PlantPromoterDB promoter information of AT5G16260.1

Summary of Gene (AT5G16260.1)

Organism	Arabidopsis thaliana
Chromosome	5
Locus	AT5G16260 TAIR NCBI
Gene model	AT5G16260.1
Description	RNA recognition motif (RRM)-containing protein; FUNCTIONS IN: RNA binding, nucleotide binding, nucleic acid binding; EXPRESSED IN: 25 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: RNA recognition motif, RNP-1 (InterPro:IPR000504), Nucleotide-binding, alpha-beta plait (InterPro:IPR012677), GYF (InterPro:IPR003169); Has 1767 Blast hits to 1758 proteins in 207 species: Archae - 0; Bacteria - 82; Metazoa - 1049; Fungi - 296; Plants - 184; Viruses - 0; Other Eukaryotes - 156 (source: NCBI BLink).

#

Overview

Focused view (chromosome 5: 5310363-5311562)

`Genome position from initiation codon` `TSS from cDNA TSS information AT5G16260.1 5'->3' (+) Promoter sequence AT5G16250.1 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 AT5G16260.1

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 A clone + 5311207 -156

TSS clone peak T clone + 5311208 -155

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone peak	`A`	clone	+	5311207	-156
TSS clone peak	`T`	clone	+	5311208	-155

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 CGTCTTCCTCCT + 5311243 5311254 -120 -109

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	`CGTCTTCCTCCT`	+	5311243	5311254	-120	-109
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 GACCGTTG + 5310989 5310996 -374 -367

AtREG553 GACCGTTG Auxin PPDB Motif CCAACGG PLACE Motif YAACKG, CNGTTR

REG TGGGCCCAATG + 5311047 5311057 -316 -306

AtREG422 TGGGCCCA    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG392 GGGCCCAA   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG352   GGCCCAAT PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG461    GCCCAATG PPDB Motif GCCCA PLACE Motif

REG GTGGGCCTAGTGGGCCGT + 5311084 5311101 -279 -262

AtREG482 GTGGGCCT           PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG358 TGGGCCTA          PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG475   GGGCCTAG         PPDB Motif GCCCA PLACE Motif GGGCC

AtREG532        TAGTGGGC    PPDB Motif GCCCA PLACE Motif

AtREG368           TGGGCCGT PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

REG GGGCCTAATGGGCCG + 5311156 5311170 -207 -193

AtREG360 GGGCCTAA        PPDB Motif GCCCA PLACE Motif GGGCC

AtREG506 GGCCTAAT       PPDB Motif PLACE Motif

AtREG558     CTAATGGG    PPDB Motif GCCCA PLACE Motif

AtREG357      TAATGGGC   PPDB Motif GCCCA PLACE Motif

AtREG361       AATGGGCC PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG380        ATGGGCCG PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`GACCGTTG`		+	5310989	5310996	-374	-367
	AtREG553	`GACCGTTG`	Auxin	PPDB Motif	`CCAACGG`	PLACE Motif	`YAACKG, CNGTTR`
REG	`TGGGCCCAATG`		+	5311047	5311057	-316	-306
	AtREG422	`TGGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG392	`GGGCCCAA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG352	`GGCCCAAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG461	`GCCCAATG`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`GTGGGCCTAGTGGGCCGT`		+	5311084	5311101	-279	-262
	AtREG482	`GTGGGCCT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG358	`TGGGCCTA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG475	`GGGCCTAG`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG532	`TAGTGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG368	`TGGGCCGT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
REG	`GGGCCTAATGGGCCG`		+	5311156	5311170	-207	-193
	AtREG360	`GGGCCTAA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC`
	AtREG506	`GGCCTAAT`		PPDB Motif		PLACE Motif
	AtREG558	`CTAATGGG`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG357	`TAATGGGC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG361	`AATGGGCC`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG380	`ATGGGCCG`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak A 13 - 5310907 AT5G16250.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`A`	13	-	5310907	AT5G16250.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone A clone - 5310951 AT5G16250.1

TSS clone C clone - 5310908 AT5G16250.1

TSS clone A clone - 5310907 AT5G16250.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`A`	clone	-	5310951	AT5G16250.1
TSS clone	`C`	clone	-	5310908	AT5G16250.1
TSS clone	`A`	clone	-	5310907	AT5G16250.1

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 CTCTTCTTCTTCTTCT - 5310880 5310895 AT5G16250.1

Y Patch CTCTTCTC - 5310914 5310921 AT5G16250.1

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	`CTCTTCTTCTTCTTCT`	-	5310880	5310895	AT5G16250.1
Y Patch	`CTCTTCTC`	-	5310914	5310921	AT5G16250.1
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG CAACGGTC - 5310989 5310996 AT5G16250.1

AtREG553 CAACGGTC Auxin PPDB Motif CCAACGG PLACE Motif YAACKG, CNGTTR

REG CATTGGGCCCA - 5311047 5311057 AT5G16250.1

AtREG461 CATTGGGC    PPDB Motif GCCCA PLACE Motif

AtREG352 ATTGGGCC   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG392   TTGGGCCC PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG422    TGGGCCCA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

REG ACGGCCCACTAGGCCCAC - 5311084 5311101 AT5G16250.1

AtREG368 ACGGCCCA           PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG532    GCCCACTA        PPDB Motif GCCCA PLACE Motif

AtREG475         CTAGGCCC   PPDB Motif GCCCA PLACE Motif GGGCC

AtREG358          TAGGCCCA PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG482           AGGCCCAC PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

REG ACGGCCCATTAGGCCC - 5311156 5311171 AT5G16250.1

AtREG368 ACGGCCCA         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    GCCCATTA      PPDB Motif GCCCA PLACE Motif

AtREG558     CCCATTAG     PPDB Motif GCCCA PLACE Motif

AtREG506        ATTAGGCC PPDB Motif PLACE Motif

AtREG360         TTAGGCCC PPDB Motif GCCCA PLACE Motif GGGCC