Plant Transcription Factor Database
Previous version: v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT4G16780.1
Common NameATHB2, ATHB-2, dl4415w, FCAALL.101, HAT4, HB-2
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 HD-ZIP
Protein Properties Length: 284aa    MW: 31852.5 Da    PI: 9.0241
Description homeobox protein 2
Gene Model
Gene Model ID Type Source Coding Sequence
AT4G16780.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
     Homeobox   2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                  rk+ +++k+q  +Lee F+ +++++ ++++ LAk+lgL  rqV vWFqNrRa+ k
                  788899***********************************************98 PP

  HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeveeLreel 91 
                  +kk+rlsk+q+++LEe+F+ +++L+p++K++la++Lgl++rqv+vWFqnrRARtk+kq+E+d+e+L+r++++l+een+rL+kev+eLr +l
                  69*************************************************************************************9.55 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046185.0E-302107IPR006712HD-ZIP protein, N-terminal
PROSITE profilePS5007117.427124184IPR001356Homeobox domain
SMARTSM003895.2E-16126188IPR001356Homeobox domain
PfamPF000467.7E-17128182IPR001356Homeobox domain
CDDcd000865.70E-15128185No hitNo description
PRINTSPR000311.1E-5155164IPR000047Helix-turn-helix motif
PROSITE patternPS000270159182IPR017970Homeobox, conserved site
PRINTSPR000311.1E-5164180IPR000047Helix-turn-helix motif
PfamPF021838.3E-11184218IPR003106Leucine zipper, homeobox-associated
SMARTSM003403.8E-26184227IPR003106Leucine zipper, homeobox-associated
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0008283Biological Processcell proliferation
GO:0009585Biological Processred, far-red light phototransduction
GO:0009641Biological Processshade avoidance
GO:0009733Biological Processresponse to auxin
GO:0009735Biological Processresponse to cytokinin
GO:0009826Biological Processunidimensional cell growth
GO:0010016Biological Processshoot system morphogenesis
GO:0010017Biological Processred or far-red light signaling pathway
GO:0010218Biological Processresponse to far red light
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:0048364Biological Processroot development
GO:0005634Cellular Componentnucleus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0042803Molecular Functionprotein homodimerization activity
GO:0043565Molecular Functionsequence-specific DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0009025anatomyvascular leaf
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
PO:0001054developmental stagevascular leaf senescent 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
Sequence ? help Back to Top
Protein Sequence    Length: 284 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 AtlasAT4G16780-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Predominantly expressed in leaves and stems. {ECO:0000269|PubMed:8106086}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a homeodomain-leucine zipper protein that is rapidly and strongly induced by changes in the ratio of red to far-red light. It is also involved in cell expansion and cell proliferation and in the response to auxin.
UniProtProbable transcription factor involved in the negative regulation of cell elongation and specific cell proliferation processes such as lateral root formation and secondary growth of the vascular system. Acts as mediator of the red/far-red light effects on leaf cell expansion in the shading response. Binds to the DNA sequence 5'-CAAT[GC]ATTG-3'. Negatively regulates its own expression. {ECO:0000269|PubMed:10477292, ECO:0000269|PubMed:11260495, ECO:0000269|PubMed:8449400}.
Function -- GeneRIF ? help Back to Top
  1. Arabidopsis thaliana homeobox protein2 (ATHB2)together with auxin-inducible IAA29, is diurnally expressed with a peak at dawn under the control of PHYTOCHROME-INTERACTING FACTOR4 (PIF4) and PIF5.
    [PMID: 21666227]
  2. a genetic system consisting of HD-Zip II and HD-Zip III genes (ATHB2, ATHB4) cooperates in establishing bilateral symmetry and patterning along the adaxial-abaxial axis in the embryo as well as in controlling SAM activity
    [PMID: 23578926]
Cis-element ? help Back to Top
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Rapidly and strongly induced by lowering the ratio of red to far-red light. {ECO:0000269|PubMed:8106086}.
