PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

AT4G23750.2

Common Name

CRF2, ERF064, F9D16.220, TMO3

Organism

Arabidopsis thaliana

Taxonomic ID

3702

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis

Family

ERF

Protein Properties

Length: 343aa MW: 37872.5 Da PI: 6.6849

Description

cytokinin response factor 2

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT4G23750.2	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	AP2	59.8	6.3e-19	120	170	1	55
AP2 1 sgykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkleg 55 ++++GVr+++ +g+W+AeIrdp + r r +lg++ taeeAa +++a+ +l+g AT4G23750.2 120 KKFRGVRQRP-WGKWAAEIRDPLK---RVRLWLGTYNTAEEAAMVYDNAAIQLRG 170 59******.******754...5***********************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
CDD	cd00018	2.13E-32	120	177	No hit	No description
SuperFamily	SSF54171	1.11E-21	121	179	IPR016177	DNA-binding domain
Pfam	PF00847	6.8E-12	121	170	IPR001471	AP2/ERF domain
PROSITE profile	PS51032	23.406	121	178	IPR001471	AP2/ERF domain
Gene3D	G3DSA:3.30.730.10	1.0E-29	121	178	IPR001471	AP2/ERF domain
SMART	SM00380	2.1E-37	121	184	IPR001471	AP2/ERF domain
PRINTS	PR00367	7.7E-10	122	133	IPR001471	AP2/ERF domain
PRINTS	PR00367	7.7E-10	144	160	IPR001471	AP2/ERF domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009736	Biological Process	cytokinin-activated signaling pathway
GO:0009873	Biological Process	ethylene-activated signaling pathway
GO:0042991	Biological Process	transcription factor import into nucleus
GO:0048364	Biological Process	root development
GO:0048825	Biological Process	cotyledon development
GO:0005634	Cellular Component	nucleus
GO:0005737	Cellular Component	cytoplasm
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0042802	Molecular Function	identical protein binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000037	anatomy	shoot apex
PO:0000293	anatomy	guard cell
PO:0008019	anatomy	leaf lamina base
PO:0009005	anatomy	root
PO:0009006	anatomy	shoot system
PO:0009009	anatomy	plant embryo
PO:0009010	anatomy	seed
PO:0009025	anatomy	vascular leaf
PO:0009030	anatomy	carpel
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0009046	anatomy	flower
PO:0009052	anatomy	flower pedicel
PO:0020038	anatomy	petiole
PO:0020137	anatomy	leaf apex
PO:0025022	anatomy	collective leaf structure
PO:0001078	developmental stage	plant embryo cotyledonary stage
PO:0001081	developmental stage	mature plant embryo stage
PO:0001185	developmental stage	plant embryo globular stage
PO:0004507	developmental stage	plant embryo bilateral stage
PO:0007115	developmental stage	LP.04 four leaves visible stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 343 aa Download sequence Send to blast
MEAEKKMVLP RIKFTEHKTN TTTIVSELTN THQTRILRIS VTDPDATDSS SDDEEEEHQR 60 FVSKRRRVKK FVNEVYLDSG AVVTGSCGQM ESKKRQKRAV KSESTVSPVV SATTTTTGEK 120 KFRGVRQRPW GKWAAEIRDP LKRVRLWLGT YNTAEEAAMV YDNAAIQLRG PDALTNFSVT 180 PTTATEKKAP PPSPVKKKKK KNNKSKKSVT ASSSISRSSS NDCLCSPVSV LRSPFAVDEF 240 SGISSSPVAA VVVKEEPSMT TVSETFSDFS APLFSDDDVF DFRSSVVPDY LGGDLFGEDL 300 FTADMCTDMN FGFDFGSGLS SWHMEDHFQD IGDLFGSDPL LAV

