PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT1G30490.1
Common NameATHB9, ATHB-9, F26G16.11, HB9, PHV
Organism
Arabidopsis thaliana
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: 841aa    MW: 92401.7 Da    PI: 6.3674
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT1G30490.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox58.98.6e-192179357
                 --SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHC....TS-HHHHHHHHHHHHHHHHC CS
     Homeobox  3 kRttftkeqleeLeelFeknrypsaeereeLAkkl....gLterqVkvWFqNrRakekk 57
                 k  ++t+eq+e+Le++++++++ps  +r++L +++    +++ rq+kvWFqNrR +ek+
  AT1G30490.1 21 KYVRYTPEQVEALERVYAECPKPSSLRRQQLIRECpilcNIEPRQIKVWFQNRRCREKQ 79
                 5678*****************************************************97 PP
2START172.82.2e-541703782205
                  HHHHHHHHHHHHHHHC-TT-EEEEEXCCTTEEEEEEESSS.SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-SEEEEEEEECTT..EEEEEEEEX CS
        START   2 laeeaaqelvkkalaeepgWvkssesengdevlqkfeeskvdsgealrasgvvdmvlallveellddkeqWdetlakaetlevissg..galqlmvae 97 
                  +aee+++e++ ka+ ++  Wv++  +++g++++ +++ s+++sg a+ra+g+v  +++  v+e+l+d++ W ++++ +etl+vi +g  g+++l +++
  AT1G30490.1 170 IAEETLAEFLCKATGTAVDWVQMIGMKPGPDSIGIVAVSRNCSGIAARACGLVSLEPM-KVAEILKDRPSWFRDCRCVETLNVIPTGngGTIELVNTQ 266
                  7899******************************************************.8888888888***************************** PP

                  XTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--....-TTSEE-EESSEEEEEEEECTCEEEEEEEE-EE--SSXXHHHHHHHHHHHHHH CS
        START  98 lqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppe...sssvvRaellpSgiliepksnghskvtwvehvdlkgrlphwllrslvksglae 191
                   +a+++l++ Rdf+++Ry+ +l++g++v++++S++s +  p+   sss+vRa++l Sg+li+p+++g+s +++v+hvdl+ ++++++lr+l++s+ + 
  AT1G30490.1 267 IYAPTTLAAaRDFWTLRYSTSLEDGSYVVCERSLTSATGGPNgplSSSFVRAKMLSSGFLIRPCDGGGSIIHIVDHVDLDVSSVPEVLRPLYESSKIL 364
                  *****************************************99******************************************************* PP

                  HHHHHHHHTXXXXX CS
        START 192 gaktwvatlqrqce 205
                  ++k++va+l++ ++
  AT1G30490.1 365 AQKMTVAALRHVRQ 378
                  *********98765 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.606.3E-19479IPR009057Homeodomain-like
PROSITE profilePS5007115.4511680IPR001356Homeobox domain
SMARTSM003894.2E-161884IPR001356Homeobox domain
SuperFamilySSF466891.41E-162082IPR009057Homeodomain-like
CDDcd000865.83E-172181No hitNo description
PfamPF000462.5E-162279IPR001356Homeobox domain
CDDcd146863.22E-673112No hitNo description
PROSITE profilePS5084824.922160388IPR002913START domain
CDDcd088759.86E-70164380No hitNo description
Gene3DG3DSA:3.30.530.206.4E-19169374IPR023393START-like domain
SuperFamilySSF559611.51E-34169381No hitNo description
SMARTSM002342.7E-51169379IPR002913START domain
PfamPF018521.3E-51170378IPR002913START domain
PfamPF086707.2E-49694840IPR013978MEKHLA
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009855Biological Processdetermination of bilateral symmetry
GO:0009880Biological Processembryonic pattern specification
GO:0009944Biological Processpolarity specification of adaxial/abaxial axis
GO:0010072Biological Processprimary shoot apical meristem specification
GO:0030154Biological Processcell differentiation
GO:0080060Biological Processintegument development
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
GO:0008289Molecular Functionlipid binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000229anatomyflower meristem
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009005anatomyroot
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009015anatomyportion of vascular tissue
PO:0009025anatomyvascular leaf
PO:0009029anatomystamen
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0009052anatomyflower pedicel
PO:0020022anatomyinner integument
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:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 841 aa     Download sequence    Send to blast