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 AT1G02340 (R)
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT1G02340(A)
Regulation -- Hormone ? help Back to Top
Source Hormone
Interaction ? help Back to Top
Source Intact With
BioGRIDAT4G16780, AT4G37790, AT5G06710, AT5G47370
IntActSearch Q05466
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT4G16780
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF3754530.0AF375453.1 Arabidopsis thaliana AT4g16780/dl4415w mRNA, complete cds.
GenBankAY0817470.0AY081747.1 Arabidopsis thaliana AT4g16780/dl4415w mRNA, complete cds.
GenBankX681450.0X68145.1 A.thaliana Athb-2 mRNA.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_193411.10.0homeobox protein 2
SwissprotQ054660.0HAT4_ARATH; Homeobox-leucine zipper protein HAT4
TrEMBLA0A0D3A7H31e-177A0A0D3A7H3_BRAOL; Uncharacterized protein (Fragment)
STRINGAT4G16780.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP19616156
Publications ? help Back to Top
  1. Steindler C, et al.
    Shade avoidance responses are mediated by the ATHB-2 HD-zip protein, a negative regulator of gene expression.
    Development, 1999. 126(19): p. 4235-45
  2. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
  3. Ohgishi M,Oka A,Morelli G,Ruberti I,Aoyama T
    Negative autoregulation of the Arabidopsis homeobox gene ATHB-2.
    Plant J., 2001. 25(4): p. 389-98
  4. Morelli G,Ruberti I
    Light and shade in the photocontrol of Arabidopsis growth.
    Trends Plant Sci., 2002. 7(9): p. 399-404
  5. Franklin KA, et al.
    Phytochromes B, D, and E act redundantly to control multiple physiological responses in Arabidopsis.
    Plant Physiol., 2003. 131(3): p. 1340-6
  6. Wright SI,Lauga B,Charlesworth D
    Subdivision and haplotype structure in natural populations of Arabidopsis lyrata.
    Mol. Ecol., 2003. 12(5): p. 1247-63
  7. Schena M,Davis RW
    HD-Zip proteins: members of an Arabidopsis homeodomain protein superfamily.
    Proc. Natl. Acad. Sci. U.S.A., 1992. 89(9): p. 3894-8
  8. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
  9. Jiao Y, et al.
    A genome-wide analysis of blue-light regulation of Arabidopsis transcription factor gene expression during seedling development.
    Plant Physiol., 2003. 133(4): p. 1480-93
  10. Koroleva OA,Tomlinson ML,Leader D,Shaw P,Doonan JH
    High-throughput protein localization in Arabidopsis using Agrobacterium-mediated transient expression of GFP-ORF fusions.
    Plant J., 2005. 41(1): p. 162-74
  11. Henriksson E, et al.
    Homeodomain leucine zipper class I genes in Arabidopsis. Expression patterns and phylogenetic relationships.
    Plant Physiol., 2005. 139(1): p. 509-18
  12. Brenner WG,Romanov GA,K
    Immediate-early and delayed cytokinin response genes of Arabidopsis thaliana identified by genome-wide expression profiling reveal novel cytokinin-sensitive processes and suggest cytokinin action through transcriptional cascades.
    Plant J., 2005. 44(2): p. 314-33
  13. Sessa G, et al.
    A dynamic balance between gene activation and repression regulates the shade avoidance response in Arabidopsis.
    Genes Dev., 2005. 19(23): p. 2811-5
  14. Roig-Villanova I,Bou J,Sorin C,Devlin PF,Martínez-García JF
    Identification of primary target genes of phytochrome signaling. Early transcriptional control during shade avoidance responses in Arabidopsis.
    Plant Physiol., 2006. 141(1): p. 85-96
  15. Ruberti I,Sessa G,Lucchetti S,Morelli G
    A novel class of plant proteins containing a homeodomain with a closely linked leucine zipper motif.
    EMBO J., 1991. 10(7): p. 1787-91
  16. Brock MT,Tiffin P,Weinig C
    Sequence diversity and haplotype associations with phenotypic responses to crowding: GIGANTEA affects fruit set in Arabidopsis thaliana.
