PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT5G02030.1
Common NameBLH9, BLR, HB-6, LSN, PNY, RPL, T7H20_80, VAN
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: 575aa    MW: 62006.6 Da    PI: 7.9444
Description TALE family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT5G02030.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
     Homeobox  22 nrypsaeereeLAkklgLterqVkvWFqNrRak 54 
                  ++yp+ +++  LAk++gL+ +qV++WF N R +
                  89*****************************87 PP

         BELL   4 elqkkkakLlslleeVdkrYkqyveqlqtvissFeavaglgsakpYtslAlkaiSrhFrcLkdaiaeqi 72 
                  ++ kkk+kL+s+l+eV+krYkqy+eqlq+v++sFe+vaglg+a+pY++lAlka+S+hF+cLk+ai++q+
                  5789**************************************************************997 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005745.7E-70165292IPR006563POX domain
PfamPF075267.3E-35170291IPR006563POX domain
CDDcd000862.02E-11349410No hitNo description
SMARTSM003894.0E-9349413IPR001356Homeobox domain
PfamPF059201.8E-18366405IPR008422Homeobox KN domain
PROSITE profilePS5007111.645368409IPR001356Homeobox domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0010051Biological Processxylem and phloem pattern formation
GO:0010076Biological Processmaintenance of floral meristem identity
GO:0010077Biological Processmaintenance of inflorescence meristem identity
GO:0010089Biological Processxylem development
GO:0010154Biological Processfruit development
GO:0010223Biological Processsecondary shoot formation
GO:0010228Biological Processvegetative to reproductive phase transition of meristem
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:0048457Biological Processfloral whorl morphogenesis
GO:0048645Biological Processorgan formation
GO:0080006Biological Processinternode patterning
GO:0005634Cellular Componentnucleus
GO:0005829Cellular Componentcytosol
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:0000037anatomyshoot apex
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0008016anatomyvegetative shoot apical meristem
PO:0008019anatomyleaf lamina base
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009025anatomyvascular leaf
PO:0009052anatomyflower pedicel
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
PO:0025272anatomyovary replum
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: 575 aa     Download sequence    Send to blast
3D Structure ? help Back to Top
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5bng_A9e-17355413159Homeobox protein Meis2
5bng_B9e-17355413159Homeobox protein Meis2
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.48020.0floral meristem| silique
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT5G02030-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed during late heart stage embryo in the SAM region between the two developing cotyledons. Expression is initially down-regulated in incipient floral primordia but a strong expression is subsequently detected in the central region of young floral primordia and the inner whorl of developing flowers. In fruit, is expressed in the replum of developing ovaries. {ECO:0000269|PubMed:12874117}.
UniprotTISSUE SPECIFICITY: Predominantly expressed in stems, inflorescences and flowers. {ECO:0000269|PubMed:12874117, ECO:0000269|PubMed:12897247, ECO:0000269|PubMed:13678595, ECO:0000269|PubMed:15019989}.
Functional Description ? help Back to Top
Source Description
TAIRMutant has additional lateral organs and phyllotaxy defect. Encodes a homeodomain transcription factor. Has sequence similarity to the Arabidopsis ovule development regulator Bell1. Binds directly to the AGAMOUS cis-regulatory element. Its localization to the nucleus is dependent on the coexpression of either STM or BP.
UniProtTranscription factor that is involved in the preservation of the spiral phyllotactic arrangement leading to a regular pattern of organ initiation. Required for maintenance of stem cell fate in the shoot apical meristem, and is essential for specifying floral primordia and establishing early internode patterning events during inflorescence development. Acts as transcription repressor of AG expression in floral and inflorescence meristems. Is also responsive of the nuclear import of SHOOT MERISTEMLESS (STM). In the fruit, plays a central role in patterning by negatively regulating SHP expression in order to prevent replum cells from adopting a valve margin cell fate. {ECO:0000269|PubMed:12874117, ECO:0000269|PubMed:12897247, ECO:0000269|PubMed:13678595, ECO:0000269|PubMed:15019989, ECO:0000269|PubMed:15120075, ECO:0000269|PubMed:15155890, ECO:0000269|PubMed:16741748}.
Function -- GeneRIF ? help Back to Top
  1. floral phenotype of blr mutants is caused by derepression of AGAMOUS, suggesting that BLR functions as a transcription repressor
    [PMID: 15155890]
  2. results from this study support a model in which PNY and PNF promote LFY expression during reproductive development
    [PMID: 18298668]
  3. data showed that BP and PNY restrict KNAT6 and KNAT2 expression to promote correct inflorescence development
    [PMID: 18390591]
  4. PNY functions in the inner whorls to regulate flower patterning events.
    [PMID: 19082619]
  5. combined lesions in ATH1, PNY and PNF result in a full phenocopy of shoot apical meristem loss-of-function mutants.
    [PMID: 19175771]
  6. PNY and PNF act to restrict organogenesis to the peripheral zone by maintaining a boundary between the central zone and peripheral zone.