Sequence ? help Back to Top

Protein Sequence Length: 343 aa Download sequence Send to blast

MEAEKKMVLP RIKFTEHKTN TTTIVSELTN THQTRILRIS VTDPDATDSS SDDEEEEHQR  60
FVSKRRRVKK FVNEVYLDSG AVVTGSCGQM ESKKRQKRAV KSESTVSPVV SATTTTTGEK  120
KFRGVRQRPW GKWAAEIRDP LKRVRLWLGT YNTAEEAAMV YDNAAIQLRG PDALTNFSVT  180
PTTATEKKAP PPSPVKKKKK KNNKSKKSVT ASSSISRSSS NDCLCSPVSV LRSPFAVDEF  240
SGISSSPVAA VVVKEEPSMT TVSETFSDFS APLFSDDDVF DFRSSVVPDY LGGDLFGEDL  300
FTADMCTDMN FGFDFGSGLS SWHMEDHFQD IGDLFGSDPL LAV

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1gcc_A	2e-20	120	177	1	59	ETHYLENE RESPONSIVE ELEMENT BINDING FACTOR 1
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	63	67	KRRRV
2	196	206	KKKKKNNKSKK

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.26323	0.0	flower\| seed

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	254235_at	0.0
Expression Atlas	AT4G23750	-
AtGenExpress	AT4G23750	-
ATTED-II	AT4G23750	-

Functional Description ? help Back to Top
Source	Description
TAIR	encodes a member of the ERF (ethylene response factor) subfamily B-5 of ERF/AP2 transcription factor family. The protein contains one AP2 domain. There are 7 members in this subfamily. Monopteros target gene.
UniProt	Component of the cytokinin signaling pathway involved in cotyledons, leaves, and embryos development. Probably acts as a transcriptional activator. Binds to the GCC-box pathogenesis-related promoter element. May be involved in the regulation of gene expression by stress factors and by components of stress signal transduction pathways (By similarity). {ECO:0000250, ECO:0000269\|PubMed:16832061}.

Function -- GeneRIF ? help Back to Top
Findings indicate that CRF2 signaling controls cellular organization and may promote metastatic potential of human CRC cells through an epithelial-mesenchymal transition like process. [PMID: 24260200] Results suggest that CRF2 and CRF3 respond to cold via TCS-dependent and TCS-independent pathways and control LR initiation and development, contributing to LR adaptation to cold stress. [PMID: 27432872]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00027	PBM	25215497	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT4G23750.2

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By cytokinins. {ECO:0000269\|PubMed:16832061}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source	Upstream Regulator (A: Activate/R: Repress)
ATRM	AT2G20180 (R)

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT4G23750, AT4G27950, AT5G53290, AT1G22985, AT1G71130
IntAct	Search Q9SUQ2

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT4G23750

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AL035394	0.0	AL035394.1 Arabidopsis thaliana DNA chromosome 4, BAC clone F9D16 (ESSAII project).
GenBank	AL161560	0.0	AL161560.2 Arabidopsis thaliana DNA chromosome 4, contig fragment No. 60.
GenBank	AY057475	0.0	AY057475.1 Arabidopsis thaliana AT4g23750/F9D16_220 mRNA, complete cds.
GenBank	BT015038	0.0	BT015038.1 Arabidopsis thaliana At4g23750 gene, complete cds.
GenBank	CP002687	0.0	CP002687.1 Arabidopsis thaliana chromosome 4 sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_194106.1	0.0	cytokinin response factor 2
Refseq	NP_974599.1	0.0	cytokinin response factor 2
Swissprot	Q9SUQ2	0.0	CRF2_ARATH; Ethylene-responsive transcription factor CRF2
TrEMBL	A0A178V319	0.0	A0A178V319_ARATH; TMO3
STRING	AT4G23750.1	0.0	(Arabidopsis thaliana)

Link Out ? help Back to Top
Phytozome	AT4G23750.2
Entrez Gene	828475
iHOP	AT4G23750
wikigenes	AT4G23750

