PlantPromoterDB promoter information of AT3G09480.1

Summary of Gene (AT3G09480.1)

Organism	Arabidopsis thaliana
Chromosome	3
Locus	AT3G09480 TAIR NCBI
Gene model	AT3G09480.1
Description	histone H2B, putative; FUNCTIONS IN: DNA binding; INVOLVED IN: nucleosome assembly; LOCATED IN: nucleus, nucleosome; EXPRESSED IN: 18 plant structures; EXPRESSED DURING: 8 growth stages; CONTAINS InterPro DOMAIN/s: Histone H2B (InterPro:IPR000558), Histone-fold (InterPro:IPR009072), Histone core (InterPro:IPR007125); BEST Arabidopsis thaliana protein match is: histone H2B, putative (TAIR:AT5G02570.1); Has 2678 Blast hits to 2678 proteins in 284 species: Archae - 0; Bacteria - 0; Metazoa - 1868; Fungi - 162; Plants - 357; Viruses - 0; Other Eukaryotes - 291 (source: NCBI BLink).

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Overview

Focused view (chromosome 3: 2916270-2915071)

`Genome position from initiation codon` `TSS from cDNA TSS information AT3G09480.1 5'->3' (-) Promoter sequence AT3G09490.1 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 AT3G09480.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

Not Available Not Available Not Available Not Available Not Available

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
Not Available	Not Available	Not Available	Not Available	Not Available

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone peak T clone - 2915320 -50

TSS clone peak C clone - 2915312 -42

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone peak	`T`	clone	-	2915320	-50
TSS clone peak	`C`	clone	-	2915312	-42

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 CCTCTATATATATCT - 2915344 2915358 -74 -88

Y Patch None None None

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	`CCTCTATATATATCT`	-	2915344	2915358	-74	-88
Y Patch	None	None	None
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 ACGCCACGTAG - 2915404 2915414 -134 -144

AtREG508 ACGCCACG    PPDB Motif PLACE Motif GCCAC

AtREG371 CGCCACGT   ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, GCCAC, ACGTGKC

AtREG413   GCCACGTA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, GCCAC, ACGTGKC

AtREG495    CCACGTAG PPDB Motif ACGT PLACE Motif ACGT, ACGTG

REG CGCACGTG - 2915418 2915425 -148 -155

AtREG541 CGCACGTG PPDB Motif ACGT PLACE Motif ACGT, ACGTG, CACGTG

REG GTTCGGTT - 2915463 2915470 -193 -200

AtREG556 GTTCGGTT PPDB Motif AACCG(G/A) PLACE Motif

REG TGAGCCCA - 2915477 2915484 -207 -214

AtREG485 TGAGCCCA PPDB Motif GCCCA PLACE Motif TGGGCY

REG AAAAGGCCAAGGCCCATTAG - 2915486 2915505 -216 -235

AtREG459 AAAAGGCC             PPDB Motif PLACE Motif

AtREG398        CAAGGCCC      PPDB Motif GCCCA PLACE Motif GGGCC

AtREG353         AAGGCCCA     PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG354          AGGCCCAT    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG361           GGCCCATT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG357            GCCCATTA PPDB Motif GCCCA PLACE Motif

AtREG558             CCCATTAG PPDB Motif GCCCA PLACE Motif

REG CCCAATAA - 2915611 2915618 -341 -348

AtREG417 CCCAATAA PPDB Motif GCCCA PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`ACGCCACGTAG`		-	2915404	2915414	-134	-144
	AtREG508	`ACGCCACG`		PPDB Motif		PLACE Motif	`GCCAC`
	AtREG371	`CGCCACGT`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, GCCAC, ACGTGKC`
	AtREG413	`GCCACGTA`		PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, GCCAC, ACGTGKC`
	AtREG495	`CCACGTAG`		PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG`
REG	`CGCACGTG`		-	2915418	2915425	-148	-155
	AtREG541	`CGCACGTG`		PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, CACGTG`
REG	`GTTCGGTT`		-	2915463	2915470	-193	-200
	AtREG556	`GTTCGGTT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
REG	`TGAGCCCA`		-	2915477	2915484	-207	-214
	AtREG485	`TGAGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
REG	`AAAAGGCCAAGGCCCATTAG`		-	2915486	2915505	-216	-235
	AtREG459	`AAAAGGCC`		PPDB Motif		PLACE Motif
	AtREG398	`CAAGGCCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG353	`AAGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG354	`AGGCCCAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG361	`GGCCCATT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG357	`GCCCATTA`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG558	`CCCATTAG`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`CCCAATAA`		-	2915611	2915618	-341	-348
	AtREG417	`CCCAATAA`		PPDB Motif	`GCCCA`	PLACE Motif

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak A 5 + 2915598 AT3G09490.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`A`	5	+	2915598	AT3G09490.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone G clone + 2915559 AT3G09490.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`G`	clone	+	2915559	AT3G09490.1

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 CTCTTCTT + 2915560 2915567 AT3G09490.1

Y Patch TTCTTCTCTTTC + 2915580 2915591 AT3G09490.1

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	`CTCTTCTT`	+	2915560	2915567	AT3G09490.1
Y Patch	`TTCTTCTCTTTC`	+	2915580	2915591	AT3G09490.1
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG CTACGTGGCGT + 2915404 2915414 AT3G09490.1

AtREG495 CTACGTGG    PPDB Motif ACGT PLACE Motif ACGT, ACGTG

AtREG413 TACGTGGC   PPDB Motif ACGT PLACE Motif ACGT, ACGTG, GCCAC, ACGTGKC

AtREG371   ACGTGGCG ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, GCCAC, ACGTGKC

AtREG508    CGTGGCGT PPDB Motif PLACE Motif GCCAC

REG CACGTGCG + 2915418 2915425 AT3G09490.1

AtREG541 CACGTGCG PPDB Motif ACGT PLACE Motif ACGT, ACGTG, CACGTG

REG AACCGAAC + 2915463 2915470 AT3G09490.1

AtREG556 AACCGAAC PPDB Motif AACCG(G/A) PLACE Motif

REG TGGGCTCA + 2915477 2915484 AT3G09490.1

AtREG485 TGGGCTCA PPDB Motif GCCCA PLACE Motif TGGGCY

REG CTAATGGGCCTTGGCCTTTT + 2915486 2915505 AT3G09490.1

AtREG558 CTAATGGG             PPDB Motif GCCCA PLACE Motif

AtREG357 TAATGGGC            PPDB Motif GCCCA PLACE Motif

AtREG361   AATGGGCC           PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG354    ATGGGCCT          PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG353     TGGGCCTT         PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG398      GGGCCTTG        PPDB Motif GCCCA PLACE Motif GGGCC

AtREG459             GGCCTTTT PPDB Motif PLACE Motif