MMAHHSMDDR DSPDKGFDSG KYVRYTPEQV EALERVYAEC PKPSSLRRQQ LIRECPILCN  60
IEPRQIKVWF QNRRCREKQR KESARLQTVN RKLSAMNKLL MEENDRLQKQ VSNLVYENGF  120
MKHRIHTASG TTTDNSCESV VVSGQQRQQQ NPTHQHPQRD VNNPANLLSI AEETLAEFLC  180
KATGTAVDWV QMIGMKPGPD SIGIVAVSRN CSGIAARACG LVSLEPMKVA EILKDRPSWF  240
RDCRCVETLN VIPTGNGGTI ELVNTQIYAP TTLAAARDFW TLRYSTSLED GSYVVCERSL  300
TSATGGPNGP LSSSFVRAKM LSSGFLIRPC DGGGSIIHIV DHVDLDVSSV PEVLRPLYES  360
SKILAQKMTV AALRHVRQIA QETSGEVQYS GGRQPAVLRT FSQRLCRGFN DAVNGFVDDG  420
WSPMSSDGGE DITIMINSSS AKFAGSQYGS SFLPSFGSGV LCAKASMLLQ NVPPLVLIRF  480
LREHRAEWAD YGVDAYSAAS LRATPYAVPC VRTGGFPSNQ VILPLAQTLE HEEFLEVVRL  540
GGHAYSPEDM GLSRDMYLLQ LCSGVDENVV GGCAQLVFAP IDESFADDAP LLPSGFRVIP  600
LDQKTNPNDH QSASRTRDLA SSLDGSTKTD SETNSRLVLT IAFQFTFDNH SRDNVATMAR  660
QYVRNVVGSI QRVALAITPR PGSMQLPTSP EALTLVRWIT RSYSIHTGAD LFGADSQSCG  720
GDTLLKQLWD HSDAILCCSL KTNASPVFTF ANQAGLDMLE TTLVALQDIM LDKTLDDSGR  780
RALCSEFAKI MQQGYANLPA GICVSSMGRP VSYEQATVWK VVDDNESNHC LAFTLVSWSF  840
V
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.279610.0cell culture| flower| root| seed| silique| vegetative tissue
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible261800_at0.0
Expression AtlasAT1G30490-
AtGenExpressAT1G30490-
ATTED-IIAT1G30490-
Functional Description ? help Back to Top
Source Description
TAIRDominant PHV mutations cause transformation of abaxial leaf fates into adaxial leaf fates. Has overlapping functions with PHABULOSA, REVOLUTA and CORONA/ATHB15 in patterning the apical portion of the embryo. Encodes a member of HD-Zip family which contains homeodomain-leucine zipper domains and domain similar to a mammalian sterol binding domain.
UniProtProbable transcription factor involved in the determination of adaxial-abaxial polarity in ovule primordium. Specifies adaxial leaf fates. Binds to the DNA sequence 5'-GTAAT[GC]ATTAC-3'. {ECO:0000269|PubMed:11395776, ECO:0000269|PubMed:15598805, ECO:0000269|PubMed:17900520, ECO:0000269|PubMed:9747806}.
Function -- GeneRIF ? help Back to Top
  1. Class III HD-Zip AND KANADI genes required for root development [PHAVOLUTA (PHV)]
    [PMID: 15286295]
  2. A yeast two-hybrid screen with DRN followed by co-immunoprecipitation and bimolecular fluorescence complementation revealed PHAVOLUTA (PHV) to be a protein interaction partner in planta
    [PMID: 17376809]
  3. Athb-9 is sensitive to redox conditions
    [PMID: 17900520]
  4. stem cell specification pathway is normally repressed by the activity of the HD-zip III transcription factors PHABULOSA (PHB), PHAVOLUTA (PHV) and CORONA (CNA).
    [PMID: 26011610]
  5. The branching ovules of the mutant resemble those of some fossil gymnosperms, implicating BEL1 and HD-ZIPIII genes as players in the evolution of the unbranched ovule form in extant angiosperms.
    [PMID: 26700684]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00170DAP27203113Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT1G30490.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By auxin. Repressed by miR165 and miR166. {ECO:0000269|PubMed:14999284, ECO:0000269|PubMed:16033795, ECO:0000269|PubMed:17237362}.
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 AT2G17950(R), AT5G16560(R)
Interaction ? help Back to Top
Source Intact With
IntActSearch O04292
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT1G30490
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAJ4409670.0AJ440967.1 Arabidopsis thaliana mRNA for homeodomain-leucine zipper protein (hb9 gene).
GenBankAK2265700.0AK226570.1 Arabidopsis thaliana mRNA for HD-Zip protein, complete cds, clone: RAFL07-12-P11.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_174337.10.0Homeobox-leucine zipper family protein / lipid-binding START domain-containing protein
SwissprotO042920.0ATBH9_ARATH; Homeobox-leucine zipper protein ATHB-9
TrEMBLA0A178WF170.0A0A178WF17_ARATH; PHV
STRINGAT1G30490.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM42562653
Representative plantOGRP6511671
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. McConnell JR, et al.
