PlantPromoterDB promoter information of AT5G38420.1

Summary of Gene (AT5G38420.1)

Organism	Arabidopsis thaliana
Chromosome	5
Locus	AT5G38420 TAIR NCBI
Gene model	AT5G38420.1
Description	ribulose bisphosphate carboxylase small chain 2B / RuBisCO small subunit 2B (RBCS-2B) (ATS2B); FUNCTIONS IN: ribulose-bisphosphate carboxylase activity; INVOLVED IN: response to blue light, carbon utilization by fixation of carbon dioxide, response to red light, response to far red light; LOCATED IN: in 8 components; EXPRESSED IN: 10 plant structures; CONTAINS InterPro DOMAIN/s: Ribulose bisphosphate carboxylase, small chain (InterPro:IPR000894); BEST Arabidopsis thaliana protein match is: ribulose bisphosphate carboxylase small chain 1B / RuBisCO small subunit 1B (RBCS-1B) (ATS1B) (TAIR:AT5G38430.1); Has 1722 Blast hits to 1701 proteins in 391 species: Archae - 0; Bacteria - 341; Metazoa - 0; Fungi - 0; Plants - 874; Viruses - 0; Other Eukaryotes - 507 (source: NCBI BLink).

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Overview

Focused view (chromosome 5: 15382978-15381779)

`Genome position from initiation codon` `TSS from cDNA TSS information AT5G38420.1 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 AT5G38420.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 446 - 15382029 -51

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	446	-	15382029	-51

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone C clone - 15382030 -52

TSS clone A clone - 15382029 -51

TSS clone A clone - 15382028 -50

TSS clone G clone - 15382027 -49

TSS clone T clone - 15382026 -48

TSS clone A clone - 15382025 -47

TSS clone A clone - 15382024 -46

TSS clone A clone - 15382020 -42

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`C`	clone	-	15382030	-52
TSS clone	`A`	clone	-	15382029	-51
TSS clone	`A`	clone	-	15382028	-50
TSS clone	`G`	clone	-	15382027	-49
TSS clone	`T`	clone	-	15382026	-48
TSS clone	`A`	clone	-	15382025	-47
TSS clone	`A`	clone	-	15382024	-46
TSS clone	`A`	clone	-	15382020	-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 CCACTATATAAAGA - 15382051 15382064 -73 -86

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	`CCACTATATAAAGA`	-	15382051	15382064	-73	-86
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 TATGGCCC - 15382100 15382107 -122 -129

AtREG479 TATGGCCC PPDB Motif GCCCA PLACE Motif GGGCC

REG AACGACGT - 15382118 15382125 -140 -147

AtREG493 AACGACGT PPDB Motif ACGT PLACE Motif ACGT

REG GTGGCAAT - 15382127 15382134 -149 -156

AtREG654 GTGGCAAT PPDB Motif PLACE Motif GCCAC

REG CTGCCACGTG - 15382189 15382198 -211 -220

AtREG468 CTGCCACG ABA PPDB Motif PLACE Motif GCCAC

AtREG379 TGCCACGT ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, GCCAC, ACGTGKC

AtREG367 GCCACGTG ABA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, GCCAC, CACGTG, ACGTGKC, CACGTGGC

REG TACCCTTA - 15382227 15382234 -249 -256

AtREG570 TACCCTTA PPDB Motif ACCCT PLACE Motif

REG CCCAATTG - 15382291 15382298 -313 -320

AtREG647 CCCAATTG PPDB Motif PLACE Motif

REG TTTAACCG - 15382319 15382326 -341 -348

AtREG645 TTTAACCG PPDB Motif AACCG(G/A) PLACE Motif CNGTTR

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`TATGGCCC`		-	15382100	15382107	-122	-129
	AtREG479	`TATGGCCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
REG	`AACGACGT`		-	15382118	15382125	-140	-147
	AtREG493	`AACGACGT`		PPDB Motif	`ACGT`	PLACE Motif	`ACGT`
REG	`GTGGCAAT`		-	15382127	15382134	-149	-156
	AtREG654	`GTGGCAAT`		PPDB Motif		PLACE Motif	`GCCAC`
REG	`CTGCCACGTG`		-	15382189	15382198	-211	-220
	AtREG468	`CTGCCACG`	ABA	PPDB Motif		PLACE Motif	`GCCAC`
	AtREG379	`TGCCACGT`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, GCCAC, ACGTGKC`
	AtREG367	`GCCACGTG`	ABA	PPDB Motif	`ACGT`	PLACE Motif	`ACGT, ACGTG, GCCAC, CACGTG, ACGTGKC, CACGTGGC`
REG	`TACCCTTA`		-	15382227	15382234	-249	-256
	AtREG570	`TACCCTTA`		PPDB Motif	`ACCCT`	PLACE Motif
REG	`CCCAATTG`		-	15382291	15382298	-313	-320
	AtREG647	`CCCAATTG`		PPDB Motif		PLACE Motif
REG	`TTTAACCG`		-	15382319	15382326	-341	-348
	AtREG645	`TTTAACCG`		PPDB Motif	`AACCG(G/A)`	PLACE Motif	`CNGTTR`

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