PlantPromoterDB promoter information of AT4G36480.2

Summary of Gene (AT4G36480.2)

Organism	Arabidopsis thaliana
Chromosome	4
Locus	AT4G36480 TAIR NCBI
Gene model	AT4G36480.2
Description	Encodes the LCB1 subunit of serine palmitoyltransferase. Together with the LCB2 subunit, forms a functional serine palmitoyltransferase complex, which catalyzes the first reaction of sphingolipid biosynthesis. Knockout of LCB1 was embryo lethal. Partial suppression of LCB1 expression led to smaller plants due to reduced cell expansion.

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Overview

Focused view (chromosome 4: 17217598-17218797)

`Genome position from initiation codon` `AT4G36480.1 TSS from cDNA TSS information AT4G36480.2 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 AT4G36480.2

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 4 + 17218174 -424

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	4	+	17218174	-424

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone T clone + 17218091 -507

TSS clone T clone + 17218367 -231

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`T`	clone	+	17218091	-507
TSS clone	`T`	clone	+	17218367	-231

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 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	None	None	None
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 CATTGGGCCTCTAGGCCCATAT + 17217965 17217986 -633 -612

AtREG461 CATTGGGC               PPDB Motif GCCCA PLACE Motif

AtREG352 ATTGGGCC              PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG356   TTGGGCCT             PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG447    TGGGCCTC            PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG411     GGGCCTCT           PPDB Motif GCCCA PLACE Motif GGGCC

AtREG475           CTAGGCCC     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

AtREG432               GCCCATAT PPDB Motif GCCCA PLACE Motif

REG TAAACGGCGTCGT + 17217995 17218007 -603 -591

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

AtREG524 AAACGGCG     PPDB Motif AAACG(C/G) PLACE Motif

AtREG497   AACGGCGT    PPDB Motif AAACG(C/G), CCAACGG PLACE Motif

AtREG540    ACGGCGTC   PPDB Motif PLACE Motif

AtREG537      GGCGTCGT PPDB Motif PLACE Motif

REG TCTGGGCCCAG + 17218029 17218039 -569 -559

AtREG397 TCTGGGCC    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG363 CTGGGCCCAG PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG422   TGGGCCCA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`CATTGGGCCTCTAGGCCCATAT`		+	17217965	17217986	-633	-612
	AtREG461	`CATTGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG352	`ATTGGGCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG356	`TTGGGCCT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG447	`TGGGCCTC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG411	`GGGCCTCT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG475	`CTAGGCCC`		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`
	AtREG432	`GCCCATAT`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`TAAACGGCGTCGT`		+	17217995	17218007	-603	-591
	AtREG613	`TAAACGGC`		PPDB Motif	`AAACG(C/G)`	PLACE Motif
	AtREG524	`AAACGGCG`		PPDB Motif	`AAACG(C/G)`	PLACE Motif
	AtREG497	`AACGGCGT`		PPDB Motif	`AAACG(C/G), CCAACGG`	PLACE Motif
	AtREG540	`ACGGCGTC`		PPDB Motif		PLACE Motif
	AtREG537	`GGCGTCGT`		PPDB Motif		PLACE Motif
REG	`TCTGGGCCCAG`		+	17218029	17218039	-569	-559
	AtREG397	`TCTGGGCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG363	`CTGGGCCCAG`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG422	`TGGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`

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