT`		-	12400177	12400187	-127	-137
	AtREG479	`TATGGCCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG401	`GGCCCGTT`		PPDB Motif	`AAACG(C/G), ACGGGC, CCAACGG`	PLACE Motif	`GGGCC`
REG	`CTTATTGGGCCACTAAAGCCCAAAC`		-	12400200	12400224	-150	-174
	AtREG611	`CTTATTGG`		PPDB Motif		PLACE Motif
	AtREG417	`TTATTGGG`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG355	`TATTGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG352	`ATTGGGCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG420	`TTGGGCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG445	`TGGGCCAC`		PPDB Motif	`GCCCA`	PLACE Motif	`GCCAC, GGGCC, TGGGCY`
	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`
	AtREG474	`GCCCAAAC`		PPDB Motif	`GCCCA`	PLACE Motif

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak G 4 + 12400339 AT4G23840.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`G`	4	+	12400339	AT4G23840.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone A clone + 12400345 AT4G23840.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`A`	clone	+	12400345	AT4G23840.1

Core promoter information

Type Sequence Genome position Gene model

Strand Start End

initiator Not Available Not Available Not Available

TATA Box ATTATATAAAGG + 12400306 12400317 AT4G23840.1

Y Patch None None None

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	`ATTATATAAAGG`	+	12400306	12400317	AT4G23840.1
Y Patch	None	None	None
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG TACACGTGA + 12400165 12400173 AT4G23840.1

AtREG453 TACACGTG ABA, DREB1Aox PPDB Motif ACGT PLACE Motif ACGT, ACGTG, ACACNNG

AtREG628 ACACGTGA DREB1Aox PPDB Motif ACGT PLACE Motif ACGT, ACGTG, CACGTG, ACACNNG

REG AACGGGCCATA + 12400177 12400187 AT4G23840.1

AtREG401 AACGGGCC    PPDB Motif AAACG(C/G), ACGGGC, CCAACGG PLACE Motif GGGCC

AtREG479    GGGCCATA PPDB Motif GCCCA PLACE Motif GGGCC

REG GTTTGGGCTTTAGTGGCCCAATAAG + 12400200 12400224 AT4G23840.1

AtREG474 GTTTGGGC                  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

AtREG445             GTGGCCCA      PPDB Motif GCCCA PLACE Motif GCCAC, GGGCC, TGGGCY

AtREG420              TGGCCCAA     PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG352               GGCCCAAT    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG355                GCCCAATA   PPDB Motif GCCCA PLACE Motif

AtREG417                 CCCAATAA PPDB Motif GCCCA PLACE Motif

AtREG611                  CCAATAAG PPDB Motif PLACE Motif