Plant Transcription Factor Database
Previous version: v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT3G26744.1
Common NameATICE1, BHLH116, EN45, ICE1, MDJ14.1, MLJ15.14, SCRM
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 bHLH
Protein Properties Length: 494aa    MW: 53538.9 Da    PI: 5.1164
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT3G26744.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
          HLH   7 erErrRRdriNsafeeLrellPk.askapskKlsKaeiLekAveYIksL 54 
                  ++ErrRR+++N+++  Lr+++Pk +      K++ a+iL  A++Y+k+L
                  79*********************66......****************98 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5088815.866303352IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474591.01E-16306373IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003534.2E-14309358IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000103.3E-9309352IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000833.97E-13310356No hitNo description
Gene3DG3DSA:, basic helix-loop-helix (bHLH) domain
CDDcd048737.80E-7423483No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0010440Biological Processstomatal lineage progression
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0050826Biological Processresponse to freezing
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
GO:0046983Molecular Functionprotein dimerization activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000230anatomyinflorescence meristem
PO:0000263anatomynon-hair root epidermal cell
PO:0000293anatomyguard cell
PO:0002000anatomystomatal complex
PO:0008019anatomyleaf lamina base
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009025anatomyvascular leaf
PO:0009052anatomyflower pedicel
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
PO:0025195anatomypollen tube cell
PO:0001054developmental stagevascular leaf senescent stage
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007064developmental stageLP.12 twelve leaves visible stage
PO:0007095developmental stageLP.08 eight leaves visible stage
PO:0007098developmental stageLP.02 two leaves visible stage
PO:0007103developmental stageLP.10 ten leaves visible stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 494 aa     Download sequence    Send to blast
Nucleic Localization Signal ? help Back to Top
No. Start End Sequence
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.253020.0bud| flower| seed| silique
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT3G26744-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Widely expressed in the whole plant with high expression in leaves and stem. Broad expression within stomatal cell lineages of leaf epidermis. {ECO:0000269|PubMed:18641265}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a MYC-like bHLH transcriptional activator that binds specifically to the MYC recognition sequences in the CBF3 promoter. Mutants are defective in cold-regulated gene expression. Cold stress triggers protein degradation of nuclear GFPICE1 protein, and the RING finger protein HOS1 is required. Sumoylation of ICE1 controls CBF3/DREB1A expression and freezing tolerance.
UniProtTranscriptional activator that regulates the cold-induced transcription of CBF/DREB1 genes. Binds specifically to the MYC recognition sites (5'-CANNTG-3') found in the CBF3/DREB1A promoter. Mediates stomatal differentiation in the epidermis probably by controlling successive roles of SPCH, MUTE, and FAMA. {ECO:0000269|PubMed:17416732, ECO:0000269|PubMed:18641265}.
Function -- GeneRIF ? help Back to Top
  1. cold stress responses in Arabidopsis are attenuated by a ubiquitination/proteasome pathway in which HOS1 mediates the degradation of the ICE1 protein
    [PMID: 16702557]
  2. Regulon genes repressed by siz1 did not affect expression of ICE1, which encodes a MYC transcription factor.
    [PMID: 17416732]
  3. The inducer of CBF expression1 (ICE1) protein that is involved in transcriptional control of cold responses is found to bind to a MYC element in this BAP1 promoter and is required for the cooling induction of BAP1.
    [PMID: 21098676]
  4. The serine 403 to alanine substitution increases the transactivation activity of ICE1 and the freezing tolerance of Arabidopsis.
    [PMID: 21447070]
  5. Jasmonate functions as a critical upstream signal of the ICE-CBF/DREB1 pathway to positively regulate Arabidopsis freezing tolerance.
    [PMID: 23933884]
  6. propose that the ZHOUPI/ICE1 complex might have ancient origins, acquiring novel megagametophyte-specific functions in heterosporous land plants that were conserved in the angiosperm endosperm
    [PMID: 24553285]
  7. ICE2 gene has originated from a duplication event about 17.9MYA followed by sub- and neofunctionalization of the ancestral ICE1 gene.
    [PMID: 25443829]
  8. uncover the unexpected roles of OST1 in modulating C-repeat-binding factor-dependent cold signaling in Arabidopsis
    [PMID: 25669882]
  9. Seedling growth was severely reduced in a T-DNA insertion mutant of ICE1, ice1-2, when grown on 1/2 MS medium lacking sugars, but was restored to wild-type (WT) levels by supplementation with 56 mM glucose.
    [PMID: 26048037]
  10. unified ICE-CBF pathway provides transcriptional feedback control of freezing tolerance during cold acclimation
    [PMID: 26311645]
Cis-element ? help Back to Top
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By high-salt stress, cold stress and abscisic acid (ABA) treatment.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source Upstream Regulator (A: Activate/R: Repress)
ATRM AT5G53210 (A)
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT2G42540(A), AT3G23250(R), AT3G61190(A), AT4G25470(A), AT4G25480(A), AT4G25490(A), AT5G52310(A), AT5G53210(A)
Interaction ? help Back to Top
Source Intact With
BioGRIDAT5G53210, AT1G49770
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT3G26744
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY0790160.0AY079016.1 Arabidopsis thaliana AT3g26744/MLJ15_15 mRNA, complete cds.
