PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v1.0, v2.0, v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT4G32980.1
Common NameATH1, F26P21.100
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 TALE
Protein Properties Length: 473aa    MW: 53899.7 Da    PI: 6.902
Description homeobox gene 1
Gene Model
Gene Model ID Type Source Coding Sequence
AT4G32980.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox25.62.1e-083914291854
                  HHHH..SSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHH CS
     Homeobox  18 lFek..nrypsaeereeLAkklgLterqVkvWFqNrRak 54 
                  +F++  ++yp+ +e+  LA + gLt +qV++WF N R +
  AT4G32980.1 391 MFQNflHPYPKDSEKHLLAIRSGLTRSQVSNWFINARVR 429
                  6887779******************************88 PP

2BELL93.32.3e-30266336172
         BELL   1 erqelqkkkakLlslleeVdkrYkqyveqlqtvissFeavaglgsakpYtslAlkaiSrhFrcLkdaiaeqi 72 
                  +r++l++kk++Ll+ll++Vd+rY+++v++++tvis+F+a+++l++ +++t++Al+++S+ +++L+++i+++i
  AT4G32980.1 266 QRRALEAKKTHLLDLLQMVDDRYSHCVDEIHTVISAFHAATELDP-QLHTRFALQTVSFLYKNLRERICKKI 336
                  6899*****************************************.************************98 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005742.9E-64196334IPR006563POX domain
PfamPF075262.0E-27202332IPR006563POX domain
PROSITE profilePS5007111.078370433IPR001356Homeobox domain
SMARTSM003893.0E-5373437IPR001356Homeobox domain
CDDcd000861.73E-10373434No hitNo description
SuperFamilySSF466892.74E-15374442IPR009057Homeodomain-like
Gene3DG3DSA:1.10.10.601.4E-25376439IPR009057Homeodomain-like
PfamPF059201.6E-14390429IPR008422Homeobox KN domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0008285Biological Processnegative regulation of cell proliferation
GO:0009640Biological Processphotomorphogenesis
GO:0010073Biological Processmeristem maintenance
GO:0010227Biological Processfloral organ abscission
GO:0010228Biological Processvegetative to reproductive phase transition of meristem
GO:0010371Biological Processregulation of gibberellin biosynthetic process
GO:0090470Biological Processshoot organ boundary specification
GO:0005634Cellular Componentnucleus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
GO:0043565Molecular Functionsequence-specific DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000017anatomyvascular leaf primordium
PO:0000035anatomycotyledon vascular system
PO:0000036anatomyleaf vascular system
PO:0000037anatomyshoot apex
PO:0000230anatomyinflorescence meristem
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:0020148anatomyshoot apical meristem
PO:0025022anatomycollective leaf structure
PO:0025281anatomypollen
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:0007131developmental stageseedling development stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 473 aa     Download sequence    Send to blast
MDNNNNNNTF SSLDNVMTNQ NPLLMDFIPS REDSTSFSTM LPWNTIRSDP LQMGGFDIFN  60
SMLTNKYLSS SPRSIDVQDN RNVEFMAPPP HPPPLHPLDH LRHYDDSSNN MWGFEANSEF  120
QAFSGVVGPS EPMMSTFGEE DFPFLISNKR NNELSLSLAS DVSDECSEIS LCAATRLASE  180
QASCSSKDIS NNVVTQGFSQ LIFGSKYLHS VQEILSHFAA YSLDYSSRGT ESGAASSAFT  240
SRFENITEFL DGDSNNSEAG FGSTFQRRAL EAKKTHLLDL LQMVDDRYSH CVDEIHTVIS  300
AFHAATELDP QLHTRFALQT VSFLYKNLRE RICKKIISMG SVLERGKDKT QETSMFHQHC  360
LLQQLKRKNH QIWRPQRGLP EKSVSVLRNW MFQNFLHPYP KDSEKHLLAI RSGLTRSQVS  420
NWFINARVRL WKPMIEEMYA EMNKRKLNNS HIQPNGPTLR MPKSVMMSQA MHK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
3k2a_A1e-13379437563Homeobox protein Meis2
3k2a_B1e-13379437563Homeobox protein Meis2
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.760.0flower| leaf
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible253411_at0.0
Expression AtlasAT4G32980-
AtGenExpressAT4G32980-
ATTED-IIAT4G32980-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Down-regulated in the shoot apical meristem (SAM) upon floral induction. {ECO:0000269|PubMed:17908157}.
