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

AT3G47500.1

Common Name

CDF3, DOF3.3, F1P2.50, HPPBF-2A

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

Dof

Protein Properties

Length: 448aa MW: 49730.3 Da PI: 7.0586

Description

cycling DOF factor 3

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT3G47500.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-Dof	125.7	1.4e-39	106	166	2	62
zf-Dof 2 kekalkcprCdstntkfCyynnyslsqPryfCkaCrryWtkGGalrnvPvGggrrknkkss 62 ++k+l+cprC+s++tkfCyynny+++qPr+fCkaC+ryWt+GG++rnvPvG+grrknk+ss AT3G47500.1 106 PTKILPCPRCKSMETKFCYYNNYNINQPRHFCKACQRYWTAGGTMRNVPVGAGRRKNKSSS 166 67899*****************************************************987 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
ProDom	PD007478	1.0E-31	103	163	IPR003851	Zinc finger, Dof-type
Pfam	PF02701	7.4E-32	108	164	IPR003851	Zinc finger, Dof-type
PROSITE profile	PS50884	28.556	110	164	IPR003851	Zinc finger, Dof-type
PROSITE pattern	PS01361	0	112	148	IPR003851	Zinc finger, Dof-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009908	Biological Process	flower development
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0005515	Molecular Function	protein binding
GO:0046872	Molecular Function	metal ion binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000013	anatomy	cauline leaf
PO:0000037	anatomy	shoot apex
PO:0000084	anatomy	plant sperm cell
PO:0000230	anatomy	inflorescence meristem
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:0009029	anatomy	stamen
PO:0009030	anatomy	carpel
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0009046	anatomy	flower
PO:0009047	anatomy	stem
PO:0009052	anatomy	flower pedicel
PO:0020030	anatomy	cotyledon
PO:0020038	anatomy	petiole
PO:0020100	anatomy	hypocotyl
PO:0020137	anatomy	leaf apex
PO:0025022	anatomy	collective leaf structure
PO:0025195	anatomy	pollen tube cell
PO:0025281	anatomy	pollen
PO:0001054	developmental stage	vascular leaf senescent stage
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:0007064	developmental stage	LP.12 twelve leaves visible stage
PO:0007095	developmental stage	LP.08 eight leaves visible stage
PO:0007098	developmental stage	LP.02 two leaves visible stage
PO:0007103	developmental stage	LP.10 ten leaves visible stage
PO:0007115	developmental stage	LP.04 four leaves visible stage
PO:0007123	developmental stage	LP.06 six 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: 448 aa Download sequence Send to blast
MMMETRDPAI KLFGMKIPFP SVFESAVTVE DDEEDDWSGG DDKSPEKVTP ELSDKNNNNC 60 NDNSFNNSKP ETLDKEEATS TDQIESSDTP EDNQQTTPDG KTLKKPTKIL PCPRCKSMET 120 KFCYYNNYNI NQPRHFCKAC QRYWTAGGTM RNVPVGAGRR KNKSSSSHYR HITISEALEA 180 ARLDPGLQAN TRVLSFGLEA QQQHVAAPMT PVMKLQEDQK VSNGARNRFH GLADQRLVAR 240 VENGDDCSSG SSVTTSNNHS VDESRAQSGS VVEAQMNNNN NNNMNGYACI PGVPWPYTWN 300 PAMPPPGFYP PPGYPMPFYP YWTIPMLPPH QSSSPISQKC SNTNSPTLGK HPRDEGSSKK 360 DNETERKQKA GCVLVPKTLR IDDPNEAAKS SIWTTLGIKN EAMCKAGGMF KGFDHKTKMY 420 NNDKAENSPV LSANPAALSR SHNFHEQI

Sequence ? help Back to Top

Protein Sequence Length: 448 aa Download sequence Send to blast

MMMETRDPAI KLFGMKIPFP SVFESAVTVE DDEEDDWSGG DDKSPEKVTP ELSDKNNNNC  60
NDNSFNNSKP ETLDKEEATS TDQIESSDTP EDNQQTTPDG KTLKKPTKIL PCPRCKSMET  120
KFCYYNNYNI NQPRHFCKAC QRYWTAGGTM RNVPVGAGRR KNKSSSSHYR HITISEALEA  180
ARLDPGLQAN TRVLSFGLEA QQQHVAAPMT PVMKLQEDQK VSNGARNRFH GLADQRLVAR  240
VENGDDCSSG SSVTTSNNHS VDESRAQSGS VVEAQMNNNN NNNMNGYACI PGVPWPYTWN  300
PAMPPPGFYP PPGYPMPFYP YWTIPMLPPH QSSSPISQKC SNTNSPTLGK HPRDEGSSKK  360
DNETERKQKA GCVLVPKTLR IDDPNEAAKS SIWTTLGIKN EAMCKAGGMF KGFDHKTKMY  420
NNDKAENSPV LSANPAALSR SHNFHEQI

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.519	0.0	silique

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	186510750	0.0
Genevisible	252429_at	0.0
Expression Atlas	AT3G47500	-
AtGenExpress	AT3G47500	-
ATTED-II	AT3G47500	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in the vasculature of cotyledons and hypocotyls, leaves and roots. {ECO:0000269\|PubMed:19619493}.

Functional Description ? help Back to Top
Source	Description
TAIR	Dof-type zinc finger domain-containing protein, identical to H-protein promoter binding factor-2a GI:3386546 from (Arabidopsis thaliana). Interacts with LKP2 and FKF1, but its overexpression does not change flowering time under short or long day conditions.
UniProt	Transcription factor that binds specifically to a 5'-AA[AG]G-3' consensus core sequence (By similarity). Regulates a photoperiodic flowering response. Transcriptional repressor of 'CONSTANS' expression. {ECO:0000250, ECO:0000269\|PubMed:19619493}.