GenBankAY1956210.0AY195621.1 Arabidopsis thaliana ICE1 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001030774.10.0transcription factor ICE1
RefseqNP_001030776.20.0transcription factor ICE1
RefseqNP_189309.20.0transcription factor ICE1
SwissprotQ9LSE20.0ICE1_ARATH; Transcription factor ICE1
STRINGAT3G26744.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP5571678
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
  2. Chinnusamy V, et al.
    ICE1: a regulator of cold-induced transcriptome and freezing tolerance in Arabidopsis.
    Genes Dev., 2003. 17(8): p. 1043-54
  3. Heim MA, et al.
    The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity.
    Mol. Biol. Evol., 2003. 20(5): p. 735-47
  4. Toledo-Ortiz G,Huq E,Quail PH
    The Arabidopsis basic/helix-loop-helix transcription factor family.
    Plant Cell, 2003. 15(8): p. 1749-70
  5. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
  6. Chinnusamy V,Schumaker K,Zhu JK
    Molecular genetic perspectives on cross-talk and specificity in abiotic stress signalling in plants.
    J. Exp. Bot., 2004. 55(395): p. 225-36
  7. Lee BH,Henderson DA,Zhu JK
    The Arabidopsis cold-responsive transcriptome and its regulation by ICE1.
    Plant Cell, 2005. 17(11): p. 3155-75
  8. Skinner JS, et al.
    Mapping of barley homologs to genes that regulate low temperature tolerance in Arabidopsis.
    Theor. Appl. Genet., 2006. 112(5): p. 832-42
  9. Dong CH,Agarwal M,Zhang Y,Xie Q,Zhu JK
    The negative regulator of plant cold responses, HOS1, is a RING E3 ligase that mediates the ubiquitination and degradation of ICE1.
    Proc. Natl. Acad. Sci. U.S.A., 2006. 103(21): p. 8281-6
  10. Benedict C,Geisler M,Trygg J,Huner N,Hurry V
    Consensus by democracy. Using meta-analyses of microarray and genomic data to model the cold acclimation signaling pathway in Arabidopsis.
    Plant Physiol., 2006. 141(4): p. 1219-32
  11. Agarwal M, et al.
    A R2R3 type MYB transcription factor is involved in the cold regulation of CBF genes and in acquired freezing tolerance.
    J. Biol. Chem., 2006. 281(49): p. 37636-45
  12. Xin Z,Mandaokar A,Chen J,Last RL,Browse J
    Arabidopsis ESK1 encodes a novel regulator of freezing tolerance.
    Plant J., 2007. 49(5): p. 786-99
  13. Miura K, et al.
    SIZ1-mediated sumoylation of ICE1 controls CBF3/DREB1A expression and freezing tolerance in Arabidopsis.
    Plant Cell, 2007. 19(4): p. 1403-14
  14. Badawi M, et al.
    Structure and functional analysis of wheat ICE (inducer of CBF expression) genes.
    Plant Cell Physiol., 2008. 49(8): p. 1237-49
  15. Kanaoka MM, et al.
    SCREAM/ICE1 and SCREAM2 specify three cell-state transitional steps leading to arabidopsis stomatal differentiation.
    Plant Cell, 2008. 20(7): p. 1775-85
  16. 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
  17. Fursova OV,Pogorelko GV,Tarasov VA
    Identification of ICE2, a gene involved in cold acclimation which determines freezing tolerance in Arabidopsis thaliana.
    Gene, 2009. 429(1-2): p. 98-103
  18. Serna L
    Emerging parallels between stomatal and muscle cell lineages.
    Plant Physiol., 2009. 149(4): p. 1625-31
  19. Lippold F, et al.
    AtMyb41 regulates transcriptional and metabolic responses to osmotic stress in Arabidopsis.
    Plant Physiol., 2009. 149(4): p. 1761-72
  20. Zhou J, et al.
    Basic helix-loop-helix transcription factor from wild rice (OrbHLH2) improves tolerance to salt- and osmotic stress in Arabidopsis.
    J. Plant Physiol., 2009. 166(12): p. 1296-306
  21. Serna L
    Cell fate transitions during stomatal development.
    Bioessays, 2009. 31(8): p. 865-73
  22. Miura K,Hasegawa PM
    Regulation of cold signaling by sumoylation of ICE1.
    Plant Signal Behav, 2008. 3(1): p. 52-3
  23. Miura K,Ohta M
    SIZ1, a small ubiquitin-related modifier ligase, controls cold signaling through regulation of salicylic acid accumulation.
    J. Plant Physiol., 2010. 167(7): p. 555-60
  24. Peterson KM,Rychel AL,Torii KU
    Out of the mouths of plants: the molecular basis of the evolution and diversity of stomatal development.
