PlantPromoterDB promoter information of AT4G12640.1

Summary of Gene (AT4G12640.1)

Organism	Arabidopsis thaliana
Chromosome	4
Locus	AT4G12640 TAIR NCBI
Gene model	AT4G12640.1
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: Spen paralogue and orthologue C-terminal (InterPro:IPR012921), RNA recognition motif, RNP-1 (InterPro:IPR000504), Nucleotide-binding, alpha-beta plait (InterPro:IPR012677); BEST Arabidopsis thaliana protein match is: FPA; RNA binding (TAIR:AT2G43410.4); Has 6679 Blast hits to 5578 proteins in 311 species: Archae - 8; Bacteria - 143; Metazoa - 3956; Fungi - 1074; Plants - 834; Viruses - 0; Other Eukaryotes - 664 (source: NCBI BLink).

#

Overview

Focused view (chromosome 4: 7461697-7462896)

`Genome position from initiation codon` `TSS from cDNA TSS information AT4G12640.1 5'->3' (+) Promoter sequence AT4G12620.1 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 AT4G12640.1

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 C clone + 7462599 -98

TSS clone peak A clone + 7462601 -96

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone peak	`C`	clone	+	7462599	-98
TSS clone peak	`A`	clone	+	7462601	-96

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 TTTGGGCCGAATATTGGGCTTAT + 7462426 7462448 -271 -249

AtREG373 TTTGGGCC                PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG414 TTGGGCCG               PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG393   TGGGCCGA              PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG427    GGGCCGAA             PPDB Motif GCCCA PLACE Motif GGGCC

AtREG509           ATATTGGG      PPDB Motif PLACE Motif

AtREG355            TATTGGGC     PPDB Motif GCCCA PLACE Motif

AtREG402             ATTGGGCT    PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG407              TTGGGCTT   PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG426               TGGGCTTA PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG462                GGGCTTAT PPDB Motif GCCCA PLACE Motif

REG TTTTGGGCCGAT + 7462493 7462504 -204 -193

AtREG529 TTTTGGGC     PPDB Motif GCCCA PLACE Motif

AtREG373 TTTGGGCC    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG414   TTGGGCCG   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG393    TGGGCCGA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG555     GGGCCGAT PPDB Motif GCCCA PLACE Motif GGGCC

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`TTTGGGCCGAATATTGGGCTTAT`		+	7462426	7462448	-271	-249
	AtREG373	`TTTGGGCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG414	`TTGGGCCG`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG393	`TGGGCCGA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG427	`GGGCCGAA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG509	`ATATTGGG`		PPDB Motif		PLACE Motif
	AtREG355	`TATTGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG402	`ATTGGGCT`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG407	`TTGGGCTT`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG426	`TGGGCTTA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG462	`GGGCTTAT`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`TTTTGGGCCGAT`		+	7462493	7462504	-204	-193
	AtREG529	`TTTTGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG373	`TTTGGGCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG414	`TTGGGCCG`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG393	`TGGGCCGA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG555	`GGGCCGAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak C 4 - 7462357 AT4G12620.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`C`	4	-	7462357	AT4G12620.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone A clone - 7462300 AT4G12620.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`A`	clone	-	7462300	AT4G12620.1

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 CGTCTTCTTCTT - 7462308 7462319 AT4G12620.1

Y Patch CCTCCTTCTTC - 7462331 7462341 AT4G12620.1

Y Patch CTTTCTCTCTCT - 7462343 7462354 AT4G12620.1

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	`CGTCTTCTTCTT`	-	7462308	7462319	AT4G12620.1
Y Patch	`CCTCCTTCTTC`	-	7462331	7462341	AT4G12620.1
Y Patch	`CTTTCTCTCTCT`	-	7462343	7462354	AT4G12620.1
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG ATAAGCCCAATATTCGGCCCAAA - 7462426 7462448 AT4G12620.1

AtREG462 ATAAGCCC                PPDB Motif GCCCA PLACE Motif

AtREG426 TAAGCCCA               PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG407   AAGCCCAA              PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG402    AGCCCAAT             PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG355     GCCCAATA            PPDB Motif GCCCA PLACE Motif

AtREG509      CCCAATAT           PPDB Motif PLACE Motif

AtREG427             TTCGGCCC    PPDB Motif GCCCA PLACE Motif GGGCC

AtREG393              TCGGCCCA   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

REG ATCGGCCCAAAA - 7462493 7462504 AT4G12620.1

AtREG555 ATCGGCCC     PPDB Motif GCCCA PLACE Motif GGGCC

AtREG393 TCGGCCCA    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

AtREG529     GCCCAAAA PPDB Motif GCCCA PLACE Motif