PlantPromoterDB promoter information of AT3G62250.1

Summary of Gene (AT3G62250.1)

Organism	Arabidopsis thaliana
Chromosome	3
Locus	AT3G62250 TAIR NCBI
Gene model	AT3G62250.1
Description	ubiquitin 5 (UBQ5); FUNCTIONS IN: protein binding, structural constituent of ribosome; INVOLVED IN: protein ubiquitination during ubiquitin-dependent protein catabolic process, protein modification process, translation; LOCATED IN: cytosolic small ribosomal subunit; CONTAINS InterPro DOMAIN/s: Ribosomal protein S27a (InterPro:IPR002906), Ubiquitin (InterPro:IPR000626); BEST Arabidopsis thaliana protein match is: UBQ6; protein binding (TAIR:AT2G47110.1); Has 9355 Blast hits to 5604 proteins in 655 species: Archae - 78; Bacteria - 7; Metazoa - 4233; Fungi - 952; Plants - 1981; Viruses - 176; Other Eukaryotes - 1928 (source: NCBI BLink).

#

Overview

Focused view (chromosome 3: 23036138-23037337)

`Genome position from initiation codon` `AT3G62245 AT3G62245.1 TSS from cDNA TSS information AT3G62250.1 5'->3' (+) Promoter sequence AT3G62240.1 AT3G62245.1 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 AT3G62250.1

TSS information

Type Sequence TPM score Genome position Position from initiation codon

Strand Position Position

TSS peak G 81 + 23037125 -13

Type	Sequence	TPM score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS peak	`G`	81	+	23037125	-13

TSS information from cDNA

Type Sequence Score Genome position Position from initiation codon

Strand Position Position

TSS clone G clone + 23037119 -19

TSS clone G clone + 23037122 -16

TSS clone C clone + 23037123 -15

TSS clone G clone + 23037125 -13

TSS clone T clone + 23037126 -12

TSS clone C clone + 23037129 -9

Type	Sequence	Score	Genome position	Position from initiation codon
			Strand	Position	Position
TSS clone	`G`	clone	+	23037119	-19
TSS clone	`G`	clone	+	23037122	-16
TSS clone	`C`	clone	+	23037123	-15
TSS clone	`G`	clone	+	23037125	-13
TSS clone	`T`	clone	+	23037126	-12
TSS clone	`C`	clone	+	23037129	-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 TCTCCTTC + 23037080 23037087 -58 -51

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	`TCTCCTTC`	+	23037080	23037087	-58	-51
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 CTTAATGGCCCAATAG + 23036987 23037002 -151 -136

AtREG604 CTTAATGG         PPDB Motif PLACE Motif TTAATGG

AtREG437     ATGGCCCA     PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG420      TGGCCCAA    PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG352       GGCCCAAT   PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG355        GCCCAATA PPDB Motif GCCCA PLACE Motif

AtREG624         CCCAATAG PPDB Motif GCCCA PLACE Motif

REG AAAGCCCAAAACTAAGCCCAAAT + 23037014 23037036 -124 -102

AtREG376 AAAGCCCA                PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG407 AAGCCCAA    AAGCCCAA   PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG469   AGCCCAAA    AGCCCAAA PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG529    GCCCAAAA             PPDB Motif GCCCA PLACE Motif

AtREG634            CTAAGCCC     PPDB Motif GCCCA PLACE Motif

AtREG426             TAAGCCCA    PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG421                GCCCAAAT PPDB Motif GCCCA PLACE Motif