Publications ? help Back to Top
Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Ma L, et al. Genomic evidence for COP1 as a repressor of light-regulated gene expression and development in Arabidopsis. Plant Cell, 2002. 14(10): p. 2383-98 [PMID:12368493] Che P,Gingerich DJ,Lall S,Howell SH Global and hormone-induced gene expression changes during shoot development in Arabidopsis. Plant Cell, 2002. 14(11): p. 2771-85 [PMID:12417700] Rashotte AM,Carson SD,To JP,Kieber JJ Expression profiling of cytokinin action in Arabidopsis. Plant Physiol., 2003. 132(4): p. 1998-2011 [PMID:12913156] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] Wang R, et al. Genomic analysis of the nitrate response using a nitrate reductase-null mutant of Arabidopsis. Plant Physiol., 2004. 136(1): p. 2512-22 [PMID:15333754] Kiba T,Aoki K,Sakakibara H,Mizuno T Arabidopsis response regulator, ARR22, ectopic expression of which results in phenotypes similar to the wol cytokinin-receptor mutant. Plant Cell Physiol., 2004. 45(8): p. 1063-77 [PMID:15356332] Kiba T, et al. Combinatorial microarray analysis revealing arabidopsis genes implicated in cytokinin responses through the His->Asp Phosphorelay circuitry. Plant Cell Physiol., 2005. 46(2): p. 339-55 [PMID:15695462] Duarte JM, et al. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol., 2006. 23(2): p. 469-78 [PMID:16280546] Nakano T,Suzuki K,Fujimura T,Shinshi H Genome-wide analysis of the ERF gene family in Arabidopsis and rice. Plant Physiol., 2006. 140(2): p. 411-32 [PMID:16407444] Rashotte AM, et al. A subset of Arabidopsis AP2 transcription factors mediates cytokinin responses in concert with a two-component pathway. Proc. Natl. Acad. Sci. U.S.A., 2006. 103(29): p. 11081-5 [PMID:16832061] Lee DJ, et al. Genome-wide expression profiling of ARABIDOPSIS RESPONSE REGULATOR 7(ARR7) overexpression in cytokinin response. Mol. Genet. Genomics, 2007. 277(2): p. 115-37 [PMID:17061125] Soitamo AJ,Piippo M,Allahverdiyeva Y,Battchikova N,Aro EM Light has a specific role in modulating Arabidopsis gene expression at low temperature. BMC Plant Biol., 2008. 8: p. 13 [PMID:18230142] Ascencio-Ib Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection. Plant Physiol., 2008. 148(1): p. 436-54 [PMID:18650403] Day RC,Herridge RP,Ambrose BA,Macknight RC Transcriptome analysis of proliferating Arabidopsis endosperm reveals biological implications for the control of syncytial division, cytokinin signaling, and gene expression regulation. Plant Physiol., 2008. 148(4): p. 1964-84 [PMID:18923020] Oh E, et al. Genome-wide analysis of genes targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during seed germination in Arabidopsis. Plant Cell, 2009. 21(2): p. 403-19 [PMID:19244139] Schlereth A, et al. MONOPTEROS controls embryonic root initiation by regulating a mobile transcription factor. Nature, 2010. 464(7290): p. 913-6 [PMID:20220754] Cutcliffe JW,Hellmann E,Heyl A,Rashotte AM CRFs form protein-protein interactions with each other and with members of the cytokinin signalling pathway in Arabidopsis via the CRF domain. J. Exp. Bot., 2011. 62(14): p. 4995-5002 [PMID:21705390] Ducarouge B, et al. CRF2 signaling is a novel regulator of cellular adhesion and migration in colorectal cancer cells. PLoS ONE, 2013. 8(11): p. e79335 [PMID:24260200] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Jin J, et al. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors. Mol. Biol. Evol., 2015. 32(7): p. 1767-73 [PMID:25750178] Ckurshumova W,Berleth T Overcoming recalcitrance - Auxin response factor functions in plant regeneration. Plant Signal Behav, 2015. 10(7): p. e993293 [PMID:26098229] Raines T, et al. The cytokinin response factors modulate root and shoot growth and promote leaf senescence in Arabidopsis. Plant J., 2016. 85(1): p. 134-47 [PMID:26662515] Jeon J,Cho C,Lee MR,Van Binh N,Kim J CYTOKININ RESPONSE FACTOR2 (CRF2) and CRF3 Regulate Lateral Root Development in Response to Cold Stress in Arabidopsis. Plant Cell, 2016. 28(8): p. 1828-43 [PMID:27432872]