Function -- GeneRIF ? help Back to Top
CDF3 plays a multifaceted role acting on both flowering time and abiotic stress tolerance, in part by controlling the CBF/DREB2A-CRT/DRE and ZAT10/12 modules. [PMID: 28044345]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00394	DAP	27203113	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT3G47500.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Circadian-regulation. Highly expressed at the beginning of the light period, then decreases, reaching a minimum between 16 and 29 hours after dawn before rising again at the end of the day. {ECO:0000269\|PubMed:19619493}.

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

Interaction ? help Back to Top
Source	Intact With
IntAct	Search Q8LFV3

Phenotype -- Disruption Phenotype ? help Back to Top
Source	Description
UniProt	DISRUPTION PHENOTYPE: No alteration in flowering time, probably due to the redundancy with CDF1, CDF2 and CDF5. {ECO:0000269\|PubMed:19619493}.

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT3G47500

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AY065152	0.0	AY065152.1 Arabidopsis thaliana H-protein promoter binding factor-2a (At3g47500; F1P2.50) mRNA, complete cds.
GenBank	AY128757	0.0	AY128757.1 Arabidopsis thaliana H-protein promoter binding factor-2a (At3g47500) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_190334.1	0.0	cycling DOF factor 3
Swissprot	Q8LFV3	0.0	CDF3_ARATH; Cyclic dof factor 3
TrEMBL	A0A178VE67	0.0	A0A178VE67_ARATH; CDF3
STRING	AT3G47500.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5441	28	48
Representative plant	OGRP38	17	445

Link Out ? help Back to Top
Phytozome	AT3G47500.1
Entrez Gene	823904
iHOP	AT3G47500
wikigenes	AT3G47500

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] Yanagisawa S The Dof family of plant transcription factors. Trends Plant Sci., 2002. 7(12): p. 555-60 [PMID:12475498] Kreps JA, et al. Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiol., 2002. 130(4): p. 2129-41 [PMID:12481097] Hudson ME,Lisch DR,Quail PH The FHY3 and FAR1 genes encode transposase-related proteins involved in regulation of gene expression by the phytochrome A-signaling pathway. Plant J., 2003. 34(4): p. 453-71 [PMID:12753585] Lijavetzky D,Carbonero P,Vicente-Carbajosa J Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families. BMC Evol. Biol., 2003. 3: p. 17 [PMID:12877745] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] Tepperman JM, et al. Expression profiling of phyB mutant demonstrates substantial contribution of other phytochromes to red-light-regulated gene expression during seedling de-etiolation. Plant J., 2004. 38(5): p. 725-39 [PMID:15144375] Vogel JT,Zarka DG,Van Buskirk HA,Fowler SG,Thomashow MF Roles of the CBF2 and ZAT12 transcription factors in configuring the low temperature transcriptome of Arabidopsis. Plant J., 2005. 41(2): p. 195-211 [PMID:15634197] Imaizumi T,Schultz TF,Harmon FG,Ho LA,Kay SA FKF1 F-box protein mediates cyclic degradation of a repressor of CONSTANS in Arabidopsis. Science, 2005. 309(5732): p. 293-7 [PMID:16002617] Delessert C, et al. The transcription factor ATAF2 represses the expression of pathogenesis-related genes in Arabidopsis. Plant J., 2005. 43(5): p. 745-57 [PMID:16115070] 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] Khanna R, et al. Functional profiling reveals that only a small number of phytochrome-regulated early-response genes in Arabidopsis are necessary for optimal deetiolation. Plant Cell, 2006. 18(9): p. 2157-71 [PMID:16891401] Chawade A,Br Putative cold acclimation pathways in Arabidopsis thaliana identified by a combined analysis of mRNA co-expression patterns, promoter motifs and transcription factors. BMC Genomics, 2007. 8: p. 304 [PMID:17764576] 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] Borges F, et al. Comparative transcriptomics of Arabidopsis sperm cells. Plant Physiol., 2008. 148(2): p. 1168-81 [PMID:18667720] Wang Y, et al. Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis. Plant Physiol., 2008. 148(3): p. 1201-11 [PMID:18775970] Fornara F, et al. Arabidopsis DOF transcription factors act redundantly to reduce CONSTANS expression and are essential for a photoperiodic flowering response. Dev. Cell, 2009. 17(1): p. 75-86 [PMID:19619493] Jung CH,Wong CE,Singh MB,Bhalla PL Comparative genomic analysis of soybean flowering genes. PLoS ONE, 2012. 7(6): p. e38250 [PMID:22679494] Ding Y, et al. Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biol., 2013. 13: p. 229 [PMID:24377444] Corrales AR, et al. Multifaceted role of cycling DOF factor 3 (CDF3) in the regulation of flowering time and abiotic stress responses in Arabidopsis. Plant Cell Environ., 2017. 40(5): p. 748-764 [PMID:28044345] Renau-Morata B, et al. Ectopic Expression of CDF3 Genes in Tomato Enhances Biomass Production and Yield under Salinity Stress Conditions. Front Plant Sci, 2017. 8: p. 660 [PMID:28515731] Henriques R, et al. The antiphasic regulatory module comprising CDF5 and its antisense RNA FLORE links the circadian clock to photoperiodic flowering. New Phytol., 2017. 216(3): p. 854-867 [PMID:28758689]