PlantPromoterDB promoter information of AT5G58130.1

Summary of Gene (AT5G58130.1)

Organism	Arabidopsis thaliana
Chromosome	5
Locus	AT5G58130 TAIR NCBI
Gene model	AT5G58130.1
Description	RNA recognition motif (RRM)-containing protein; FUNCTIONS IN: nucleotide binding, nucleic acid binding; INVOLVED IN: biological_process unknown; LOCATED IN: cellular_component unknown; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: RNA recognition motif, RNP-1 (InterPro:IPR000504), Nucleotide-binding, alpha-beta plait (InterPro:IPR012677); BEST Arabidopsis thaliana protein match is: leucine-rich repeat family protein (TAIR:AT3G50690.1); Has 13214 Blast hits to 6289 proteins in 622 species: Archae - 145; Bacteria - 5890; Metazoa - 2525; Fungi - 1196; Plants - 360; Viruses - 129; Other Eukaryotes - 2969 (source: NCBI BLink).

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Overview

Focused view (chromosome 5: 23524766-23523567)

`Genome position from initiation codon` `TSS from cDNA TSS information AT5G58130.1 5'->3' (-) Promoter sequence AT5G58140.1 AT5G58140.2 AT5G58140.3 AT5G58140.4 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 AT5G58130.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak G 4 - 23523800 -34

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`G`	4	-	23523800	-34

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone G clone - 23523797 -31

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`G`	clone	-	23523797	-31

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 CTAATGGGCCTTA - 23523840 23523852 -74 -86

AtREG558 CTAATGGG      PPDB Motif GCCCA PLACE Motif

AtREG357 TAATGGGC     PPDB Motif GCCCA PLACE Motif

AtREG361   AATGGGCC    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG354    ATGGGCCT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG353     TGGGCCTT PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG351      GGGCCTTA PPDB Motif GCCCA PLACE Motif GGGCC

REG TAAAAGCCCATTAAG - 23523869 23523883 -103 -117

AtREG549 TAAAAGCC        PPDB Motif PLACE Motif

AtREG409 AAAAGCCC       PPDB Motif GCCCA PLACE Motif

AtREG376   AAAGCCCA      PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG378    AAGCCCAT     PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG372     AGCCCATT    PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG357      GCCCATTA   PPDB Motif GCCCA PLACE Motif

AtREG396       CCCATTAA PPDB Motif GCCCA PLACE Motif TTAATGG

AtREG604        CCATTAAG PPDB Motif PLACE Motif TTAATGG

REG GTTAGGCCTTAT - 23523895 23523906 -129 -140

AtREG535 GTTAGGCC     PPDB Motif PLACE Motif

AtREG425     GGCCTTAT PPDB Motif AACCG(G/A) PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`CTAATGGGCCTTA`		-	23523840	23523852	-74	-86
	AtREG558	`CTAATGGG`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG357	`TAATGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG361	`AATGGGCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG354	`ATGGGCCT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG353	`TGGGCCTT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG351	`GGGCCTTA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
REG	`TAAAAGCCCATTAAG`		-	23523869	23523883	-103	-117
	AtREG549	`TAAAAGCC`		PPDB Motif		PLACE Motif
	AtREG409	`AAAAGCCC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG376	`AAAGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG378	`AAGCCCAT`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG372	`AGCCCATT`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG357	`GCCCATTA`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG396	`CCCATTAA`		PPDB Motif	`GCCCA`	PLACE Motif	`TTAATGG`
	AtREG604	`CCATTAAG`		PPDB Motif		PLACE Motif	`TTAATGG`
REG	`GTTAGGCCTTAT`		-	23523895	23523906	-129	-140
	AtREG535	`GTTAGGCC`		PPDB Motif		PLACE Motif
	AtREG425	`GGCCTTAT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak G 4 + 23523980 AT5G58140.4, AT5G58140.2, AT5G58140.3, AT5G58140.1

TSS peak T 4 + 23524444 AT5G58140.4, AT5G58140.2, AT5G58140.3, AT5G58140.1

TSS peak G 15 + 23524719 AT5G58140.4, AT5G58140.2, AT5G58140.3, AT5G58140.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`G`	4	+	23523980	AT5G58140.4, AT5G58140.2, AT5G58140.3, AT5G58140.1
TSS peak	`T`	4	+	23524444	AT5G58140.4, AT5G58140.2, AT5G58140.3, AT5G58140.1
TSS peak	`G`	15	+	23524719	AT5G58140.4, AT5G58140.2, AT5G58140.3, AT5G58140.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone T clone + 23524427 AT5G58140.4, AT5G58140.2, AT5G58140.3, AT5G58140.1

TSS clone G clone + 23524522 AT5G58140.4, AT5G58140.2, AT5G58140.3, AT5G58140.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`T`	clone	+	23524427	AT5G58140.4, AT5G58140.2, AT5G58140.3, AT5G58140.1
TSS clone	`G`	clone	+	23524522	AT5G58140.4, AT5G58140.2, AT5G58140.3, AT5G58140.1

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 TCTTTCTC + 23524470 23524477 AT5G58140.1, AT5G58140.2, AT5G58140.3, AT5G58140.4

Y Patch CCTCTTCTT + 23524672 23524680 AT5G58140.1, AT5G58140.2, AT5G58140.3, AT5G58140.4

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	`TCTTTCTC`	+	23524470	23524477	AT5G58140.1, AT5G58140.2, AT5G58140.3, AT5G58140.4
Y Patch	`CCTCTTCTT`	+	23524672	23524680	AT5G58140.1, AT5G58140.2, AT5G58140.3, AT5G58140.4
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG ATAAGGCCCATTAG + 23523839 23523852 AT5G58140.1, AT5G58140.2, AT5G58140.3, AT5G58140.4

AtREG425 ATAAGGCC       PPDB Motif AACCG(G/A) PLACE Motif

AtREG351 TAAGGCCC      PPDB Motif GCCCA PLACE Motif GGGCC

AtREG353   AAGGCCCA     PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG354    AGGCCCAT    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG361     GGCCCATT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG357      GCCCATTA PPDB Motif GCCCA PLACE Motif

AtREG558       CCCATTAG PPDB Motif GCCCA PLACE Motif

REG CTTAATGGGCTTTTA + 23523869 23523883 AT5G58140.1, AT5G58140.2, AT5G58140.3, AT5G58140.4

AtREG604 CTTAATGG        PPDB Motif PLACE Motif TTAATGG

AtREG396 TTAATGGG       PPDB Motif GCCCA PLACE Motif TTAATGG

AtREG357   TAATGGGC      PPDB Motif GCCCA PLACE Motif

AtREG372    AATGGGCT     PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG378     ATGGGCTT    PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG376      TGGGCTTT   PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG409       GGGCTTTT PPDB Motif GCCCA PLACE Motif

AtREG549        GGCTTTTA PPDB Motif PLACE Motif

REG ATAAGGCCTAAC + 23523895 23523906 AT5G58140.1, AT5G58140.2, AT5G58140.3, AT5G58140.4

AtREG425 ATAAGGCC     PPDB Motif AACCG(G/A) PLACE Motif

AtREG535     GGCCTAAC PPDB Motif PLACE Motif