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

AT5G51990.1

Common Name

CBF4, DREB1D, ERF028, MSG15.7

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: 224aa MW: 24955.9 Da PI: 5.4406

Description

C-repeat-binding factor 4

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT5G51990.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	AP2	57.5	3.4e-18	53	102	2	55
AP2 2 gykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkleg 55 y+GVr++ +g+Wv+e+r+p +k+ r++lg+f t e+Aa+a++ a+++l+g AT5G51990.1 53 IYRGVRQRN-SGKWVCEVREP---NKKSRIWLGTFPTVEMAARAHDVAALALRG 102 69**999.7**9998...347***********************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
CDD	cd00018	3.62E-31	52	112	No hit	No description
Pfam	PF00847	3.2E-14	52	102	IPR001471	AP2/ERF domain
Gene3D	G3DSA:3.30.730.10	5.7E-32	53	112	IPR001471	AP2/ERF domain
SuperFamily	SSF54171	2.55E-21	53	112	IPR016177	DNA-binding domain
PROSITE profile	PS51032	22.247	53	110	IPR001471	AP2/ERF domain
SMART	SM00380	6.8E-31	53	116	IPR001471	AP2/ERF domain
PRINTS	PR00367	8.4E-9	54	65	IPR001471	AP2/ERF domain
PRINTS	PR00367	8.4E-9	76	92	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:0009738	Biological Process	abscisic acid-activated signaling pathway
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000293	anatomy	guard cell
PO:0009005	anatomy	root
PO:0009030	anatomy	carpel
PO:0009047	anatomy	stem
PO:0009052	anatomy	flower pedicel
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 224 aa Download sequence Send to blast
MNPFYSTFPD SFLSISDHRS PVSDSSECSP KLASSCPKKR AGRKKFRETR HPIYRGVRQR 60 NSGKWVCEVR EPNKKSRIWL GTFPTVEMAA RAHDVAALAL RGRSACLNFA DSAWRLRIPE 120 TTCPKEIQKA ASEAAMAFQN ETTTEGSKTA AEAEEAAGEG VREGERRAEE QNGGVFYMDD 180 EALLGMPNFF ENMAEGMLLP PPEVGWNHND FDGVGDVSLW SFDE

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5wx9_A	6e-14	51	109	12	71	Ethylene-responsive transcription factor ERF096
Search in ModeBase

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	248389_at	0.0
Expression Atlas	AT5G51990	-
AtGenExpress	AT5G51990	-
ATTED-II	AT5G51990	-

Functional Description ? help Back to Top
Source	Description
TAIR	encodes a member of the DREB subfamily A-1 of ERF/AP2 transcription factor family (CBF4). The protein contains one AP2 domain. There are six members in this subfamily, including CBF1, CBF2, and CBF3. This gene is involved in response to drought stress and abscisic acid treatment, but not to low temperature.
UniProt	Transcriptional activator that binds specifically to the DNA sequence 5'-[AG]CCGAC-3'. Binding to the C-repeat/DRE element mediates abscisic acid- and dehydration-inducible transcription. CBF/DREB1 factors play a key role in freezing tolerance and cold acclimation. {ECO:0000269\|PubMed:11798174, ECO:0000269\|PubMed:12376631}.

Function -- GeneRIF ? help Back to Top
Vascular plant one-zinc-finger proteins (VOZs) negatively affect CBF4 expression in an activating abscisic acid-mediated (ABA)-independent manner. [PMID: 23167462]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00557	DAP	27203113	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT5G51990.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By high-salt stress, drought stress and abscisic acid (ABA) treatment. {ECO:0000269\|PubMed:11798174, ECO:0000269\|PubMed:12376631}.

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

Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source	Target Gene (A: Activate/R: Repress)
ATRM	AT2G42540(A), AT5G52310(A)

