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 AT1G12860.1
Common NameBHLH33, EN44, F13K23.12, ICE2, SCRM2
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 bHLH
Protein Properties Length: 450aa    MW: 49795.7 Da    PI: 6.1898
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT1G12860.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH361.2e-11270312754
                  HHHHHHHHHHHHHHHHHHCTSCC.C...TTS-STCHHHHHHHHHHHHHH CS
          HLH   7 erErrRRdriNsafeeLrellPk.askapskKlsKaeiLekAveYIksL 54 
                  ++ErrRR+++N+++  Lr+++Pk +      K++ a+iL  A++Y+k+L
  AT1G12860.1 270 MAERRRRKKLNDRLYMLRSVVPKiS------KMDRASILGDAIDYLKEL 312
                  79*********************66......****************98 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5088815.866263312IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474595.63E-17266337IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000102.9E-9269312IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003534.2E-14269318IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000834.54E-13270316No hitNo description
Gene3DG3DSA:4.10.280.107.6E-16270327IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profilePS516718.734378450IPR002912ACT domain
CDDcd048738.58E-7379420No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010444Biological Processguard mother cell differentiation
GO:0050826Biological Processresponse to freezing
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0016597Molecular Functionamino acid 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:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009005anatomyroot
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009025anatomyvascular leaf
PO:0009029anatomystamen
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0009052anatomyflower pedicel
PO:0020030anatomycotyledon
PO:0020038anatomypetiole
PO:0020100anatomyhypocotyl
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
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: 450 aa     Download sequence    Send to blast
MNSDGVWLDG SGESPEVNNG EAASWVRNPD EDWFNNPPPP QHTNQNDFRF NGGFPLNPSE  60
NLLLLLQQSI DSSSSSSPLL HPFTLDAASQ QQQQQQQQQE QSFLATKACI VSLLNVPTIN  120
NNTFDDFGFD SGFLGQQFHG NHQSPNSMNF TGLNHSVPDF LPAPENSSGS CGLSPLFSNR  180
AKVLKPLQVM ASSGSQPTLF QKRAAMRQSS SSKMCNSESS SEMRKSSYER EIDDTSTGII  240
DISGLNYESD DHNTNNNKGK KKGMPAKNLM AERRRRKKLN DRLYMLRSVV PKISKMDRAS  300
ILGDAIDYLK ELLQRINDLH TELESTPPSS SSLHPLTPTP QTLSYRVKEE LCPSSSLPSP  360
KGQQPRVEVR LREGKAVNIH MFCGRRPGLL LSTMRALDNL GLDVQQAVIS CFNGFALDVF  420
RAEQCQEDHD VLPEQIKAVL LDTAGYAGLV
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1259277KKKGMPAKNLMAERRRRKK
2271278ERRRRKKL
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.420570.0floral meristem| flower| leaf| seed| vegetative tissue
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO3341825340.0
Genevisible261196_at0.0
Expression AtlasAT1G12860-
AtGenExpressAT1G12860-
ATTED-IIAT1G12860-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed constitutively in roots, leaves, stems, and flowers. Broad expression within stomatal cell lineages of leaf epidermis, except in mature guard-cells. {ECO:0000269|PubMed:12679534, ECO:0000269|PubMed:18641265}.
Functional Description ? help Back to Top
Source Description
TAIREncodes ICE2 (Inducer of CBF Expression 2), a transcription factor of the bHLH family that participates in the response to deep freezing through the cold acclimation-dependent pathway. Overexpression of ICE2 results in increased tolerance to deep freezing stress after cold acclimation.
UniProtMediates stomatal differentiation in the epidermis probably by controlling successive roles of SPCH, MUTE, and FAMA (PubMed:18641265). Functions as a dimer with SPCH during stomatal initiation (PubMed:18641265, PubMed:28507175). {ECO:0000269|PubMed:18641265, ECO:0000269|PubMed:28507175}.
Function -- GeneRIF ? help Back to Top
  1. These results suggested that the CBF1 transcription factor, known as one of the regulators of the cold stress response, has a dominant role in providing freezing tolerance in transgenic plants characterized by overexpression of ICE2.
    [PMID: 19026725]
  2. Jasmonate functions as a critical upstream signal of the ICE-CBF/DREB1 pathway to positively regulate Arabidopsis freezing tolerance.
    [PMID: 23933884]
  3. ICE2 gene has originated from a duplication event about 17.9MYA followed by sub- and neofunctionalization of the ancestral ICE1 gene.
