PlantPromoterDB promoter information of AT5G27470.1

Summary of Gene (AT5G27470.1)

Organism	Arabidopsis thaliana
Chromosome	5
Locus	AT5G27470 TAIR NCBI
Gene model	AT5G27470.1
Description	seryl-tRNA synthetase / serine--tRNA ligase; FUNCTIONS IN: serine-tRNA ligase activity, aminoacyl-tRNA ligase activity, nucleotide binding, ATP binding; INVOLVED IN: response to cadmium ion, seryl-tRNA aminoacylation; LOCATED IN: cytosol; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 14 growth stages; CONTAINS InterPro DOMAIN/s: tRNA-binding arm (InterPro:IPR010978), Seryl-tRNA synthetase, class IIa, N-terminal (InterPro:IPR015866), Aminoacyl-tRNA synthetase, class II (G, H, P and S), conserved region (InterPro:IPR002314), Seryl-tRNA synthetase, class IIa (InterPro:IPR002317), Aminoacyl-tRNA synthetase, class II, conserved region (InterPro:IPR006195), Seryl-tRNA synthetase, class IIa, C-terminal (InterPro:IPR018156); BEST Arabidopsis thaliana protein match is: SRS (SERYL-TRNA SYNTHETASE); serine-tRNA ligase (TAIR:AT1G11870.2); Has 7169 Blast hits to 7168 proteins in 1635 species: Archae - 140; Bacteria - 3036; Metazoa - 295; Fungi - 180; Plants - 68; Viruses - 0; Other Eukaryotes - 3450 (source: NCBI BLink).

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Overview

Focused view (chromosome 5: 9694087-9695286)

`Genome position from initiation codon` `TSS from cDNA TSS information AT5G27470.1 5'->3' (+) Promoter sequence AT5G27460.1 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 AT5G27470.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak G 8 + 9695027 -60

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`G`	8	+	9695027	-60

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone A clone + 9695008 -79

TSS clone C clone + 9695019 -68

TSS clone T clone + 9695028 -59

TSS clone G clone + 9695036 -51

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`A`	clone	+	9695008	-79
TSS clone	`C`	clone	+	9695019	-68
TSS clone	`T`	clone	+	9695028	-59
TSS clone	`G`	clone	+	9695036	-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 CTTCCTTCTTCTTCCTC + 9694991 9695007 -96 -80

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	`CTTCCTTCTTCTTCCTC`	+	9694991	9695007	-96	-80
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 TGGTTCGGT + 9694841 9694849 -246 -238

AtREG655 TGGTTCGG PPDB Motif PLACE Motif

AtREG451 GGTTCGGT PPDB Motif PLACE Motif

REG ATTTGGGCCGTA + 9694888 9694899 -199 -188

AtREG421 ATTTGGGC     PPDB Motif GCCCA PLACE Motif

AtREG373 TTTGGGCC    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG414   TTGGGCCG   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG368    TGGGCCGT PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG499     GGGCCGTA PPDB Motif GCCCA PLACE Motif GGGCC

REG AGTTGGGCTTACCCGGCCCATAT + 9694908 9694930 -179 -157

AtREG607 AGTTGGGC                PPDB Motif GCCCA PLACE Motif

AtREG574 GTTGGGCT               PPDB Motif GCCCA, CCAACGG PLACE Motif TGGGCY

AtREG407   TTGGGCTT              PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG426    TGGGCTTA             PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG404            CCCGGCCC     CK PPDB Motif GCCCA PLACE Motif GGGCC

AtREG457             CCGGCCCA    CK PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG380              CGGCCCAT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG364               GGCCCATA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG432                GCCCATAT PPDB Motif GCCCA PLACE Motif

REG ATAAGCCC + 9694939 9694946 -148 -141

AtREG462 ATAAGCCC PPDB Motif GCCCA PLACE Motif

REG GACGTCGT + 9694959 9694966 -128 -121

AtREG431 GACGTCGT PPDB Motif ACGT PLACE Motif ACGT

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`TGGTTCGGT`		+	9694841	9694849	-246	-238
	AtREG655	`TGGTTCGG`		PPDB Motif		PLACE Motif
	AtREG451	`GGTTCGGT`		PPDB Motif		PLACE Motif
REG	`ATTTGGGCCGTA`		+	9694888	9694899	-199	-188
	AtREG421	`ATTTGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG373	`TTTGGGCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG414	`TTGGGCCG`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG368	`TGGGCCGT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG499	`GGGCCGTA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
REG	`AGTTGGGCTTACCCGGCCCATAT`		+	9694908	9694930	-179	-157
	AtREG607	`AGTTGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG574	`GTTGGGCT`		PPDB Motif	`GCCCA, CCAACGG`	PLACE Motif	`TGGGCY`
	AtREG407	`TTGGGCTT`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG426	`TGGGCTTA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG404	`CCCGGCCC`	CK	PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG457	`CCGGCCCA`	CK	PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG380	`CGGCCCAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG364	`GGCCCATA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG432	`GCCCATAT`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`ATAAGCCC`		+	9694939	9694946	-148	-141
	AtREG462	`ATAAGCCC`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`GACGTCGT`		+	9694959	9694966	-128	-121
	AtREG431	`GACGTCGT`		PPDB Motif	`ACGT`	PLACE Motif	`ACGT`

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

TSS clone G clone - 9694840 AT5G27460.1

TSS clone peak A clone - 9694823 AT5G27460.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`G`	clone	-	9694840	AT5G27460.1
TSS clone peak	`A`	clone	-	9694823	AT5G27460.1

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 TCTCTTCTCT - 9694866 9694875 AT5G27460.1

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	`TCTCTTCTCT`	-	9694866	9694875	AT5G27460.1
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG TACGGCCCAAAT - 9694888 9694899 AT5G27460.1

AtREG499 TACGGCCC     PPDB Motif GCCCA PLACE Motif GGGCC

AtREG368 ACGGCCCA    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG414   CGGCCCAA   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG373    GGCCCAAA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG421     GCCCAAAT PPDB Motif GCCCA PLACE Motif

REG ATATGGGCCGGGTAAGCCCAACT - 9694908 9694930 AT5G27460.1

AtREG432 ATATGGGC                PPDB Motif GCCCA PLACE Motif

AtREG364 TATGGGCC               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

AtREG404     GGGCCGGG            CK PPDB Motif GCCCA PLACE Motif GGGCC

AtREG426             TAAGCCCA    PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG407              AAGCCCAA   PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG574               AGCCCAAC PPDB Motif GCCCA, CCAACGG PLACE Motif TGGGCY

AtREG607                GCCCAACT PPDB Motif GCCCA PLACE Motif

REG GGGCTTAT - 9694939 9694946 AT5G27460.1

AtREG462 GGGCTTAT PPDB Motif GCCCA PLACE Motif

REG ACGACGTC - 9694959 9694966 AT5G27460.1

AtREG431 ACGACGTC PPDB Motif ACGT PLACE Motif ACGT