    Mol. Ecol., 2007. 16(14): p. 3050-62
  17. Franklin KA,Whitelam GC
    Light-quality regulation of freezing tolerance in Arabidopsis thaliana.
    Nat. Genet., 2007. 39(11): p. 1410-3
  18. Ciarbelli AR, et al.
    The Arabidopsis homeodomain-leucine zipper II gene family: diversity and redundancy.
    Plant Mol. Biol., 2008. 68(4-5): p. 465-78
  19. Finlayson SA,Krishnareddy SR,Kebrom TH,Casal JJ
    Phytochrome regulation of branching in Arabidopsis.
    Plant Physiol., 2010. 152(4): p. 1914-27
  20. K
    Ectopic expression of different cytokinin-regulated transcription factor genes of Arabidopsis thaliana alters plant growth and development.
    J. Plant Physiol., 2011. 168(12): p. 1320-7
  21. Kunihiro A, et al.
    Phytochrome-interacting factor 4 and 5 (PIF4 and PIF5) activate the homeobox ATHB2 and auxin-inducible IAA29 genes in the coincidence mechanism underlying photoperiodic control of plant growth of Arabidopsis thaliana.
    Plant Cell Physiol., 2011. 52(8): p. 1315-29
  22. Arabidopsis Interactome Mapping Consortium
    Evidence for network evolution in an Arabidopsis interactome map.
    Science, 2011. 333(6042): p. 601-7
  23. Tiwari SB, et al.
    The EDLL motif: a potent plant transcriptional activation domain from AP2/ERF transcription factors.
    Plant J., 2012. 70(5): p. 855-65
  24. Bou-Torrent J, et al.
    ATHB4 and HAT3, two class II HD-ZIP transcription factors, control leaf development in Arabidopsis.
    Plant Signal Behav, 2012. 7(11): p. 1382-7
  25. Turchi L, et al.
    Arabidopsis HD-Zip II transcription factors control apical embryo development and meristem function.
    Development, 2013. 140(10): p. 2118-29
  26. Jung CG, et al.
    Molecular characterization of the cold- and heat-induced Arabidopsis PXL1 gene and its potential role in transduction pathways under temperature fluctuations.
    J. Plant Physiol., 2015. 176: p. 138-46
  27. 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
  28. Schena M,Davis RW
    Structure of homeobox-leucine zipper genes suggests a model for the evolution of gene families.
    Proc. Natl. Acad. Sci. U.S.A., 1994. 91(18): p. 8393-7
  29. S
    Expression patterns of novel genes encoding homeodomain leucine-zipper proteins in Arabidopsis thaliana.
    Plant Mol. Biol., 1994. 26(1): p. 145-54
  30. Carabelli M,Sessa G,Baima S,Morelli G,Ruberti I
    The Arabidopsis Athb-2 and -4 genes are strongly induced by far-red-rich light.
    Plant J., 1993. 4(3): p. 469-79
  31. Sessa G,Morelli G,Ruberti I
    The Athb-1 and -2 HD-Zip domains homodimerize forming complexes of different DNA binding specificities.
    EMBO J., 1993. 12(9): p. 3507-17
  32. Schena M,Lloyd AM,Davis RW
    The HAT4 gene of Arabidopsis encodes a developmental regulator.
    Genes Dev., 1993. 7(3): p. 367-79
  33. Di Cristina M, et al.
    The Arabidopsis Athb-10 (GLABRA2) is an HD-Zip protein required for regulation of root hair development.
    Plant J., 1996. 10(3): p. 393-402
  34. Sessa G,Morelli G,Ruberti I
    DNA-binding specificity of the homeodomain-leucine zipper domain.
    J. Mol. Biol., 1997. 274(3): p. 303-9
  35. Sessa G,Steindler C,Morelli G,Ruberti I
    The Arabidopsis Athb-8, -9 and -14 genes are members of a small gene family coding for highly related HD-ZIP proteins.
    Plant Mol. Biol., 1998. 38(4): p. 609-22