    [PMID: 25443829]
  4. unified ICE-CBF pathway provides transcriptional feedback control of freezing tolerance during cold acclimation
    [PMID: 26311645]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT1G12860.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT5G53210(A)
Interaction ? help Back to Top
Source Intact With
IntActSearch Q9LPW3
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT1G12860
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1180110.0AK118011.1 Arabidopsis thaliana At1g12860 mRNA for putative bHLH transcription factor (bHLH033), complete cds, clone: RAFL19-21-N13.
GenBankBT0053770.0BT005377.1 Arabidopsis thaliana At1g12860 mRNA, complete cds.
GenBankEU3696700.0EU369670.1 Arabidopsis thaliana bHLH protein (SCREAM2) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_172746.20.0basic helix-loop-helix (bHLH) DNA-binding superfamily protein
SwissprotQ9LPW30.0SCRM2_ARATH; Transcription factor SCREAM2
TrEMBLA0A1P8AMV90.0A0A1P8AMV9_ARATH; Basic helix-loop-helix (BHLH) DNA-binding superfamily protein
STRINGAT1G12860.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM19522782
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
    [PMID:11118137]
  2. Seki M, et al.
    Functional annotation of a full-length Arabidopsis cDNA collection.
    Science, 2002. 296(5565): p. 141-5
    [PMID:11910074]
  3. Chinnusamy V, et al.
    ICE1: a regulator of cold-induced transcriptome and freezing tolerance in Arabidopsis.
    Genes Dev., 2003. 17(8): p. 1043-54
    [PMID:12672693]
  4. 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
    [PMID:12679534]
  5. Toledo-Ortiz G,Huq E,Quail PH
    The Arabidopsis basic/helix-loop-helix transcription factor family.
    Plant Cell, 2003. 15(8): p. 1749-70
    [PMID:12897250]
  6. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  7. Bailey PC, et al.
    Update on the basic helix-loop-helix transcription factor gene family in Arabidopsis thaliana.
    Plant Cell, 2003. 15(11): p. 2497-502
    [PMID:14600211]
  8. Nawy T, et al.
    Transcriptional profile of the Arabidopsis root quiescent center.
    Plant Cell, 2005. 17(7): p. 1908-25
    [PMID:15937229]
  9. 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
    [PMID:18641265]
  10. 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]
  11. 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
    [PMID:19026725]
  12. Tarasov VA,Khadeeva NV,Mel'nik VA,Ezhova TA,Shestakov SV
    The Atlg12860 gene of Arabidopsis thaliana determines cathelicidin-like antimicrobial activity.
    Dokl. Biol. Sci., 2009.
    [PMID:19760875]
  13. Skinner MK,Rawls A,Wilson-Rawls J,Roalson EH
    Basic helix-loop-helix transcription factor gene family phylogenetics and nomenclature.
    Differentiation, 2010. 80(1): p. 1-8
    [PMID:20219281]
  14. Hanada K, et al.
    Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana.
    Mol. Biol. Evol., 2011. 28(1): p. 377-82
    [PMID:20736450]
  15. Arabidopsis Interactome Mapping Consortium
    Evidence for network evolution in an Arabidopsis interactome map.
    Science, 2011. 333(6042): p. 601-7
    [PMID:21798944]
  16. 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
    [PMID:23933884]
  17. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  18. 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
    [PMID:25443829]
  19. Emmerstorfer A, et al.
    Over-expression of ICE2 stabilizes cytochrome P450 reductase in Saccharomyces cerevisiae and Pichia pastoris.
    Biotechnol J, 2015. 10(4): p. 623-35
    [PMID:25641738]
  20. 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]
  21. Lee HG,Seo PJ
    The MYB96-HHP module integrates cold and abscisic acid signaling to activate the CBF-COR pathway in Arabidopsis.
    Plant J., 2015. 82(6): p. 962-77
    [PMID:25912720]
  22. 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
    [PMID:26311645]
  23. Raissig MT,Abrash E,Bettadapur A,Vogel JP,Bergmann DC
    Grasses use an alternatively wired bHLH transcription factor network to establish stomatal identity.
    Proc. Natl. Acad. Sci. U.S.A., 2016. 113(29): p. 8326-31
    [PMID:27382177]
  24. Fu ZW,Wang YL,Lu YT,Yuan TT
    Nitric oxide is involved in stomatal development by modulating the expression of stomatal regulator genes in Arabidopsis.
    Plant Sci., 2016. 252: p. 282-289
    [PMID:27717464]
  25. de Marcos A, et al.
    A Mutation in the bHLH Domain of the SPCH Transcription Factor Uncovers a BR-Dependent Mechanism for Stomatal Development.
    Plant Physiol., 2017. 174(2): p. 823-842
    [PMID:28507175]