PlantPromoterDB promoter information of AT3G12260.1

Summary of Gene (AT3G12260.1)

Organism	Arabidopsis thaliana
Chromosome	3
Locus	AT3G12260 TAIR NCBI
Gene model	AT3G12260.1
Description	complex 1 family protein / LVR family protein; FUNCTIONS IN: catalytic activity; LOCATED IN: mitochondrion, respiratory chain complex I, membrane; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 14 growth stages; CONTAINS InterPro DOMAIN/s: Complex 1 LYR protein (InterPro:IPR008011); Has 192 Blast hits to 192 proteins in 85 species: Archae - 0; Bacteria - 0; Metazoa - 102; Fungi - 33; Plants - 31; Viruses - 0; Other Eukaryotes - 26 (source: NCBI BLink).

#

Overview

Focused view (chromosome 3: 3911337-3910138)

`Genome position from initiation codon` `TSS from cDNA TSS information AT3G12260.1 5'->3' (-) Promoter sequence AT3G12270.1 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 AT3G12260.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak A 5 - 3910404 -67

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`A`	5	-	3910404	-67

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone G clone - 3910399 -62

TSS clone A clone - 3910392 -55

TSS clone T clone - 3910391 -54

TSS clone A clone - 3910380 -43

TSS clone A clone - 3910375 -38

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`G`	clone	-	3910399	-62
TSS clone	`A`	clone	-	3910392	-55
TSS clone	`T`	clone	-	3910391	-54
TSS clone	`A`	clone	-	3910380	-43
TSS clone	`A`	clone	-	3910375	-38

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 GAAACGACGTCGTC - 3910449 3910462 -112 -125

AtREG576 GAAACGAC       PPDB Motif PLACE Motif

AtREG415 AAACGACG      PPDB Motif PLACE Motif

AtREG493   AACGACGT     PPDB Motif ACGT PLACE Motif ACGT

AtREG431    ACGACGTCGT PPDB Motif ACGT PLACE Motif ACGT

AtREG526       ACGTCGTC PPDB Motif ACGT PLACE Motif ACGT

REG CTTAGGCCCATAAAAAGCCCATTAG - 3910474 3910498 -137 -161

AtREG563 CTTAGGCC                  PPDB Motif PLACE Motif

AtREG360 TTAGGCCC                 PPDB Motif GCCCA PLACE Motif GGGCC

AtREG358   TAGGCCCA                PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG354    AGGCCCAT               PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG364     GGCCCATA              PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG394      GCCCATAA             PPDB Motif GCCCA PLACE Motif

AtREG589            AAAAAGCC       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

AtREG558                  CCCATTAG PPDB Motif GCCCA PLACE Motif

REG TAACCGGAAATAATTACG - 3910516 3910533 -179 -196

AtREG621 TAACCGGA           PPDB Motif AACCG(G/A) PLACE Motif CNGTTR

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

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

AtREG646           TAATTACG ABA PPDB Motif PLACE Motif

REG GTAAACCGAA - 3910536 3910545 -199 -208

AtREG519 GTAAACCG   PPDB Motif AACCG(G/A) PLACE Motif

AtREG514 TAAACCGA PPDB Motif AACCG(G/A) PLACE Motif

AtREG568   AAACCGAA PPDB Motif AACCG(G/A) PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`GAAACGACGTCGTC`		-	3910449	3910462	-112	-125
	AtREG576	`GAAACGAC`		PPDB Motif		PLACE Motif
	AtREG415	`AAACGACG`		PPDB Motif		PLACE Motif
	AtREG493	`AACGACGT`		PPDB Motif	`ACGT`	PLACE Motif	`ACGT`
	AtREG431	`ACGACGTCGT`		PPDB Motif	`ACGT`	PLACE Motif	`ACGT`
	AtREG526	`ACGTCGTC`		PPDB Motif	`ACGT`	PLACE Motif	`ACGT`
REG	`CTTAGGCCCATAAAAAGCCCATTAG`		-	3910474	3910498	-137	-161
	AtREG563	`CTTAGGCC`		PPDB Motif		PLACE Motif
	AtREG360	`TTAGGCCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG358	`TAGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG354	`AGGCCCAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG364	`GGCCCATA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG394	`GCCCATAA`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG589	`AAAAAGCC`		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
	AtREG558	`CCCATTAG`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`TAACCGGAAATAATTACG`		-	3910516	3910533	-179	-196
	AtREG621	`TAACCGGA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif	`CNGTTR`
	AtREG534	`AACCGGAA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG644	`ACCGGAAA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG646	`TAATTACG`	ABA	PPDB Motif		PLACE Motif
REG	`GTAAACCGAA`		-	3910536	3910545	-199	-208
	AtREG519	`GTAAACCG`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG514	`TAAACCGA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG568	`AAACCGAA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif

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

Not Available Not Available Not Available Not Available Not Available

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
Not Available	Not Available	Not Available	Not Available	Not Available

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 None None None

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	None	None	None
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG None None None