PlantPromoterDB promoter information of AT5G19960.1

Summary of Gene (AT5G19960.1)

Organism	Arabidopsis thaliana
Chromosome	5
Locus	AT5G19960 TAIR NCBI
Gene model	AT5G19960.1
Description	RNA recognition motif (RRM)-containing protein; FUNCTIONS IN: RNA binding, 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, glycine rich protein (InterPro:IPR015465), RNA recognition motif, RNP-1 (InterPro:IPR000504), Nucleotide-binding, alpha-beta plait (InterPro:IPR012677); BEST Arabidopsis thaliana protein match is: GR-RBP8; RNA binding / nucleic acid binding / nucleotide binding (TAIR:AT4G39260.2); Has 17397 Blast hits to 14212 proteins in 592 species: Archae - 12; Bacteria - 964; Metazoa - 9774; Fungi - 1887; Plants - 2774; Viruses - 3; Other Eukaryotes - 1983 (source: NCBI BLink).

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Overview

Focused view (chromosome 5: 6739479-6740678)

`Genome position from initiation codon` `AT5G19940.1 AT5G19940.2 TSS from cDNA TSS information AT5G19960.1 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 AT5G19960.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

Not Available Not Available Not Available Not Available Not Available

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
Not Available	Not Available	Not Available	Not Available	Not Available

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone peak A clone + 6744021 -8

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone peak	`A`	clone	+	6744021	-8

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 CAATTGGG + 6743730 6743737 -299 -292

AtREG647 CAATTGGG PPDB Motif PLACE Motif

REG CGTTTTGA + 6743832 6743839 -197 -190

AtREG653 CGTTTTGA PPDB Motif AAACG(C/G) PLACE Motif

REG TTTCCGGTTT + 6743910 6743919 -119 -110

AtREG644 TTTCCGGT   PPDB Motif AACCG(G/A) PLACE Motif

AtREG534 TTCCGGTT PPDB Motif AACCG(G/A) PLACE Motif

AtREG521   TCCGGTTT PPDB Motif AACCG(G/A) PLACE Motif

REG TAGTGGGCCTAATGGCCCATAT + 6743925 6743946 -104 -83

AtREG532 TAGTGGGC               PPDB Motif GCCCA PLACE Motif

AtREG482   GTGGGCCT             PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG358    TGGGCCTA            PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG360     GGGCCTAA           PPDB Motif GCCCA PLACE Motif GGGCC

AtREG506      GGCCTAAT          PPDB Motif PLACE Motif

AtREG437            ATGGCCCA    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG490             TGGCCCAT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG364              GGCCCATA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG432               GCCCATAT PPDB Motif GCCCA PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`CAATTGGG`		+	6743730	6743737	-299	-292
	AtREG647	`CAATTGGG`		PPDB Motif		PLACE Motif
REG	`CGTTTTGA`		+	6743832	6743839	-197	-190
	AtREG653	`CGTTTTGA`		PPDB Motif	`AAACG(C/G)`	PLACE Motif
REG	`TTTCCGGTTT`		+	6743910	6743919	-119	-110
	AtREG644	`TTTCCGGT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG534	`TTCCGGTT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG521	`TCCGGTTT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
REG	`TAGTGGGCCTAATGGCCCATAT`		+	6743925	6743946	-104	-83
	AtREG532	`TAGTGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG482	`GTGGGCCT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG358	`TGGGCCTA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG360	`GGGCCTAA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG506	`GGCCTAAT`		PPDB Motif		PLACE Motif
	AtREG437	`ATGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG490	`TGGCCCAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG364	`GGCCCATA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG432	`GCCCATAT`		PPDB Motif	`GCCCA`	PLACE Motif

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak A 17 + 6739689 AT5G19940.1, AT5G19940.2

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`A`	17	+	6739689	AT5G19940.1, AT5G19940.2

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone T clone + 6739634 AT5G19940.1, AT5G19940.2