    [PMID: 21505100]
  7. SPL3, SPL4, and SPL5 function is dependent upon PNY and PNF
    [PMID: 21653282]
  8. Reduced repla resembling Arabidopsis rpl mutant correlated across the Brassicaceae with a point mutation in a conserved cis-element of RPL. When introduced in Arabidopsis, this nucleotide change specifically reduced RPL expression + function in the fruit.
    [PMID: 21737279]
  9. Regulation of meristem central zone integrity by PNY and PNF is crucial for vegetative and reproductive development.
    [PMID: 21822063]
  10. Results report a dual function for the homeodomain transcription factor BELLRINGER (BLR) in the establishment and maintenance of the phyllotactic pattern in Arabidopsis.
    [PMID: 21965608]
  11. These data support a role for BLR in ordering the shoot apex.
    [PMID: 23148846]
  12. NTT loss of function leads to reduced replum width and cell number, whereas increased expression promotes replum enlargement. NTT activates the homeobox gene BP, which, together with RPL, is important for replum development.
    [PMID: 25039392]
  13. The data reveal a potential mechanism by which repression of lateral organ boundary genes by PNY-PNF is essential for flowering.
    [PMID: 26417006]
Cis-element ? help Back to Top
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT1G26310(A), AT1G69120(A), AT2G42830(R), AT3G58780(R), AT4G08150(A), AT4G18960(R), AT5G61850(A), AT5G67110(R)
Interaction -- BIND ? help Back to Top
Source Intact With Description
BINDAT1G62360PNY interacts with STM.
Interaction ? help Back to Top
Source Intact With
BioGRIDAT5G02030, AT5G25220, AT1G23380, AT1G26260, AT1G62360, AT1G69120, AT1G70510, AT1G75410
IntActSearch Q9LZM8
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT5G02030
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY3283140.0AY328314.1 Arabidopsis thaliana bellringer homeodomain protein mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_195823.10.0POX (plant homeobox) family protein
SwissprotQ9LZM80.0BLH9_ARATH; BEL1-like homeodomain protein 9
TrEMBLR0FE520.0R0FE52_9BRAS; Uncharacterized protein
STRINGAT5G02030.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP13316172
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. Byrne ME,Groover AT,Fontana JR,Martienssen RA
    Phyllotactic pattern and stem cell fate are determined by the Arabidopsis homeobox gene BELLRINGER.
    Development, 2003. 130(17): p. 3941-50
  3. Smith HM,Hake S
    The interaction of two homeobox genes, BREVIPEDICELLUS and PENNYWISE, regulates internode patterning in the Arabidopsis inflorescence.
    Plant Cell, 2003. 15(8): p. 1717-27
  4. Roeder AH,Ferr
    The role of the REPLUMLESS homeodomain protein in patterning the Arabidopsis fruit.
    Curr. Biol., 2003. 13(18): p. 1630-5
  5. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
  6. Bhatt AM,Etchells JP,Canales C,Lagodienko A,Dickinson H
    VAAMANA--a BEL1-like homeodomain protein, interacts with KNOX proteins BP and STM and regulates inflorescence stem growth in Arabidopsis.
    Gene, 2004. 328: p. 103-11
  7. 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
  8. Bao X,Franks RG,Levin JZ,Liu Z
    Repression of AGAMOUS by BELLRINGER in floral and inflorescence meristems.
    Plant Cell, 2004. 16(6): p. 1478-89
  9. Son O, et al.
    Induction of a homeodomain-leucine zipper gene by auxin is inhibited by cytokinin in Arabidopsis roots.
    Biochem. Biophys. Res. Commun., 2005. 326(1): p. 203-9
  10. Kooiker M, et al.
    BASIC PENTACYSTEINE1, a GA binding protein that induces conformational changes in the regulatory region of the homeotic Arabidopsis gene SEEDSTICK.
    Plant Cell, 2005. 17(3): p. 722-9
  11. 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
  12. Robles P,Pelaz S
    Flower and fruit development in Arabidopsis thaliana.
    Int. J. Dev. Biol., 2005. 49(5-6): p. 633-43
  13. Dinneny JR,Weigel D,Yanofsky MF
    A genetic framework for fruit patterning in Arabidopsis thaliana.
    Development, 2005. 132(21): p. 4687-96
  14. 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
  15. Gregis V,Sessa A,Colombo L,Kater MM
    AGL24, SHORT VEGETATIVE PHASE, and APETALA1 redundantly control AGAMOUS during early stages of flower development in Arabidopsis.
    Plant Cell, 2006. 18(6): p. 1373-82
  16. Kanrar S,Onguka O,Smith HM
    Arabidopsis inflorescence architecture requires the activities of KNOX-BELL homeodomain heterodimers.
    Planta, 2006. 224(5): p. 1163-73
  17. Alonso-Cantabrana H, et al.
    Common regulatory networks in leaf and fruit patterning revealed by mutations in the Arabidopsis ASYMMETRIC LEAVES1 gene.
