PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT3G25730.1
Common NameEDF3, K13N2.14, K13N2.7
Organism
Arabidopsis thaliana
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family RAV
Protein Properties Length: 333aa    MW: 37755.8 Da    PI: 9.7218
Description ethylene response DNA binding factor 3
Gene Model
Gene Model ID Type Source Coding Sequence
AT3G25730.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1AP240.66.5e-1360108155
          AP2   1 sgykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkleg 55 
                  s++kGV   + +grW A+I++      ++r++lg+f  ++eAa+a++ a+ +++g
  AT3G25730.1  60 SRFKGVVPQP-NGRWGAQIYEK-----HQRVWLGTFNEEDEAARAYDVAAHRFRG 108
                  689***9788.8*********3.....5**********99************998 PP
2B31023.3e-32183288199
                  EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE. CS
           B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefe 91 
                  f+k+ tpsdv+k++rlv+pk+ ae+h       ++++ +++ l +ed +g++W+++++y+++s++yvltkGW++Fvk+++L++gD + Fk++++++++
  AT3G25730.1 183 FEKTVTPSDVGKLNRLVIPKHQAEKHfplplgnNNVSVKGMLLNFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKRLCAGDLISFKRSNDQDQK 280
                  99*****************************9977888****************************************************99999999 PP

                  .EEEEE-S CS
           B3  92 lvvkvfrk 99 
                  +++++ +k
  AT3G25730.1 281 FFIGWKSK 288
                  99999876 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF008472.9E-860108IPR001471AP2/ERF domain
CDDcd000185.79E-2660118No hitNo description
SuperFamilySSF541713.66E-1760117IPR016177DNA-binding domain
Gene3DG3DSA:3.30.730.102.2E-2061117IPR001471AP2/ERF domain
SMARTSM003803.8E-2861122IPR001471AP2/ERF domain
PROSITE profilePS5103220.08661116IPR001471AP2/ERF domain
Gene3DG3DSA:2.40.330.105.2E-39176289IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019361.96E-31181290IPR015300DNA-binding pseudobarrel domain
CDDcd100177.54E-27182276No hitNo description
PfamPF023622.9E-28183288IPR003340B3 DNA binding domain
PROSITE profilePS5086313.987183289IPR003340B3 DNA binding domain
SMARTSM010193.6E-25183289IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009873Biological Processethylene-activated signaling pathway
GO:0005634Cellular Componentnucleus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0044212Molecular Functiontranscription regulatory region DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000293anatomyguard cell
PO:0009005anatomyroot
PO:0009010anatomyseed
PO:0009046anatomyflower
PO:0020030anatomycotyledon
PO:0020100anatomyhypocotyl
PO:0007611developmental stagepetal differentiation and expansion stage
Sequence ? help Back to Top
Protein Sequence    Length: 333 aa     Download sequence    Send to blast
MDAMSSVDES STTTDSIPAR KSSSPASLLY RMGSGTSVVL DSENGVEVEV EAESRKLPSS  60
RFKGVVPQPN GRWGAQIYEK HQRVWLGTFN EEDEAARAYD VAAHRFRGRD AVTNFKDTTF  120
EEEVEFLNAH SKSEIVDMLR KHTYKEELDQ RKRNRDGNGK ETTAFALASM VVMTGFKTAE  180
LLFEKTVTPS DVGKLNRLVI PKHQAEKHFP LPLGNNNVSV KGMLLNFEDV NGKVWRFRYS  240
YWNSSQSYVL TKGWSRFVKE KRLCAGDLIS FKRSNDQDQK FFIGWKSKSG LDLETGRVMR  300
LFGVDISLNA VVVVKETTEV LMSSLRCKKQ RVL
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1wid_A9e-6517929510124DNA-binding protein RAV1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.373310.0seed
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO1865104230.0
Genevisible257643_at0.0
Expression AtlasAT3G25730-
AtGenExpressAT3G25730-
ATTED-IIAT3G25730-
Functional Description ? help Back to Top
Source Description
UniProtProbably 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}.
Function -- GeneRIF ? help Back to Top
  1. Data show that FOREVER YOUNG FLOWER UP-REGULATING FACTOR1 (FUF1; At1g71450) acts as an activator in suppressing ETHYLENE RESPONSE DNA BINDING FACTORs EDF1/2/3/4 function and senescence/abscission of the flowers.
    [PMID: 26063506]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00031PBM25215497Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT3G25730.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT3G25730
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB0286070.0AB028607.1 Arabidopsis thaliana genomic DNA, chromosome 3, TAC clone:K13N2.
GenBankAJ4410730.0AJ441073.1 Arabidopsis thaliana mRNA for putative auxin response factor 14 (arf14 gene).
GenBankAK2294150.0AK229415.1 Arabidopsis thaliana mRNA for AP2 domain transcription factor, complete cds, clone: RAFL16-68-B16.
GenBankCP0026860.0CP002686.1 Arabidopsis thaliana chromosome 3, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_189201.10.0ethylene response DNA binding factor 3
SwissprotQ9LS060.0RAVL4_ARATH; AP2/ERF and B3 domain-containing transcription factor ARF14
TrEMBLA0A178VJD40.0A0A178VJD4_ARATH; EDF3
STRINGAT3G25730.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM84827121
Representative plantOGRP36516108
Publications ? help Back to Top
  1. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  2. 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]
  3. Hu YX,Wang YX,Liu XF,Li JY
    Arabidopsis RAV1 is down-regulated by brassinosteroid and may act as a negative regulator during plant development.
    Cell Res., 2004. 14(1): p. 8-15
    [PMID:15040885]
  4. Stepanova AN,Hoyt JM,Hamilton AA,Alonso JM
    A Link between ethylene and auxin uncovered by the characterization of two root-specific ethylene-insensitive mutants in Arabidopsis.
    Plant Cell, 2005. 17(8): p. 2230-42
    [PMID:15980261]
  5. 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]
  6. Swaminathan K,Peterson K,Jack T
    The plant B3 superfamily.
    Trends Plant Sci., 2008. 13(12): p. 647-55
    [PMID:18986826]
  7. Ikeda M,Ohme-Takagi M
    A novel group of transcriptional repressors in Arabidopsis.
    Plant Cell Physiol., 2009. 50(5): p. 970-5
    [PMID:19324928]
  8. Gaudinier A, et al.
    Enhanced Y1H assays for Arabidopsis.
    Nat. Methods, 2011. 8(12): p. 1053-5
    [PMID:22037706]
  9. Chen WH,Li PF,Chen MK,Lee YI,Yang CH
    FOREVER YOUNG FLOWER Negatively Regulates Ethylene Response DNA-Binding Factors by Activating an Ethylene-Responsive Factor to Control Arabidopsis Floral Organ Senescence and Abscission.
    Plant Physiol., 2015. 168(4): p. 1666-83
    [PMID:26063506]