PlantPromoterDB promoter information of AT1G09760.1

Summary of Gene (AT1G09760.1)

Organism	Arabidopsis thaliana
Chromosome	1
Locus	AT1G09760 TAIR NCBI
Gene model	AT1G09760.1
Description	U2 small nuclear ribonucleoprotein A (U2A'); FUNCTIONS IN: protein binding; INVOLVED IN: nuclear mRNA splicing, via spliceosome, response to cold; LOCATED IN: in 6 components; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: U2A'/phosphoprotein 32 family A, C-terminal (InterPro:IPR003603); Has 5479 Blast hits to 4495 proteins in 302 species: Archae - 0; Bacteria - 1581; Metazoa - 2979; Fungi - 220; Plants - 106; Viruses - 2; Other Eukaryotes - 591 (source: NCBI BLink).

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Overview

Focused view (chromosome 1: 3162603-3161404)

`Genome position from initiation codon` `TSS from cDNA TSS information AT1G09760.1 5'->3' (-) Promoter sequence AT1G09770.1 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 AT1G09760.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak G 8 - 3161655 -52

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`G`	8	-	3161655	-52

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone G clone - 3161674 -71

TSS clone T clone - 3161656 -53

TSS clone G clone - 3161655 -52

TSS clone A clone - 3161654 -51

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`G`	clone	-	3161674	-71
TSS clone	`T`	clone	-	3161656	-53
TSS clone	`G`	clone	-	3161655	-52
TSS clone	`A`	clone	-	3161654	-51

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 TCTCTTTCCT - 3161658 3161667 -55 -64

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	`TCTCTTTCCT`	-	3161658	3161667	-55	-64
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 CAATGGGCCGTTTA - 3161737 3161750 -134 -147

AtREG551 CAATGGGC       PPDB Motif GCCCA PLACE Motif

AtREG361 AATGGGCC      PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG380   ATGGGCCG     PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG368    TGGGCCGT    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG377     GGGCCGTT   PPDB Motif GCCCA, AAACG(C/G) PLACE Motif GGGCC

AtREG613       GCCGTTTA PPDB Motif AAACG(C/G) PLACE Motif

REG TTATGGGCCTAACCGACTGGGCCAAT - 3161752 3161777 -149 -174

AtREG394 TTATGGGC                   PPDB Motif GCCCA PLACE Motif

AtREG364 TATGGGCC                  PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG354   ATGGGCCT                 PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG358    TGGGCCTA                PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG360     GGGCCTAA               PPDB Motif GCCCA PLACE Motif GGGCC

AtREG535      GGCCTAAC              PPDB Motif PLACE Motif

AtREG641           AACCGACT         PPDB Motif AACCG(G/A), CCGAC PLACE Motif CCGAC, RCCGAC

AtREG384                ACTGGGCC    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG458                 CTGGGCCA   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG484                  TGGGCCAA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG446                   GGGCCAAT CK PPDB Motif GCCCA PLACE Motif GGGCC

REG ACCCTAGA - 3161885 3161892 -282 -289

AtREG658 ACCCTAGA PPDB Motif ACCCT PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`CAATGGGCCGTTTA`		-	3161737	3161750	-134	-147
	AtREG551	`CAATGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG361	`AATGGGCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG380	`ATGGGCCG`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG368	`TGGGCCGT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG377	`GGGCCGTT`		PPDB Motif	`GCCCA, AAACG(C/G)`	PLACE Motif	`GGGCC`
	AtREG613	`GCCGTTTA`		PPDB Motif	`AAACG(C/G)`	PLACE Motif
REG	`TTATGGGCCTAACCGACTGGGCCAAT`		-	3161752	3161777	-149	-174
	AtREG394	`TTATGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG364	`TATGGGCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG354	`ATGGGCCT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG358	`TGGGCCTA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG360	`GGGCCTAA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG535	`GGCCTAAC`		PPDB Motif		PLACE Motif
	AtREG641	`AACCGACT`		PPDB Motif	`AACCG(G/A), CCGAC`	PLACE Motif	`CCGAC, RCCGAC`
	AtREG384	`ACTGGGCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG458	`CTGGGCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG484	`TGGGCCAA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG446	`GGGCCAAT`	CK	PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
REG	`ACCCTAGA`		-	3161885	3161892	-282	-289
	AtREG658	`ACCCTAGA`		PPDB Motif	`ACCCT`	PLACE Motif

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak G 2 + 3161844 AT1G09770.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`G`	2	+	3161844	AT1G09770.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone A clone + 3161841 AT1G09770.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`A`	clone	+	3161841	AT1G09770.1

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 TTTCTTCTTC + 3161858 3161867 AT1G09770.1

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	`TTTCTTCTTC`	+	3161858	3161867	AT1G09770.1
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG TAAACGGCCCATTG + 3161737 3161750 AT1G09770.1

AtREG613 TAAACGGC       PPDB Motif AAACG(C/G) PLACE Motif

AtREG377   AACGGCCC     PPDB Motif GCCCA, AAACG(C/G) PLACE Motif GGGCC

AtREG368    ACGGCCCA    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG380     CGGCCCAT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG361      GGCCCATT PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG551       GCCCATTG PPDB Motif GCCCA PLACE Motif

REG ATTGGCCCAGTCGGTTAGGCCCATAA + 3161752 3161777 AT1G09770.1

AtREG446 ATTGGCCC                   CK PPDB Motif GCCCA PLACE Motif GGGCC

AtREG484 TTGGCCCA                  PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG458   TGGCCCAG                 PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG384    GGCCCAGT                PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG641         AGTCGGTT           PPDB Motif AACCG(G/A), CCGAC PLACE Motif CCGAC, RCCGAC

AtREG535              GTTAGGCC      PPDB Motif PLACE Motif

AtREG360               TTAGGCCC     PPDB Motif GCCCA PLACE Motif GGGCC

AtREG358                TAGGCCCA    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG354                 AGGCCCAT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG364                  GGCCCATA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG394                   GCCCATAA PPDB Motif GCCCA PLACE Motif