Plant Transcription Factor Database
Previous version: v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT4G34530.1
Common NameBHLH63, CIB1, EN84, T4L20.110
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: 335aa    MW: 37540.4 Da    PI: 5.6803
Description cryptochrome-interacting basic-helix-loop-helix 1
Gene Model
Gene Model ID Type Source Coding Sequence
AT4G34530.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
          HLH   4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                  +h+++Er RR++i +++  L++l+P +    +k   Ka +L + ++Y++sLq
                  8*************************9....899*****************9 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd000835.30E-11176233No hitNo description
SuperFamilySSF474591.2E-16176246IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profilePS5088815.593178228IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:, basic helix-loop-helix (bHLH) domain
PfamPF000102.5E-7182229IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003532.0E-8184234IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006351Biological Processtranscription, DNA-templated
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009637Biological Processresponse to blue light
GO:0009911Biological Processpositive regulation of flower development
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:0005020anatomyvascular bundle
Sequence ? help Back to Top
Protein Sequence    Length: 335 aa     Download sequence    Send to blast
Nucleic Localization Signal ? help Back to Top
No. Start End Sequence
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT4G34530-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed constitutively in roots, leaves, and stems. {ECO:0000269|PubMed:12679534}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a transcription factor CIB1 (cryptochrome-interacting basic-helix-loop-helix). CIB1 interacts with CRY2 (cryptochrome 2) in a blue light-specific manner in yeast and Arabidopsis cells, and it acts together with additional CIB1-related proteins to promote CRY2-dependent floral initiation. CIB1 positively regulates FT expression.
UniProtTranscription factor that binds DNA to G box 5'-CACGTG-3' and, to a lower extent, to E-box 5'-CANNTG-3' in vitro. Binds to chromatin DNA of the FT gene and promotes its expression, and thus triggers flowering in response to blue light. {ECO:0000269|PubMed:18988809, ECO:0000269|PubMed:24130508}.
Function -- GeneRIF ? help Back to Top
  1. identification & characterization of CIB1 (At4g34530) protein; CIB1 interacts with CRY2 in a blue light-specific manner & acts with additional CIB1-related proteins to promote CRY2-dependent floral initiation; CIB1 stimulates FT messenger RNA expression.
    [PMID: 18988809]
  2. Data indicate that although cryptochrome 2 physically interacts with CIB1 in response to blue light, ZEITLUPE and LOV KELCH PROTEIN 2 are required for the function and blue-light suppression of degradation of CIB1.
    [PMID: 24101505]
Cis-element ? help Back to Top
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Accumulates strongly in response to blue light due to reduced preventing 26S proteasome-mediated degradation in an ADO1/ZTL and ADO2/LKP2 dependent manner, but levels decrease in the absence of blue light via 26S proteasome degradation (at protein level). {ECO:0000269|PubMed:24101505}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
Interaction ? help Back to Top
Source Intact With
BioGRIDAT5G48560, AT1G26260
IntActSearch Q8GY61
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT4G34530
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1178460.0AK117846.1 Arabidopsis thaliana At4g34530 mRNA for putative bHLH transcription factor (bHLH063), complete cds, clone: RAFL18-04-K08.
GenBankBT0053130.0BT005313.1 Arabidopsis thaliana At4g34530 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_195179.20.0cryptochrome-interacting basic-helix-loop-helix 1
SwissprotQ8GY610.0BH063_ARATH; Transcription factor bHLH63
TrEMBLD7MED30.0D7MED3_ARALL; Putative uncharacterized protein
STRINGAT4G34530.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP5816313
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. Seki M, et al.
    Functional annotation of a full-length Arabidopsis cDNA collection.
    Science, 2002. 296(5565): p. 141-5
  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. 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
  7. Thimmapuram J,Duan H,Liu L,Schuler MA
    Bicistronic and fused monocistronic transcripts are derived from adjacent loci in the Arabidopsis genome.
    RNA, 2005. 11(2): p. 128-38
  8. Andersson-Gunner
    Biosynthesis of cellulose-enriched tension wood in Populus: global analysis of transcripts and metabolites identifies biochemical and developmental regulators in secondary wall biosynthesis.
    Plant J., 2006. 45(2): p. 144-65
  9. Kong H, et al.
    Patterns of gene duplication in the plant SKP1 gene family in angiosperms: evidence for multiple mechanisms of rapid gene birth.
    Plant J., 2007. 50(5): p. 873-85
  10. Liu H, et al.
    Photoexcited CRY2 interacts with CIB1 to regulate transcription and floral initiation in Arabidopsis.
    Science, 2008. 322(5907): p. 1535-9
  11. Kennedy MJ, et al.
    Rapid blue-light-mediated induction of protein interactions in living cells.
    Nat. Methods, 2010. 7(12): p. 973-5
  12. Arabidopsis Interactome Mapping Consortium
    Evidence for network evolution in an Arabidopsis interactome map.
    Science, 2011. 333(6042): p. 601-7
  13. Li X, et al.
    Arabidopsis cryptochrome 2 (CRY2) functions by the photoactivation mechanism distinct from the tryptophan (trp) triad-dependent photoreduction.
    Proc. Natl. Acad. Sci. U.S.A., 2011. 108(51): p. 20844-9
  14. Weidler G, et al.
    Degradation of Arabidopsis CRY2 is regulated by SPA proteins and phytochrome A.
    Plant Cell, 2012. 24(6): p. 2610-23
  15. Idevall-Hagren O,Dickson EJ,Hille B,Toomre DK,De Camilli P
    Optogenetic control of phosphoinositide metabolism.
    Proc. Natl. Acad. Sci. U.S.A., 2012. 109(35): p. E2316-23
  16. Hughes RM,Bolger S,Tapadia H,Tucker CL
    Light-mediated control of DNA transcription in yeast.
    Methods, 2012. 58(4): p. 385-91
  17. Ikeda M,Fujiwara S,Mitsuda N,Ohme-Takagi M
    A triantagonistic basic helix-loop-helix system regulates cell elongation in Arabidopsis.
    Plant Cell, 2012. 24(11): p. 4483-97
  18. Konermann S, et al.
    Optical control of mammalian endogenous transcription and epigenetic states.
    Nature, 2013. 500(7463): p. 472-6
  19. Liu H, et al.
    Arabidopsis CRY2 and ZTL mediate blue-light regulation of the transcription factor CIB1 by distinct mechanisms.
    Proc. Natl. Acad. Sci. U.S.A., 2013. 110(43): p. 17582-7
  20. Liu Y,Li X,Li K,Liu H,Lin C
    Multiple bHLH proteins form heterodimers to mediate CRY2-dependent regulation of flowering-time in Arabidopsis.
    PLoS Genet., 2013. 9(10): p. e1003861
  21. Idevall-Hagren O,Decamilli P
    Manipulation of plasma membrane phosphoinositides using photoinduced protein-protein interactions.
    Methods Mol. Biol., 2014. 1148: p. 109-28
  22. Cui Y,Choudhury SR,Irudayaraj J
    Quantitative real-time kinetics of optogenetic proteins CRY2 and CIB1/N using single-molecule tools.
    Anal. Biochem., 2014. 458: p. 58-60
  23. Duan L, et al.
    Optogenetic control of molecular motors and organelle distributions in cells.
    Chem. Biol., 2015. 22(5): p. 671-82