PlantPromoterDB promoter information of AT1G09140.1

Summary of Gene (AT1G09140.1)

Organism	Arabidopsis thaliana
Chromosome	1
Locus	AT1G09140 TAIR NCBI
Gene model	AT1G09140.1
Description	Encodes a serine-arginine rich RNA binding protein involved in regulation of splicing (including splicing of itself). Exists as 3 alternative spliced forms that are differentially expressed.

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Overview

Focused view (chromosome 1: 2946818-2945619)

`Genome position from initiation codon` `AT1G09140.2 TSS from cDNA TSS information AT1G09140.1 5'->3' (-) Promoter sequence AT1G09150.1 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 AT1G09140.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak G 8 - 2945951 -133

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`G`	8	-	2945951	-133

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone G clone - 2945954 -136

TSS clone T clone - 2945953 -135

TSS clone G clone - 2945879 -61

TSS clone A clone - 2945876 -58

TSS clone A clone - 2945872 -54

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`G`	clone	-	2945954	-136
TSS clone	`T`	clone	-	2945953	-135
TSS clone	`G`	clone	-	2945879	-61
TSS clone	`A`	clone	-	2945876	-58
TSS clone	`A`	clone	-	2945872	-54

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 TTTATAAAAG - 2945980 2945989 -162 -171

Y Patch TCTTCTTCTTCTT - 2945902 2945914 -84 -96

Y Patch CTCCTTTC - 2945942 2945949 -124 -131

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	`TTTATAAAAG`	-	2945980	2945989	-162	-171
Y Patch	`TCTTCTTCTTCTT`	-	2945902	2945914	-84	-96
Y Patch	`CTCCTTTC`	-	2945942	2945949	-124	-131
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 GGGCTATT - 2946035 2946042 -217 -224

AtREG584 GGGCTATT PPDB Motif GCCCA PLACE Motif

REG ATATGGGCCGAT - 2946054 2946065 -236 -247

AtREG432 ATATGGGC     PPDB Motif GCCCA PLACE Motif

AtREG364 TATGGGCC    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

AtREG555     GGGCCGAT PPDB Motif GCCCA PLACE Motif GGGCC

REG ACAGGCCCATTAA - 2946069 2946081 -251 -263

AtREG433 ACAGGCCC      PPDB Motif GCCCA PLACE Motif GGGCC

AtREG370 CAGGCCCA     PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG354   AGGCCCAT    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG361    GGCCCATT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG357     GCCCATTA PPDB Motif GCCCA PLACE Motif

AtREG396      CCCATTAA PPDB Motif GCCCA PLACE Motif TTAATGG

REG ATCCGGTTA - 2946095 2946103 -277 -285

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

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

REG TTCCGGTTTG - 2946127 2946136 -309 -318

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

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

AtREG496   CCGGTTTG PPDB Motif AACCG(G/A) PLACE Motif

REG TGACCCGA - 2946190 2946197 -372 -379

AtREG617 TGACCCGA PPDB Motif PLACE Motif

REG AAAACGACA - 2946224 2946232 -406 -414

AtREG520 AAAACGAC PPDB Motif PLACE Motif

AtREG569 AAACGACA PPDB Motif PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`GGGCTATT`		-	2946035	2946042	-217	-224
	AtREG584	`GGGCTATT`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`ATATGGGCCGAT`		-	2946054	2946065	-236	-247
	AtREG432	`ATATGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG364	`TATGGGCC`		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`
	AtREG555	`GGGCCGAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
REG	`ACAGGCCCATTAA`		-	2946069	2946081	-251	-263
	AtREG433	`ACAGGCCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG370	`CAGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG354	`AGGCCCAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG361	`GGCCCATT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG357	`GCCCATTA`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG396	`CCCATTAA`		PPDB Motif	`GCCCA`	PLACE Motif	`TTAATGG`
REG	`ATCCGGTTA`		-	2946095	2946103	-277	-285
	AtREG561	`ATCCGGTT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG621	`TCCGGTTA`		PPDB Motif	`AACCG(G/A)`	PLACE Motif	`CNGTTR`
REG	`TTCCGGTTTG`		-	2946127	2946136	-309	-318
	AtREG534	`TTCCGGTT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG521	`TCCGGTTT`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
	AtREG496	`CCGGTTTG`		PPDB Motif	`AACCG(G/A)`	PLACE Motif
REG	`TGACCCGA`		-	2946190	2946197	-372	-379
	AtREG617	`TGACCCGA`		PPDB Motif		PLACE Motif
REG	`AAAACGACA`		-	2946224	2946232	-406	-414
	AtREG520	`AAAACGAC`		PPDB Motif		PLACE Motif
	AtREG569	`AAACGACA`		PPDB Motif		PLACE Motif

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak A 2 + 2946303 AT1G09150.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`A`	2	+	2946303	AT1G09150.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone T clone + 2946229 AT1G09150.1

TSS clone G clone + 2946281 AT1G09150.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`T`	clone	+	2946229	AT1G09150.1
TSS clone	`G`	clone	+	2946281	AT1G09150.1

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 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 AATAGCCC + 2946035 2946042 AT1G09150.1

AtREG584 AATAGCCC PPDB Motif GCCCA PLACE Motif

REG ATCGGCCCATAT + 2946054 2946065 AT1G09150.1

AtREG555 ATCGGCCC     PPDB Motif GCCCA PLACE Motif GGGCC

AtREG393 TCGGCCCA    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG380   CGGCCCAT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG364    GGCCCATA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG432     GCCCATAT PPDB Motif GCCCA PLACE Motif

REG TTAATGGGCCTGT + 2946069 2946081 AT1G09150.1

AtREG396 TTAATGGG      PPDB Motif GCCCA PLACE Motif TTAATGG

AtREG357 TAATGGGC     PPDB Motif GCCCA PLACE Motif

AtREG361   AATGGGCC    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG354    ATGGGCCT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG370     TGGGCCTG PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG433      GGGCCTGT PPDB Motif GCCCA PLACE Motif GGGCC

REG TAACCGGAT + 2946095 2946103 AT1G09150.1

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

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

REG CAAACCGGAA + 2946127 2946136 AT1G09150.1

AtREG496 CAAACCGG   PPDB Motif AACCG(G/A) PLACE Motif

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

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

REG TCGGGTCA + 2946190 2946197 AT1G09150.1

AtREG617 TCGGGTCA PPDB Motif PLACE Motif

REG TGTCGTTTT + 2946224 2946232 AT1G09150.1

AtREG569 TGTCGTTT PPDB Motif PLACE Motif

AtREG520 GTCGTTTT PPDB Motif PLACE Motif