PlantPromoterDB promoter information of AT3G12080.2

Summary of Gene (AT3G12080.2)

Organism	Arabidopsis thaliana
Chromosome	3
Locus	AT3G12080 TAIR NCBI
Gene model	AT3G12080.2
Description	embryo defective 2738 (emb2738); FUNCTIONS IN: GTP binding; INVOLVED IN: embryonic development ending in seed dormancy; LOCATED IN: chloroplast; EXPRESSED IN: 21 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: GTP-binding (InterPro:IPR005289), Small GTP-binding protein (InterPro:IPR005225), GTP1/OBG (InterPro:IPR006073), GTP-binding protein, HSR1-related (InterPro:IPR002917); BEST Arabidopsis thaliana protein match is: GTP-binding family protein (TAIR:AT5G39960.1); Has 29827 Blast hits to 16895 proteins in 1667 species: Archae - 139; Bacteria - 20018; Metazoa - 342; Fungi - 286; Plants - 215; Viruses - 0; Other Eukaryotes - 8827 (source: NCBI BLink).

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Overview

Focused view (chromosome 3: 3846851-3848050)

`Genome position from initiation codon` `AT3G12080.1 TSS from cDNA TSS information AT3G12080.2 5'->3' (+) Promoter sequence AT3G12070.1 AT3G12070.2 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 AT3G12080.2

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 G clone + 3847792 -59

TSS clone peak T clone + 3847793 -58

TSS clone C clone + 3847842 -9

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`G`	clone	+	3847792	-59
TSS clone peak	`T`	clone	+	3847793	-58
TSS clone	`C`	clone	+	3847842	-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 TTTCTTCTTCTTCTTCTCTT + 3847812 3847831 -39 -20

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	`TTTCTTCTTCTTCTTCTCTT`	+	3847812	3847831	-39	-20
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 TTTTGGGC + 3847552 3847559 -299 -292

AtREG529 TTTTGGGC PPDB Motif GCCCA PLACE Motif

REG CTAAACCGAA + 3847628 3847637 -223 -214

AtREG511 CTAAACCG   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

REG TTGAACCG + 3847657 3847664 -194 -187

AtREG640 TTGAACCG PPDB Motif AACCG(G/A) PLACE Motif

REG TTAAACCGGTTCATCCGGTTC + 3847726 3847746 -125 -105

AtREG473 TTAAACCG              PPDB Motif AACCG(G/A) PLACE Motif

AtREG412 TAAACCGG             PPDB Motif AACCG(G/A) PLACE Motif

AtREG436   AAACCGGT            PPDB Motif AACCG(G/A) PLACE Motif

AtREG528     ACCGGTTC          PPDB Motif AACCG(G/A) PLACE Motif

AtREG480      CCGGTTCA         PPDB Motif AACCG(G/A) PLACE Motif

AtREG561             ATCCGGTT PPDB Motif AACCG(G/A) PLACE Motif

AtREG579              TCCGGTTC PPDB Motif AACCG(G/A) PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`TTTTGGGC`		+	3847552	3847559	-299	-292
	AtREG529	`TTTTGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`CTAAACCGAA`		+	3847628	3847637	-223	-214
	AtREG511	`CTAAACCG`		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
REG	`TTGAACCG`		+	3847657	3847664	-194	-187
	AtREG640	`TTGAACCG`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
REG	`TTAAACCGGTTCATCCGGTTC`		+	3847726	3847746	-125	-105
	AtREG473	`TTAAACCG`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG412	`TAAACCGG`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG436	`AAACCGGT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG528	`ACCGGTTC`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG480	`CCGGTTCA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG561	`ATCCGGTT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG579	`TCCGGTTC`		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

TSS clone peak A clone - 3847562 AT3G12070.1, AT3G12070.2

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone peak	`A`	clone	-	3847562	AT3G12070.1, AT3G12070.2

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 CTTCTCTTCTCT - 3847522 3847533 AT3G12070.1, AT3G12070.2

Y Patch TCTTCTTC - 3847568 3847575 AT3G12070.1, AT3G12070.2

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	`CTTCTCTTCTCT`	-	3847522	3847533	AT3G12070.1, AT3G12070.2
Y Patch	`TCTTCTTC`	-	3847568	3847575	AT3G12070.1, AT3G12070.2
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG TTCGGTTTAG - 3847628 3847637 AT3G12070.1, AT3G12070.2

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

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

AtREG511   CGGTTTAG PPDB Motif AACCG(G/A) PLACE Motif

REG CGGTTCAA - 3847657 3847664 AT3G12070.1, AT3G12070.2

AtREG640 CGGTTCAA PPDB Motif AACCG(G/A) PLACE Motif

REG GAACCGGATGAACCGGTTTAA - 3847726 3847746 AT3G12070.1, AT3G12070.2

AtREG579 GAACCGGA              PPDB Motif AACCG(G/A) PLACE Motif

AtREG561 AACCGGAT             PPDB Motif AACCG(G/A) PLACE Motif

AtREG480         TGAACCGG      PPDB Motif AACCG(G/A) PLACE Motif

AtREG528          GAACCGGT     PPDB Motif AACCG(G/A) PLACE Motif

AtREG436            ACCGGTTT   PPDB Motif AACCG(G/A) PLACE Motif

AtREG412             CCGGTTTA PPDB Motif AACCG(G/A) PLACE Motif

AtREG473              CGGTTTAA PPDB Motif AACCG(G/A) PLACE Motif