PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT5G53290.1
Common NameCRF3, ERF065, K19E1.9
Organism
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 ERF
Protein Properties Length: 354aa    MW: 40100.2 Da    PI: 4.2916
Description cytokinin response factor 3
Gene Model
Gene Model ID Type Source Coding Sequence
AT5G53290.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1AP262.78.2e-20123173155
          AP2   1 sgykGVrwdkkrgrWvAeIrdpsengkrkrfslgkfgtaeeAakaaiaarkkleg 55 
                  ++++GVr+++ +g+W+AeIrdp +   r+r++lg+f taeeAa  +++a+ +l+g
  AT5G53290.1 123 KKFRGVRQRP-WGKWAAEIRDPEQ---RRRIWLGTFETAEEAAVVYDNAAIRLRG 173
                  59********.**********743...5*************************99 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd000184.72E-34123180No hitNo description
Gene3DG3DSA:3.30.730.103.2E-30124181IPR001471AP2/ERF domain
PROSITE profilePS5103223.775124181IPR001471AP2/ERF domain
PfamPF008474.4E-12124173IPR001471AP2/ERF domain
SMARTSM003801.7E-39124187IPR001471AP2/ERF domain
SuperFamilySSF541711.18E-21124182IPR016177DNA-binding domain
PRINTSPR003672.6E-10125136IPR001471AP2/ERF domain
PRINTSPR003672.6E-10147163IPR001471AP2/ERF domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009736Biological Processcytokinin-activated signaling pathway
GO:0009873Biological Processethylene-activated signaling pathway
GO:0042991Biological Processtranscription factor import into nucleus
GO:0048825Biological Processcotyledon development
GO:0005634Cellular Componentnucleus
GO:0005737Cellular Componentcytoplasm
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000037anatomyshoot apex
PO:0000293anatomyguard cell
PO:0009005anatomyroot
PO:0009025anatomyvascular leaf
Sequence ? help Back to Top
Protein Sequence    Length: 354 aa     Download sequence    Send to blast
MDEYIDFRPL KYTEHKTSMT KYTKKSSEKL SGGKSLKKVS ICYTDPDATD SSSDEDEEDF  60
LFPRRRVKRF VNEITVEPSC NNVVTGVSMK DRKRLSSSSD ETQSPASSRQ RPNNKVSVSG  120
QIKKFRGVRQ RPWGKWAAEI RDPEQRRRIW LGTFETAEEA AVVYDNAAIR LRGPDALTNF  180
SIPPQEEEEE EEPEPVIEEK PVIMTTPTPT TSSSESTEED LQHLSSPTSV LNHRSEEIQQ  240
VQQPFKSAKP EPGVSNAPWW HTGFNTGLGE SDDSFPLDTP FLDNYFNESP PEMSIFDQPM  300
DQIFCENDDI FNDMLFLGGE TMNIEDELTS SSIKDMGSTF SDFDDSLISD LLVA
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1gcc_A2e-22123182161ETHYLENE RESPONSIVE ELEMENT BINDING FACTOR 1
Search in ModeBase
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible248253_at0.0
Expression AtlasAT5G53290-
AtGenExpressAT5G53290-
ATTED-IIAT5G53290-
Functional Description ? help Back to Top
Source Description
TAIRencodes 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.
UniProtComponent 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
  1. CRFs represent a missing cross-talk component that fine-tunes auxin transport capacity downstream of cytokinin signalling to control plant development via transcriptional regulation of PIN-FORMED auxin transporters..
    [PMID: 26541513]
  2. 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]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT5G53290.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
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
BioGRIDAT5G53290, AT1G22985, AT1G71130
IntActSearch Q9FK12
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT5G53290
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB0133880.0AB013388.1 Arabidopsis thaliana genomic DNA, chromosome 5, TAC clone:K19E1.
GenBankAY5608780.0AY560878.1 Arabidopsis thaliana putative AP2/EREBP transcription factor (At5g53290) mRNA, complete cds.
GenBankBT0202440.0BT020244.1 Arabidopsis thaliana At5g53290 gene, complete cds.
GenBankBT0211360.0BT021136.1 Arabidopsis thaliana At5g53290 gene, complete cds.
GenBankCP0026880.0CP002688.1 Arabidopsis thaliana chromosome 5 sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_200141.10.0cytokinin response factor 3
SwissprotQ9FK120.0CRF3_ARATH; Ethylene-responsive transcription factor CRF3
TrEMBLA0A178UA300.0A0A178UA30_ARATH; CRF3
STRINGAT5G53290.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM22292576
Representative plantOGRP6161718
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. 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]
  3. 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]
  4. 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]
  5. Osuna D, et al.
    Temporal responses of transcripts, enzyme activities and metabolites after adding sucrose to carbon-deprived Arabidopsis seedlings.
    Plant J., 2007. 49(3): p. 463-91
    [PMID:17217462]
  6. 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]
  7. 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]
  8. 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]
  9. Xu K, et al.
    A genome-wide transcriptome profiling reveals the early molecular events during callus initiation in Arabidopsis multiple organs.
    Genomics, 2012. 100(2): p. 116-24
    [PMID:22664253]
  10. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  11. 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]
  12. Šimášková M, et al.
    Cytokinin response factors regulate PIN-FORMED auxin transporters.
    Nat Commun, 2015. 6: p. 8717
    [PMID:26541513]
  13. 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]
  14. 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]