    Role of PHABULOSA and PHAVOLUTA in determining radial patterning in shoots.
    Nature, 2001. 411(6838): p. 709-13
    [PMID:11395776]
  3. Eshed Y,Baum SF,Perea JV,Bowman JL
    Establishment of polarity in lateral organs of plants.
    Curr. Biol., 2001. 11(16): p. 1251-60
    [PMID:11525739]
  4. Golz JF,Hudson A
    Signalling in plant lateral organ development.
    Plant Cell, 2002. 14 Suppl: p. S277-88
    [PMID:12045283]
  5. Tang G,Reinhart BJ,Bartel DP,Zamore PD
    A biochemical framework for RNA silencing in plants.
    Genes Dev., 2003. 17(1): p. 49-63
    [PMID:12514099]
  6. Emery JF, et al.
    Radial patterning of Arabidopsis shoots by class III HD-ZIP and KANADI genes.
    Curr. Biol., 2003. 13(20): p. 1768-74
    [PMID:14561401]
  7. Kidner CA,Martienssen RA
    Spatially restricted microRNA directs leaf polarity through ARGONAUTE1.
    Nature, 2004. 428(6978): p. 81-4
    [PMID:14999284]
  8. Juarez MT,Kui JS,Thomas J,Heller BA,Timmermans MC
    microRNA-mediated repression of rolled leaf1 specifies maize leaf polarity.
    Nature, 2004. 428(6978): p. 84-8
    [PMID:14999285]
  9. Hawker NP,Bowman JL
    Roles for Class III HD-Zip and KANADI genes in Arabidopsis root development.
    Plant Physiol., 2004. 135(4): p. 2261-70
    [PMID:15286295]
  10. Prigge MJ, et al.
    Class III homeodomain-leucine zipper gene family members have overlapping, antagonistic, and distinct roles in Arabidopsis development.
    Plant Cell, 2005. 17(1): p. 61-76
    [PMID:15598805]
  11. Williams L,Grigg SP,Xie M,Christensen S,Fletcher JC
    Regulation of Arabidopsis shoot apical meristem and lateral organ formation by microRNA miR166g and its AtHD-ZIP target genes.
    Development, 2005. 132(16): p. 3657-68
    [PMID:16033795]
  12. Ochando I, et al.
    Mutations in the microRNA complementarity site of the INCURVATA4 gene perturb meristem function and adaxialize lateral organs in arabidopsis.
    Plant Physiol., 2006. 141(2): p. 607-19
    [PMID:16617092]
  13. Prigge MJ,Clark SE
    Evolution of the class III HD-Zip gene family in land plants.
    Evol. Dev., 2006 Jul-Aug. 8(4): p. 350-61
    [PMID:16805899]
  14. Lobbes D,Rallapalli G,Schmidt DD,Martin C,Clarke J
    SERRATE: a new player on the plant microRNA scene.
    EMBO Rep., 2006. 7(10): p. 1052-8
    [PMID:16977334]
  15. Zhou GK,Kubo M,Zhong R,Demura T,Ye ZH
    Overexpression of miR165 affects apical meristem formation, organ polarity establishment and vascular development in Arabidopsis.
    Plant Cell Physiol., 2007. 48(3): p. 391-404
    [PMID:17237362]
  16. Chandler JW,Cole M,Flier A,Grewe B,Werr W
    The AP2 transcription factors DORNROSCHEN and DORNROSCHEN-LIKE redundantly control Arabidopsis embryo patterning via interaction with PHAVOLUTA.
    Development, 2007. 134(9): p. 1653-62
    [PMID:17376809]
  17. Fu Y, et al.
    Genetic interactions between leaf polarity-controlling genes and ASYMMETRIC LEAVES1 and 2 in Arabidopsis leaf patterning.
    Plant Cell Physiol., 2007. 48(5): p. 724-35
    [PMID:17395603]
  18. Baucher M,El Jaziri M,Vandeputte O
    From primary to secondary growth: origin and development of the vascular system.
    J. Exp. Bot., 2007. 58(13): p. 3485-501
    [PMID:17898423]
  19. Comelli RN,Gonzalez DH
    Conserved homeodomain cysteines confer redox sensitivity and influence the DNA binding properties of plant class III HD-Zip proteins.