UniprotTISSUE SPECIFICITY: Most abundant in flowers.
Functional Description ? help Back to Top
Source Description
TAIREncodes transcription factor involved in photomorphogenesis. Regulates gibberellin biosynthesis. Activated by AGAMOUS in a cal-1, ap1-1 background. Expressed at low levels in developing stamens. Increased levels of ATH1 severely delay flowering in the C24 accession. Most remarkably, ectopically expressed ATH1 hardly had an effect on flowering time in the Col-0 and Ler accessions. ATH1 physically interacts with STM, BP and KNAT6 and enhances the shoot apical meristem defect of some of these genes suggesting a role in SAM maintenance. Nuclear localization is dependent upon interaction with STM.
UniProtTranscription factor which may be involved in the signal transduction pathway downstream of the COP1 gene. Controls floral competency as a specific activator of FLC expression. Is responsive of the nuclear import of SHOOT MERISTEMLESS (STM). {ECO:0000269|PubMed:17908157}.
Function -- GeneRIF ? help Back to Top
  1. ATH1 controls floral competency as a specific activator of FLOWERING LOCUS C (FLC) expression.
    [PMID: 17908157]
  2. Data show that ATH1 modulates growth at the interface between the stem, meristem, and organ primordia and contributes to the compressed vegetative habit of Arabidopsis thaliana.
    [PMID: 18757555]
  3. combined lesions in ATH1, PNY and PNF result in a full phenocopy of shoot apical meristem loss-of-function mutants.
    [PMID: 19175771]
  4. The data indicate that the ATH1-KNAT2 complex acts redundantly with KNAT6, both of which are negatively regulated by BP during pedicel development.
    [PMID: 22140242]
  5. BOP1/2 gain-of-function in stems promotes expression of the boundary gene KNOTTED1-LIKE FROM ARABIDOPSIS THALIANA6 (KNAT6) and ARABIDOPSIS THALIANA HOMEOBOX GENE1 (ATH1).
    [PMID: 22751300]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT4G32980.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By light. In etiolated seedlings, maximally expressed after 3 days of illumination.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source Upstream Regulator (A: Activate/R: Repress)
ATRM AT4G18960 (A)
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT3G15170(A), AT5G10140(A)
Regulation -- Hormone ? help Back to Top
Source Hormone
AHDgibberellin
Interaction ? help Back to Top
Source Intact With
BioGRIDAT5G11060, AT1G23380, AT1G26260, AT1G62360, AT1G62990, AT1G70510
IntActSearch P48731
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT4G32980
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY0965130.0AY096513.1 Arabidopsis thaliana putative homeobox gene ATH1 protein (At4g32980) mRNA, complete cds.
GenBankAY0721740.0AY072174.1 Arabidopsis thaliana putative homeobox gene ATH1 protein (At4g32980) mRNA, complete cds.
GenBankX801260.0X80126.1 A.thaliana AtH1 mRNA.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_195024.10.0homeobox protein ATH1
SwissprotP487310.0ATH1_ARATH; Homeobox protein ATH1
TrEMBLD7M9B90.0D7M9B9_ARALL; Putative uncharacterized protein
STRINGAT4G32980.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP13316172
MalvidsOGEM82282637
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. García-Martinez JL,Gil J
    Light Regulation of Gibberellin Biosynthesis and Mode of Action.
