PlantPromoterDB promoter information of AT1G55530.1

Summary of Gene (AT1G55530.1)

Organism	Arabidopsis thaliana
Chromosome	1
Locus	AT1G55530 TAIR NCBI
Gene model	AT1G55530.1
Description	zinc finger (C3HC4-type RING finger) family protein; FUNCTIONS IN: protein binding, zinc ion binding; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Zinc finger, RING-type (InterPro:IPR001841), Zinc finger, RING/FYVE/PHD-type (InterPro:IPR013083); BEST Arabidopsis thaliana protein match is: zinc finger (C3HC4-type RING finger) family protein (TAIR:AT5G56340.1); Has 7739 Blast hits to 7642 proteins in 225 species: Archae - 0; Bacteria - 8; Metazoa - 2938; Fungi - 729; Plants - 2721; Viruses - 30; Other Eukaryotes - 1313 (source: NCBI BLink).

#

Overview

Focused view (chromosome 1: 20731527-20730328)

`Genome position from initiation codon` `TSS from cDNA TSS information AT1G55530.1 5'->3' (-) Promoter sequence 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 AT1G55530.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 2 - 20731276 -749

TSS peak A 2 - 20731122 -595

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	2	-	20731276	-749
TSS peak	`A`	2	-	20731122	-595

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone G clone - 20731257 -730

TSS clone G clone - 20731202 -675

TSS clone A clone - 20731160 -633

TSS clone C clone - 20731159 -632

TSS clone A clone - 20731122 -595

TSS clone C clone - 20731121 -594

TSS clone A clone - 20731081 -554

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`G`	clone	-	20731257	-730
TSS clone	`G`	clone	-	20731202	-675
TSS clone	`A`	clone	-	20731160	-633
TSS clone	`C`	clone	-	20731159	-632
TSS clone	`A`	clone	-	20731122	-595
TSS clone	`C`	clone	-	20731121	-594
TSS clone	`A`	clone	-	20731081	-554

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 TCTTCTTC - 20731083 20731090 -556 -563

Y Patch CCCTCTCTTT - 20731097 20731106 -570 -579

Y Patch TTCTCCTCCTTTC - 20731125 20731137 -598 -610

Y Patch TTTCTTCTTCT - 20731161 20731171 -634 -644

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	`TCTTCTTC`	-	20731083	20731090	-556	-563
Y Patch	`CCCTCTCTTT`	-	20731097	20731106	-570	-579
Y Patch	`TTCTCCTCCTTTC`	-	20731125	20731137	-598	-610
Y Patch	`TTTCTTCTTCT`	-	20731161	20731171	-634	-644
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 GTACACGTGTT - 20731351 20731361 -824 -834

AtREG562 GTACACGT    ABA, Auxin PPDB Motif ACGT PLACE Motif ACGT, ACGTG

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

AtREG590    CACGTGTT ABA, JA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, CACGTG, ACACNNG

REG TAAAAGCCCAC - 20731375 20731385 -848 -858

AtREG549 TAAAAGCC    PPDB Motif PLACE Motif

AtREG409 AAAAGCCC   PPDB Motif GCCCA PLACE Motif

AtREG376   AAAGCCCA PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG518    AAGCCCAC PPDB Motif GCCCA PLACE Motif TGGGCY

REG AAAAGGCCCATCT - 20731400 20731412 -873 -885

AtREG459 AAAAGGCC      PPDB Motif PLACE Motif

AtREG359 AAAGGCCC     PPDB Motif GCCCA PLACE Motif GGGCC

AtREG353   AAGGCCCA    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG354    AGGCCCAT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG403     GGCCCATC PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG572      GCCCATCT PPDB Motif GCCCA PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`GTACACGTGTT`		-	20731351	20731361	-824	-834
	AtREG562	`GTACACGT`	ABA, Auxin	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG`
	AtREG453	`TACACGTG`	ABA, DREB1Aox	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, ACACNNG`
	AtREG590	`CACGTGTT`	ABA, JA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, CACGTG, ACACNNG`
REG	`TAAAAGCCCAC`		-	20731375	20731385	-848	-858
	AtREG549	`TAAAAGCC`		PPDB Motif		PLACE Motif
	AtREG409	`AAAAGCCC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG376	`AAAGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG518	`AAGCCCAC`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
REG	`AAAAGGCCCATCT`		-	20731400	20731412	-873	-885
	AtREG459	`AAAAGGCC`		PPDB Motif		PLACE Motif
	AtREG359	`AAAGGCCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG353	`AAGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG354	`AGGCCCAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG403	`GGCCCATC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG572	`GCCCATCT`		PPDB Motif	`GCCCA`	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

Not Available Not Available Not Available Not Available Not Available

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
Not Available	Not Available	Not Available	Not Available	Not Available

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 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	None	None	None
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 None None None