    Plant Cell, 2010. 22(2): p. 296-306
  25. Chinnusamy V,Zhu JK,Sunkar R
    Gene regulation during cold stress acclimation in plants.
    Methods Mol. Biol., 2010. 639: p. 39-55
  26. Chen CC,Liang CS,Kao AL,Yang CC
    HHP1, a novel signalling component in the cross-talk between the cold and osmotic signalling pathways in Arabidopsis.
    J. Exp. Bot., 2010. 61(12): p. 3305-20
  27. Elrouby N,Coupland G
    Proteome-wide screens for small ubiquitin-like modifier (SUMO) substrates identify Arabidopsis proteins implicated in diverse biological processes.
    Proc. Natl. Acad. Sci. U.S.A., 2010. 107(40): p. 17415-20
  28. Yang W, et al.
    Dwarf apple MbDREB1 enhances plant tolerance to low temperature, drought, and salt stress via both ABA-dependent and ABA-independent pathways.
    Planta, 2011. 233(2): p. 219-29
  29. Zhu Y,Yang H,Mang HG,Hua J
    Induction of BAP1 by a moderate decrease in temperature is mediated by ICE1 in Arabidopsis.
    Plant Physiol., 2011. 155(1): p. 580-8
  30. Miura K,Ohta M,Nakazawa M,Ono M,Hasegawa PM
    ICE1 Ser403 is necessary for protein stabilization and regulation of cold signaling and tolerance.
    Plant J., 2011. 67(2): p. 269-79
  31. Siddiqua M,Nassuth A
    Vitis CBF1 and Vitis CBF4 differ in their effect on Arabidopsis abiotic stress tolerance, development and gene expression.
    Plant Cell Environ., 2011. 34(8): p. 1345-59
  32. Pillitteri LJ,Peterson KM,Horst RJ,Torii KU
    Molecular profiling of stomatal meristemoids reveals new component of asymmetric cell division and commonalities among stem cell populations in Arabidopsis.
    Plant Cell, 2011. 23(9): p. 3260-75
  33. Bruex A, et al.
    A gene regulatory network for root epidermis cell differentiation in Arabidopsis.
    PLoS Genet., 2012. 8(1): p. e1002446
  34. Xie C, et al.
    Overexpression of MtCAS31 enhances drought tolerance in transgenic Arabidopsis by reducing stomatal density.
    New Phytol., 2012. 195(1): p. 124-35
  35. Lee JH, et al.
    The E3 ubiquitin ligase HOS1 regulates low ambient temperature-responsive flowering in Arabidopsis thaliana.
    Plant Cell Physiol., 2012. 53(10): p. 1802-14
  36. Meinke DW
    A survey of dominant mutations in Arabidopsis thaliana.
    Trends Plant Sci., 2013. 18(2): p. 84-91
  37. Lee JH,Kim SH,Kim JJ,Ahn JH
    Alternative splicing and expression analysis of High expression of osmotically responsive genes1 (HOS1) in Arabidopsis.
    BMB Rep, 2012. 45(9): p. 515-20
  38. Arisz SA, et al.
    Rapid phosphatidic acid accumulation in response to low temperature stress in Arabidopsis is generated through diacylglycerol kinase.
    Front Plant Sci, 2013. 4: p. 1
  39. Hu Y,Jiang L,Wang F,Yu D
    Jasmonate regulates the inducer of cbf expression-C-repeat binding factor/DRE binding factor1 cascade and freezing tolerance in Arabidopsis.
    Plant Cell, 2013. 25(8): p. 2907-24
  40. Jung JH, et al.
    The cold signaling attenuator HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE1 activates FLOWERING LOCUS C transcription via chromatin remodeling under short-term cold stress in Arabidopsis.
    Plant Cell, 2013. 25(11): p. 4378-90
  41. Denay G, et al.
    Endosperm breakdown in Arabidopsis requires heterodimers of the basic helix-loop-helix proteins ZHOUPI and INDUCER OF CBP EXPRESSION 1.
    Development, 2014. 141(6): p. 1222-7
  42. Kurbidaeva A,Ezhova T,Novokreshchenova M
    Arabidopsis thaliana ICE2 gene: phylogeny, structural evolution and functional diversification from ICE1.
    Plant Sci., 2014. 229: p. 10-22
  43. Ding Y, et al.
    OST1 kinase modulates freezing tolerance by enhancing ICE1 stability in Arabidopsis.
    Dev. Cell, 2015. 32(3): p. 278-89
  44. 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
  45. Liang CH,Yang CC
    Identification of ICE1 as a negative regulator of ABA-dependent pathways in seeds and seedlings of Arabidopsis.
    Plant Mol. Biol., 2015. 88(4-5): p. 459-70
  46. Kim YS,Lee M,Lee JH,Lee HJ,Park CM
    The unified ICE-CBF pathway provides a transcriptional feedback control of freezing tolerance during cold acclimation in Arabidopsis.
    Plant Mol. Biol., 2015. 89(1-2): p. 187-201