PlantPromoterDB promoter information of AT3G16270.1

Summary of Gene (AT3G16270.1)

Organism	Arabidopsis thaliana
Chromosome	3
Locus	AT3G16270 TAIR NCBI
Gene model	AT3G16270.1
Description	INVOLVED IN: intracellular protein transport; LOCATED IN: membrane; EXPRESSED IN: 25 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: VHS (InterPro:IPR002014), ENTH/VHS (InterPro:IPR008942); Has 113 Blast hits to 112 proteins in 49 species: Archae - 0; Bacteria - 3; Metazoa - 48; Fungi - 1; Plants - 23; Viruses - 0; Other Eukaryotes - 38 (source: NCBI BLink).

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Overview

Focused view (chromosome 3: 5508251-5509450)

`Genome position from initiation codon` `AT3G16260.1 TSS from cDNA TSS information AT3G16270.1 5'->3' (+) Promoter sequence AT3G16250.1 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 AT3G16270.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 4 + 5513334 -367

TSS peak A 4 + 5513364 -337

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	4	+	5513334	-367
TSS peak	`A`	4	+	5513364	-337

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone T clone + 5513325 -376

TSS clone T clone + 5513331 -370

TSS clone T clone + 5513335 -366

TSS clone C clone + 5513365 -336

TSS clone T clone + 5513519 -182

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`T`	clone	+	5513325	-376
TSS clone	`T`	clone	+	5513331	-370
TSS clone	`T`	clone	+	5513335	-366
TSS clone	`C`	clone	+	5513365	-336
TSS clone	`T`	clone	+	5513519	-182

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 CTTCCTTCTTTCTCT + 5513342 5513356 -359 -345

Y Patch TTTCTTCTC + 5513381 5513389 -320 -312

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	`CTTCCTTCTTTCTCT`	+	5513342	5513356	-359	-345
Y Patch	`TTTCTTCTC`	+	5513381	5513389	-320	-312
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 ACGTGACA + 5513085 5513092 -616 -609

AtREG606 ACGTGACA ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`ACGTGACA`		+	5513085	5513092	-616	-609
	AtREG606	`ACGTGACA`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG`

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak G 10 - 5508364 AT3G16250.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`G`	10	-	5508364	AT3G16250.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone G clone + 5509374 AT3G16260.1

TSS clone peak T clone + 5509375 AT3G16260.1

TSS clone C clone + 5509382 AT3G16260.1

TSS clone A clone - 5508411 AT3G16250.1

TSS clone G clone - 5508363 AT3G16250.1

TSS clone A clone - 5508325 AT3G16250.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`G`	clone	+	5509374	AT3G16260.1
TSS clone peak	`T`	clone	+	5509375	AT3G16260.1
TSS clone	`C`	clone	+	5509382	AT3G16260.1
TSS clone	`A`	clone	-	5508411	AT3G16250.1
TSS clone	`G`	clone	-	5508363	AT3G16250.1
TSS clone	`A`	clone	-	5508325	AT3G16250.1

Core promoter information

Type Sequence Genome position Gene model

Strand Start End

initiator Not Available Not Available Not Available

TATA Box CATATAAAAC - 5508398 5508407 AT3G16250.1

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	`CATATAAAAC`	-	5508398	5508407	AT3G16250.1
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 TGATGGGCCGG + 5509257 5509267 AT3G16260.1

AtREG635 TGATGGGC    PPDB Motif GCCCA PLACE Motif

AtREG403 GATGGGCC   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG380   ATGGGCCG PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG457    TGGGCCGG CK PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

REG CAAAGGCCCATGGGCTAA + 5509278 5509295 AT3G16260.1

AtREG656 CAAAGGCC           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

AtREG504     GGCCCATG       PPDB Motif GCCCA, CCATGG PLACE Motif GGGCC, TGGGCY

AtREG591       CCCATGGG     PPDB Motif GCCCA, CCATGG PLACE Motif

AtREG507      GCCCATGGGC    PPDB Motif GCCCA, CCATGG PLACE Motif

AtREG581          ATGGGCTA PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG571           TGGGCTAA PPDB Motif GCCCA PLACE Motif TGGGCY

REG CTAAACCGG - 5508471 5508479 AT3G16250.1

AtREG511 CTAAACCG PPDB Motif AACCG(G/A) PLACE Motif

AtREG412 TAAACCGG PPDB Motif AACCG(G/A) PLACE Motif

REG CCCAATAT - 5508548 5508555 AT3G16250.1

AtREG509 CCCAATAT PPDB Motif PLACE Motif