TSS clone T clone + 6739645 AT5G19940.1, AT5G19940.2

TSS clone C clone + 6739649 AT5G19940.1, AT5G19940.2

TSS clone T clone + 6739651 AT5G19940.1, AT5G19940.2

TSS clone C clone + 6739654 AT5G19940.1, AT5G19940.2

TSS clone T clone + 6739655 AT5G19940.1, AT5G19940.2

TSS clone T clone + 6739657 AT5G19940.1, AT5G19940.2

TSS clone A clone + 6739661 AT5G19940.1, AT5G19940.2

TSS clone A clone + 6739684 AT5G19940.1, AT5G19940.2

TSS clone A clone + 6739690 AT5G19940.1, AT5G19940.2

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`T`	clone	+	6739634	AT5G19940.1, AT5G19940.2
TSS clone	`T`	clone	+	6739645	AT5G19940.1, AT5G19940.2
TSS clone	`C`	clone	+	6739649	AT5G19940.1, AT5G19940.2
TSS clone	`T`	clone	+	6739651	AT5G19940.1, AT5G19940.2
TSS clone	`C`	clone	+	6739654	AT5G19940.1, AT5G19940.2
TSS clone	`T`	clone	+	6739655	AT5G19940.1, AT5G19940.2
TSS clone	`T`	clone	+	6739657	AT5G19940.1, AT5G19940.2
TSS clone	`A`	clone	+	6739661	AT5G19940.1, AT5G19940.2
TSS clone	`A`	clone	+	6739684	AT5G19940.1, AT5G19940.2
TSS clone	`A`	clone	+	6739690	AT5G19940.1, AT5G19940.2

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 CTCTCTCTCCC + 6739640 6739650 AT5G19940.1, AT5G19940.2

Y Patch CTTCTCTCTCTT + 6739663 6739674 AT5G19940.1, AT5G19940.2

Y Patch CTCTCTCC + 6739676 6739683 AT5G19940.1, AT5G19940.2

Y Patch CTTCTTCTCTT + 6739706 6739716 AT5G19940.1, AT5G19940.2

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	`CTCTCTCTCCC`	+	6739640	6739650	AT5G19940.1, AT5G19940.2
Y Patch	`CTTCTCTCTCTT`	+	6739663	6739674	AT5G19940.1, AT5G19940.2
Y Patch	`CTCTCTCC`	+	6739676	6739683	AT5G19940.1, AT5G19940.2
Y Patch	`CTTCTTCTCTT`	+	6739706	6739716	AT5G19940.1, AT5G19940.2
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG ATGGCCCA - 6739502 6739509 AT5G19930.1

AtREG437 ATGGCCCA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

REG CCGCGTTA - 6739541 6739548 AT5G19930.1

AtREG488 CCGCGTTA SA PPDB Motif PLACE Motif

REG GGGCCCATA - 6739574 6739582 AT5G19930.1

AtREG391 GGGCCCAT PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG364 GGCCCATA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

REG GTGCCACGTCAT - 6739600 6739611 AT5G19930.1

AtREG444 GTGCCACG     PPDB Motif PLACE Motif GCCAC

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

AtREG388   GCCACGTC   PPDB Motif ACGT PLACE Motif ACGT, ACGTG, GCCAC, ACGTGKC

AtREG419    CCACGTCA PPDB Motif ACGT PLACE Motif ACGT, ACGTG, TGACGTGG, CCACGTCA

AtREG483     CACGTCAT PPDB Motif ACGT PLACE Motif ACGT, ACGTG

REG TGGGCCAT + 6739502 6739509 AT5G19940.1, AT5G19940.2

AtREG437 TGGGCCAT PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

REG TAACGCGG + 6739541 6739548 AT5G19940.1, AT5G19940.2

AtREG488 TAACGCGG SA PPDB Motif PLACE Motif

REG TATGGGCCC + 6739574 6739582 AT5G19940.1, AT5G19940.2

AtREG364 TATGGGCC PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG391 ATGGGCCC PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

REG ATGACGTGGCAC + 6739600 6739611 AT5G19940.1, AT5G19940.2

AtREG483 ATGACGTG     PPDB Motif ACGT PLACE Motif ACGT, ACGTG

AtREG419 TGACGTGG    PPDB Motif ACGT PLACE Motif ACGT, ACGTG, TGACGTGG, CCACGTCA

AtREG388   GACGTGGC   PPDB Motif ACGT PLACE Motif ACGT, ACGTG, GCCAC, ACGTGKC

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

AtREG444     CGTGGCAC PPDB Motif PLACE Motif GCCAC