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT5G51990

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	EF523169	0.0	EF523169.1 Arabidopsis thaliana ecotype Oy-0 C-repeat binding factor 4 (CBF4) mRNA, complete cds.
GenBank	EF523170	0.0	EF523170.1 Arabidopsis thaliana ecotype Yo-0 C-repeat binding factor 4 (CBF4) mRNA, complete cds.
GenBank	EF523171	0.0	EF523171.1 Arabidopsis thaliana ecotype Ag-0 C-repeat binding factor 4 (CBF4) mRNA, complete cds.
GenBank	EF523172	0.0	EF523172.1 Arabidopsis thaliana ecotype Ak-1 C-repeat binding factor 4 (CBF4) mRNA, complete cds.
GenBank	EF523174	0.0	EF523174.1 Arabidopsis thaliana ecotype Bs-1 C-repeat binding factor 4 (CBF4) mRNA, complete cds.
GenBank	EF523175	0.0	EF523175.1 Arabidopsis thaliana ecotype Gre-0 C-repeat binding factor 4 (CBF4) mRNA, complete cds.
GenBank	EF523176	0.0	EF523176.1 Arabidopsis thaliana ecotype Co-1 C-repeat binding factor 4 (CBF4) mRNA, complete cds.
GenBank	EF523177	0.0	EF523177.1 Arabidopsis thaliana ecotype Can-0 C-repeat binding factor 4 (CBF4) mRNA, complete cds.
GenBank	EF523178	0.0	EF523178.1 Arabidopsis thaliana ecotype Cvi-0 C-repeat binding factor 4 (CBF4) mRNA, complete cds.
GenBank	EF523179	0.0	EF523179.1 Arabidopsis thaliana ecotype Kin-0 C-repeat binding factor 4 (CBF4) mRNA, complete cds.
GenBank	EF523180	0.0	EF523180.1 Arabidopsis thaliana ecotype Lip-0 C-repeat binding factor 4 (CBF4) mRNA, complete cds.
GenBank	EF523181	0.0	EF523181.1 Arabidopsis thaliana ecotype Pog-0 C-repeat binding factor 4 (CBF4) mRNA, complete cds.
GenBank	EF523182	0.0	EF523182.1 Arabidopsis thaliana ecotype Van-0 C-repeat binding factor 4 (CBF4) mRNA, complete cds.
GenBank	EF523183	0.0	EF523183.1 Arabidopsis thaliana ecotype Bla-1 C-repeat binding factor 4 (CBF4) mRNA, complete cds.
GenBank	EF523185	0.0	EF523185.1 Arabidopsis thaliana ecotype Hau-0 C-repeat binding factor 4 (CBF4) mRNA, complete cds.
GenBank	EF523186	0.0	EF523186.1 Arabidopsis thaliana ecotype Mv-0 C-repeat binding factor 4 (CBF4) mRNA, complete cds.
GenBank	EF523188	0.0	EF523188.1 Arabidopsis thaliana ecotype Bur-0 C-repeat binding factor 4 (CBF4) mRNA, complete cds.
GenBank	EF523189	0.0	EF523189.1 Arabidopsis thaliana ecotype Per-3 C-repeat binding factor 4 (CBF4) mRNA, complete cds.
GenBank	EF523191	0.0	EF523191.1 Arabidopsis thaliana ecotype Sapporo-0 C-repeat binding factor 4 (CBF4) mRNA, complete cds.
GenBank	EF523192	0.0	EF523192.1 Arabidopsis thaliana ecotype Tscha-1 C-repeat binding factor 4 (CBF4) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_200012.1	1e-167	C-repeat-binding factor 4
Swissprot	Q9FJ93	1e-168	DRE1D_ARATH; Dehydration-responsive element-binding protein 1D
TrEMBL	B2BJ26	1e-166	B2BJ26_ARATH; C-repeat binding factor 4
STRING	AT5G51990.1	1e-167	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM355	28	187
Representative plant	OGRP6	16	1718

Link Out ? help Back to Top
Phytozome	AT5G51990.1
Entrez Gene	835274
iHOP	AT5G51990
wikigenes	AT5G51990

