PlantPromoterDB promoter information of AT5G05680.1

Summary of Gene (AT5G05680.1)

Organism	Arabidopsis thaliana
Chromosome	5
Locus	AT5G05680 TAIR NCBI
Gene model	AT5G05680.1
Description	nuclear pore complex protein-related; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: cellular_component unknown; EXPRESSED IN: 19 plant structures; EXPRESSED DURING: 7 growth stages; Has 361 Blast hits to 348 proteins in 84 species: Archae - 2; Bacteria - 20; Metazoa - 218; Fungi - 31; Plants - 27; Viruses - 0; Other Eukaryotes - 63 (source: NCBI BLink).

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Overview

Focused view (chromosome 5: 1697365-1698564)

`Genome position from initiation codon` `TSS from cDNA TSS information AT5G05680.1 5'->3' (+) Promoter sequence AT5G05670.1 AT5G05670.2 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 AT5G05680.1

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 A clone + 1698270 -95

TSS clone C clone + 1698274 -91

TSS clone peak T clone + 1698316 -49

TSS clone G clone + 1698356 -9

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`A`	clone	+	1698270	-95
TSS clone	`C`	clone	+	1698274	-91
TSS clone peak	`T`	clone	+	1698316	-49
TSS clone	`G`	clone	+	1698356	-9

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 CCTTCTCTTCC + 1698285 1698295 -80 -70

Y Patch TCTCCTTC + 1698324 1698331 -41 -34

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	`CCTTCTCTTCC`	+	1698285	1698295	-80	-70
Y Patch	`TCTCCTTC`	+	1698324	1698331	-41	-34
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 TTAATGGGCCGAATAAAAGCCCATTAA + 1698207 1698233 -158 -132

AtREG361   AATGGGCC                  PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG380    ATGGGCCG                 PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG393     TGGGCCGA                PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG427      GGGCCGAA               PPDB Motif GCCCA PLACE Motif GGGCC

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 TAATGGGC         GCCCATTA PPDB Motif GCCCA PLACE Motif

AtREG396 TTAATGGG           CCCATTAA PPDB Motif GCCCA PLACE Motif TTAATGG

REG GTCGTTTC + 1698247 1698254 -118 -111

AtREG576 GTCGTTTC PPDB Motif PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`TTAATGGGCCGAATAAAAGCCCATTAA`		+	1698207	1698233	-158	-132
	AtREG361	`AATGGGCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG380	`ATGGGCCG`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG393	`TGGGCCGA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG427	`GGGCCGAA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	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	`TAATGGGC GCCCATTA`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG396	`TTAATGGG CCCATTAA`		PPDB Motif	`GCCCA`	PLACE Motif	`TTAATGG`
REG	`GTCGTTTC`		+	1698247	1698254	-118	-111
	AtREG576	`GTCGTTTC`		PPDB Motif		PLACE Motif

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak G 2 - 1698128 AT5G05670.2, AT5G05670.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`G`	2	-	1698128	AT5G05670.2, AT5G05670.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone T clone - 1698127 AT5G05670.2, AT5G05670.1

TSS clone C clone - 1698124 AT5G05670.2, AT5G05670.1

TSS clone A clone - 1698104 AT5G05670.2, AT5G05670.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`T`	clone	-	1698127	AT5G05670.2, AT5G05670.1
TSS clone	`C`	clone	-	1698124	AT5G05670.2, AT5G05670.1
TSS clone	`A`	clone	-	1698104	AT5G05670.2, AT5G05670.1

Core promoter information

Type Sequence Genome position Gene model

Strand Start End

initiator Not Available Not Available Not Available

TATA Box AATATATAAAAT - 1698151 1698162 AT5G05670.1, AT5G05670.2

Y Patch CGTCTTCC - 1698083 1698090 AT5G05670.1, AT5G05670.2

Y Patch TTCTTCTCC - 1698111 1698119 AT5G05670.1, AT5G05670.2

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	`AATATATAAAAT`	-	1698151	1698162	AT5G05670.1, AT5G05670.2
Y Patch	`CGTCTTCC`	-	1698083	1698090	AT5G05670.1, AT5G05670.2
Y Patch	`TTCTTCTCC`	-	1698111	1698119	AT5G05670.1, AT5G05670.2
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG TTAATGGGCTTTTATTCGGCCCATTAA - 1698207 1698233 AT5G05670.1, AT5G05670.2

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

AtREG427               TTCGGCCC      PPDB Motif GCCCA PLACE Motif GGGCC

AtREG393                TCGGCCCA     PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG380                 CGGCCCAT    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG361                  GGCCCATT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG357 TAATGGGC         GCCCATTA PPDB Motif GCCCA PLACE Motif

AtREG396 TTAATGGG           CCCATTAA PPDB Motif GCCCA PLACE Motif TTAATGG

REG GAAACGAC - 1698247 1698254 AT5G05670.1, AT5G05670.2

AtREG576 GAAACGAC PPDB Motif PLACE Motif