    J. Plant Growth Regul., 2001. 20(4): p. 354-368
    [PMID:11986761]
  3. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  4. Smith HM,Campbell BC,Hake S
    Competence to respond to floral inductive signals requires the homeobox genes PENNYWISE and POUND-FOOLISH.
    Curr. Biol., 2004. 14(9): p. 812-7
    [PMID:15120075]
  5. Gómez-Mena C,de Folter S,Costa MM,Angenent GC,Sablowski R
    Transcriptional program controlled by the floral homeotic gene AGAMOUS during early organogenesis.
    Development, 2005. 132(3): p. 429-38
    [PMID:15634696]
  6. Hackbusch J,Richter K,Müller J,Salamini F,Uhrig JF
    A central role of Arabidopsis thaliana ovate family proteins in networking and subcellular localization of 3-aa loop extension homeodomain proteins.
    Proc. Natl. Acad. Sci. U.S.A., 2005. 102(13): p. 4908-12
    [PMID:15781858]
  7. Viola IL,Gonzalez DH
    Interaction of the BELL-like protein ATH1 with DNA: role of homeodomain residue 54 in specifying the different binding properties of BELL and KNOX proteins.
    Biol. Chem., 2006. 387(1): p. 31-40
    [PMID:16497162]
  8. Cole M,Nolte C,Werr W
    Nuclear import of the transcription factor SHOOT MERISTEMLESS depends on heterodimerization with BLH proteins expressed in discrete sub-domains of the shoot apical meristem of Arabidopsis thaliana.
    Nucleic Acids Res., 2006. 34(4): p. 1281-92
    [PMID:16513846]
  9. Welch D, et al.
    Arabidopsis JACKDAW and MAGPIE zinc finger proteins delimit asymmetric cell division and stabilize tissue boundaries by restricting SHORT-ROOT action.
    Genes Dev., 2007. 21(17): p. 2196-204
    [PMID:17785527]
  10. Proveniers M,Rutjens B,Brand M,Smeekens S
    The Arabidopsis TALE homeobox gene ATH1 controls floral competency through positive regulation of FLC.
    Plant J., 2007. 52(5): p. 899-913
    [PMID:17908157]
  11. Gómez-Mena C,Sablowski R
    ARABIDOPSIS THALIANA HOMEOBOX GENE1 establishes the basal boundaries of shoot organs and controls stem growth.
    Plant Cell, 2008. 20(8): p. 2059-72
    [PMID:18757555]
  12. Rutjens B, et al.
    Shoot apical meristem function in Arabidopsis requires the combined activities of three BEL1-like homeodomain proteins.
    Plant J., 2009. 58(4): p. 641-54
    [PMID:19175771]
  13. Li Y,Pi L,Huang H,Xu L
    ATH1 and KNAT2 proteins act together in regulation of plant inflorescence architecture.
    J. Exp. Bot., 2012. 63(3): p. 1423-33
    [PMID:22140242]
  14. Schmid MW, et al.
    A powerful method for transcriptional profiling of specific cell types in eukaryotes: laser-assisted microdissection and RNA sequencing.
    PLoS ONE, 2012. 7(1): p. e29685
    [PMID:22291893]
  15. Khan M,Tabb P,Hepworth SR
    BLADE-ON-PETIOLE1 and 2 regulate Arabidopsis inflorescence architecture in conjunction with homeobox genes KNAT6 and ATH1.
    Plant Signal Behav, 2012. 7(7): p. 788-92
    [PMID:22751300]
  16. 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]
  17. Quaedvlieg N,Dockx J,Rook F,Weisbeek P,Smeekens S
    The homeobox gene ATH1 of Arabidopsis is derepressed in the photomorphogenic mutants cop1 and det1.
    Plant Cell, 1995. 7(1): p. 117-29
    [PMID:7696878]
  18. van Drunen CM, et al.
    Analysis of the chromatin domain organisation around the plastocyanin gene reveals an MAR-specific sequence element in Arabidopsis thaliana.
    Nucleic Acids Res., 1997. 25(19): p. 3904-11
    [PMID:9380515]