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] Sakuma Y, et al. DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration- and cold-inducible gene expression. Biochem. Biophys. Res. Commun., 2002. 290(3): p. 998-1009 [PMID:11798174] Hanano S, et al. Analysis of gene expression in Arabidopsis thaliana by array hybridization with genomic DNA fragments aligned along chromosomal regions. Plant J., 2002. 30(2): p. 247-55 [PMID:12000460] Haake V, et al. Transcription factor CBF4 is a regulator of drought adaptation in Arabidopsis. Plant Physiol., 2002. 130(2): p. 639-48 [PMID:12376631] Vandepoele K,Simillion C,Van de Peer Y Detecting the undetectable: uncovering duplicated segments in Arabidopsis by comparison with rice. Trends Genet., 2002. 18(12): p. 606-8 [PMID:12446138] Dal Bosco C, et al. Inactivation of the chloroplast ATP synthase gamma subunit results in high non-photochemical fluorescence quenching and altered nuclear gene expression in Arabidopsis thaliana. J. Biol. Chem., 2004. 279(2): p. 1060-9 [PMID:14576160] Navarro L, et al. The transcriptional innate immune response to flg22. Interplay and overlap with Avr gene-dependent defense responses and bacterial pathogenesis. Plant Physiol., 2004. 135(2): p. 1113-28 [PMID:15181213] Lee BH,Henderson DA,Zhu JK The Arabidopsis cold-responsive transcriptome and its regulation by ICE1. Plant Cell, 2005. 17(11): p. 3155-75 [PMID:16214899] Suzuki N, et al. Enhanced tolerance to environmental stress in transgenic plants expressing the transcriptional coactivator multiprotein bridging factor 1c. Plant Physiol., 2005. 139(3): p. 1313-22 [PMID:16244138] 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] Xiong Y,Fei SZ Functional and phylogenetic analysis of a DREB/CBF-like gene in perennial ryegrass (Lolium perenne L.). Planta, 2006. 224(4): p. 878-88 [PMID:16614820] Underwood BA,Vanderhaeghen R,Whitford R,Town CD,Hilson P Simultaneous high-throughput recombinational cloning of open reading frames in closed and open configurations. Plant Biotechnol. J., 2006. 4(3): p. 317-24 [PMID:17147637] Zhou N,Robinson SJ,Huebert T,Bate NJ,Parkin IA Comparative genome organization reveals a single copy of CBF in the freezing tolerant crucifer Thlaspi arvense. Plant Mol. Biol., 2007. 65(5): p. 693-705 [PMID:17899397] Jung C, et al. Overexpression of AtMYB44 enhances stomatal closure to confer abiotic stress tolerance in transgenic Arabidopsis. Plant Physiol., 2008. 146(2): p. 623-35 [PMID:18162593] Welling A,Palva ET Involvement of CBF transcription factors in winter hardiness in birch. Plant Physiol., 2008. 147(3): p. 1199-211 [PMID:18467468] Lin YH, et al. Molecular population genetics and gene expression analysis of duplicated CBF genes of Arabidopsis thaliana. BMC Plant Biol., 2008. 8: p. 111 [PMID:18990244] Wang Y,Hua J A moderate decrease in temperature induces COR15a expression through the CBF signaling cascade and enhances freezing tolerance. Plant J., 2009. 60(2): p. 340-9 [PMID:19563440] Abdeen A,Schnell J,Miki B Transcriptome analysis reveals absence of unintended effects in drought-tolerant transgenic plants overexpressing the transcription factor ABF3. BMC Genomics, 2010. 11: p. 69 [PMID:20105335] Causier B,Ashworth M,Guo W,Davies B The TOPLESS interactome: a framework for gene repression in Arabidopsis. Plant Physiol., 2012. 158(1): p. 423-38 [PMID:22065421] Nakai Y, et al. Vascular plant one-zinc-finger protein 1/2 transcription factors regulate abiotic and biotic stress responses in Arabidopsis. Plant J., 2013. 73(5): p. 761-75 [PMID:23167462] Efroni I, et al. Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses. Dev. Cell, 2013. 24(4): p. 438-45 [PMID:23449474] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Guttikonda SK, et al. Overexpression of AtDREB1D transcription factor improves drought tolerance in soybean. Mol. Biol. Rep., 2014. 41(12): p. 7995-8008 [PMID:25192890] 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] Zhang T, et al. Overexpression of a NF-YB3 transcription factor from Picea wilsonii confers tolerance to salinity and drought stress in transformed Arabidopsis thaliana. Plant Physiol. Biochem., 2015. 94: p. 153-64 [PMID:26093308] Carlow CE, et al. Nuclear localization and transactivation by Vitis CBF transcription factors are regulated by combinations of conserved amino acid domains. Plant Physiol. Biochem., 2017. 118: p. 306-319 [PMID:28675818] Li B, et al. Network-Guided Discovery of Extensive Epistasis between Transcription Factors Involved in Aliphatic Glucosinolate Biosynthesis. Plant Cell, 2018. 30(1): p. 178-195 [PMID:29317470]