REG TAAGGGTA + 23037041 23037048 -97 -90

AtREG570 TAAGGGTA PPDB Motif ACCCT PLACE Motif

REG ACCCTAGA + 23037070 23037077 -68 -61

AtREG658 ACCCTAGA PPDB Motif ACCCT PLACE Motif

Type	Sequence	Annotation	Genome position	Position from initiation codon
			Strand	Start	End	Start	End
REG	`CTTAATGGCCCAATAG`		+	23036987	23037002	-151	-136
	AtREG604	`CTTAATGG`		PPDB Motif		PLACE Motif	`TTAATGG`
	AtREG437	`ATGGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG420	`TGGCCCAA`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG352	`GGCCCAAT`		PPDB Motif	`GCCCA`	PLACE Motif	`GGGCC, TGGGCY`
	AtREG355	`GCCCAATA`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG624	`CCCAATAG`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`AAAGCCCAAAACTAAGCCCAAAT`		+	23037014	23037036	-124	-102
	AtREG376	`AAAGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG407	`AAGCCCAA AAGCCCAA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG469	`AGCCCAAA AGCCCAAA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG529	`GCCCAAAA`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG634	`CTAAGCCC`		PPDB Motif	`GCCCA`	PLACE Motif
	AtREG426	`TAAGCCCA`		PPDB Motif	`GCCCA`	PLACE Motif	`TGGGCY`
	AtREG421	`GCCCAAAT`		PPDB Motif	`GCCCA`	PLACE Motif
REG	`TAAGGGTA`		+	23037041	23037048	-97	-90
	AtREG570	`TAAGGGTA`		PPDB Motif	`ACCCT`	PLACE Motif
REG	`ACCCTAGA`		+	23037070	23037077	-68	-61
	AtREG658	`ACCCTAGA`		PPDB Motif	`ACCCT`	PLACE Motif

Other Reliable Promoter Summary

TSS information

Type Sequence TPM score Genome position Gene model

Strand Position

TSS peak A 2 - 23036798 AT3G62240.1

Type	Sequence	TPM score	Genome position	Gene model
			Strand	Position
TSS peak	`A`	2	-	23036798	AT3G62240.1

TSS information from cDNA

Type Sequence Score Genome position Gene model

Strand Position

TSS clone T clone - 23036765 AT3G62240.1

Type	Sequence	Score	Genome position	Gene model
			Strand	Position
TSS clone	`T`	clone	-	23036765	AT3G62240.1

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 TTCTTCTTC - 23036775 23036783 AT3G62240.1

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	`TTCTTCTTC`	-	23036775	23036783	AT3G62240.1
GA	None	None	None
Inr	None	None	None

REG information

Type Sequence Annotation Genome position Gene model

Strand Start End

REG CTATTGGGCCATTAAG - 23036987 23037002 AT3G62240.1

AtREG624 CTATTGGG         PPDB Motif GCCCA PLACE Motif

AtREG355 TATTGGGC        PPDB Motif GCCCA PLACE Motif

AtREG352   ATTGGGCC       PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG420    TTGGGCCA      PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG437     TGGGCCAT     PPDB Motif GCCCA PLACE Motif GGGCC, TGGGCY

AtREG604         CCATTAAG PPDB Motif PLACE Motif TTAATGG

REG ATTTGGGCTTAGTTTTGGGCTTT - 23037014 23037036 AT3G62240.1

AtREG421 ATTTGGGC                PPDB Motif GCCCA PLACE Motif

AtREG469 TTTGGGCT    TTTGGGCT   PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG407   TTGGGCTT    TTGGGCTT PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG426    TGGGCTTA             PPDB Motif GCCCA PLACE Motif TGGGCY

AtREG634     GGGCTTAG            PPDB Motif GCCCA PLACE Motif

AtREG529             TTTTGGGC    PPDB Motif GCCCA PLACE Motif

AtREG376                TGGGCTTT PPDB Motif GCCCA PLACE Motif TGGGCY

REG TACCCTTA - 23037041 23037048 AT3G62240.1

AtREG570 TACCCTTA PPDB Motif ACCCT PLACE Motif

REG TCTAGGGT - 23037070 23037077 AT3G62240.1

AtREG658 TCTAGGGT PPDB Motif ACCCT PLACE Motif