    Arch. Biochem. Biophys., 2007. 467(1): p. 41-7
    [PMID:17900520]
  20. Wenkel S,Emery J,Hou BH,Evans MM,Barton MK
    A feedback regulatory module formed by LITTLE ZIPPER and HD-ZIPIII genes.
    Plant Cell, 2007. 19(11): p. 3379-90
    [PMID:18055602]
  21. Kim YS, et al.
    HD-ZIP III activity is modulated by competitive inhibitors via a feedback loop in Arabidopsis shoot apical meristem development.
    Plant Cell, 2008. 20(4): p. 920-33
    [PMID:18408069]
  22. 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]
  23. Yang JY, et al.
    betaC1, the pathogenicity factor of TYLCCNV, interacts with AS1 to alter leaf development and suppress selective jasmonic acid responses.
    Genes Dev., 2008. 22(18): p. 2564-77
    [PMID:18794352]
  24. Chandler JW,Cole M,Flier A,Werr W
    BIM1, a bHLH protein involved in brassinosteroid signalling, controls Arabidopsis embryonic patterning via interaction with DORNROSCHEN and DORNROSCHEN-LIKE.
    Plant Mol. Biol., 2009. 69(1-2): p. 57-68
    [PMID:18830673]
  25. Ochando I,González-Reig S,Ripoll JJ,Vera A,Martínez-Laborda A
    Alteration of the shoot radial pattern in Arabidopsis thaliana by a gain-of-function allele of the class III HD-Zip gene INCURVATA4.
    Int. J. Dev. Biol., 2008. 52(7): p. 953-61
    [PMID:18956325]
  26. Kelley DR,Skinner DJ,Gasser CS
    Roles of polarity determinants in ovule development.
    Plant J., 2009. 57(6): p. 1054-64
    [PMID:19054366]
  27. Grigg SP, et al.
    Repression of apical homeobox genes is required for embryonic root development in Arabidopsis.
    Curr. Biol., 2009. 19(17): p. 1485-90
    [PMID:19646874]
  28. Zhong R,Ye ZH
    Regulation of HD-ZIP III Genes by MicroRNA 165.
    Plant Signal Behav, 2007. 2(5): p. 351-3
    [PMID:19704656]
  29. Yao X, et al.
    Two types of cis-acting elements control the abaxial epidermis-specific transcription of the MIR165a and MIR166a genes.
    FEBS Lett., 2009. 583(22): p. 3711-7
    [PMID:19879265]
  30. Gu XL,Wang H,Huang H,Cui XF
    SPT6L encoding a putative WG/GW-repeat protein regulates apical-basal polarity of embryo in Arabidopsis.
    Mol Plant, 2012. 5(1): p. 249-59
    [PMID:21948524]
  31. Meinke DW
    A survey of dominant mutations in Arabidopsis thaliana.
    Trends Plant Sci., 2013. 18(2): p. 84-91
    [PMID:22995285]
  32. Tang X, et al.
    MicroRNA-mediated repression of the seed maturation program during vegetative development in Arabidopsis.
    PLoS Genet., 2012. 8(11): p. e1003091
    [PMID:23209442]
  33. Turchi L, et al.
    Arabidopsis HD-Zip II transcription factors control apical embryo development and meristem function.
    Development, 2013. 140(10): p. 2118-29
    [PMID:23578926]
  34. Floyd SK, et al.
    Origin of a novel regulatory module by duplication and degeneration of an ancient plant transcription factor.
    Mol. Phylogenet. Evol., 2014. 81: p. 159-73
    [PMID:25263420]
  35. Jia X, et al.
    Functional plasticity of miR165/166 in plant development revealed by small tandem target mimic.
    Plant Sci., 2015. 233: p. 11-21
    [PMID:25711809]
  36. 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]
  37. Lee C,Clark SE
    A WUSCHEL-Independent Stem Cell Specification Pathway Is Repressed by PHB, PHV and CNA in Arabidopsis.
    PLoS ONE, 2015. 10(5): p. e0126006
    [PMID:26011610]
  38. Yamada T,Sasaki Y,Hashimoto K,Nakajima K,Gasser CS
    CORONA, PHABULOSA and PHAVOLUTA collaborate with BELL1 to confine WUSCHEL expression to the nucellus in Arabidopsis ovules.
    Development, 2016. 143(3): p. 422-6
    [PMID:26700684]
  39. Wójcik AM,Nodine MD,Gaj MD
    miR160 and miR166/165 Contribute to the LEC2-Mediated Auxin Response Involved in the Somatic Embryogenesis Induction in Arabidopsis.
    Front Plant Sci, 2017. 8: p. 2024
    [PMID:29321785]
  40. 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
    [PMID:9747806]