    Development, 2007. 134(14): p. 2663-71
  18. Kumar R, et al.
    The Arabidopsis BEL1-LIKE HOMEODOMAIN proteins SAW1 and SAW2 act redundantly to regulate KNOX expression spatially in leaf margins.
    Plant Cell, 2007. 19(9): p. 2719-35
  19. 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
  20. Kanrar S,Bhattacharya M,Arthur B,Courtier J,Smith HM
    Regulatory networks that function to specify flower meristems require the function of homeobox genes PENNYWISE and POUND-FOOLISH in Arabidopsis.
    Plant J., 2008. 54(5): p. 924-37
  21. Ragni L,Belles-Boix E,Günl M,Pautot V
    Interaction of KNAT6 and KNAT2 with BREVIPEDICELLUS and PENNYWISE in Arabidopsis inflorescences.
    Plant Cell, 2008. 20(4): p. 888-900
  22. Magnani E,Hake S
    KNOX lost the OX: the Arabidopsis KNATM gene defines a novel class of KNOX transcriptional regulators missing the homeodomain.
    Plant Cell, 2008. 20(4): p. 875-87
  23. Yu L,Patibanda V,Smith HM
    A novel role of BELL1-like homeobox genes, PENNYWISE and POUND-FOOLISH, in floral patterning.
    Planta, 2009. 229(3): p. 693-707
  24. 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
  25. Takano S,Niihama M,Smith HM,Tasaka M,Aida M
    gorgon, a novel missense mutation in the SHOOT MERISTEMLESS gene, impairs shoot meristem homeostasis in Arabidopsis.
    Plant Cell Physiol., 2010. 51(4): p. 621-34
  26. Irish VF
    The flowering of Arabidopsis flower development.
    Plant J., 2010. 61(6): p. 1014-28
  27. Smith HM,Ung N,Lal S,Courtier J
    Specification of reproductive meristems requires the combined function of SHOOT MERISTEMLESS and floral integrators FLOWERING LOCUS T and FD during Arabidopsis inflorescence development.
    J. Exp. Bot., 2011. 62(2): p. 583-93
  28. Ung N,Lal S,Smith HM
    The role of PENNYWISE and POUND-FOOLISH in the maintenance of the shoot apical meristem in Arabidopsis.
    Plant Physiol., 2011. 156(2): p. 605-14
  29. Lal S,Pacis LB,Smith HM
    Regulation of the SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE genes/microRNA156 module by the homeodomain proteins PENNYWISE and POUND-FOOLISH in Arabidopsis.
    Mol Plant, 2011. 4(6): p. 1123-32
  30. Arnaud N,Lawrenson T,
    The same regulatory point mutation changed seed-dispersal structures in evolution and domestication.
    Curr. Biol., 2011. 21(14): p. 1215-9
  31. Ung N,Smith HM
    Regulation of shoot meristem integrity during Arabidopsis vegetative development.
    Plant Signal Behav, 2011. 6(8): p. 1250-2
  32. Peaucelle A, et al.
    The transcription factor BELLRINGER modulates phyllotaxis by regulating the expression of a pectin methylesterase in Arabidopsis.
    Development, 2011. 138(21): p. 4733-41
  33. Ripoll JJ,Roeder AH,Ditta GS,Yanofsky MF
    A novel role for the floral homeotic gene APETALA2 during Arabidopsis fruit development.
    Development, 2011. 138(23): p. 5167-76
  34. Khan M, et al.
    Antagonistic interaction of BLADE-ON-PETIOLE1 and 2 with BREVIPEDICELLUS and PENNYWISE regulates Arabidopsis inflorescence architecture.
    Plant Physiol., 2012. 158(2): p. 946-60
  35. Smaczniak C, et al.
    Characterization of MADS-domain transcription factor complexes in Arabidopsis flower development.
    Proc. Natl. Acad. Sci. U.S.A., 2012. 109(5): p. 1560-5
  36. 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
  37. Avino M,Kramer EM,Donohue K,Hammel AJ,Hall JC
    Understanding the basis of a novel fruit type in Brassicaceae: conservation and deviation in expression patterns of six genes.
    Evodevo, 2012. 3(1): p. 20
  38. Romera-Branchat M,Ripoll JJ,Yanofsky MF,Pelaz S
    The WOX13 homeobox gene promotes replum formation in the Arabidopsis thaliana fruit.
    Plant J., 2013. 73(1): p. 37-49
  39. Gonz
    Antagonistic gene activities determine the formation of pattern elements along the mediolateral axis of the Arabidopsis fruit.
    PLoS Genet., 2012. 8(11): p. e1003020
  40. Etchells JP, et al.
    A role for BELLRINGER in cell wall development is supported by loss-of-function phenotypes.
    BMC Plant Biol., 2012. 12: p. 212
  41. M
    Evidence that an evolutionary transition from dehiscent to indehiscent fruits in Lepidium (Brassicaceae) was caused by a change in the control of valve margin identity genes.
    Plant J., 2013. 73(5): p. 824-35
  42. Salemme M,Sica M,Gaudio L,Aceto S
    The OitaAG and OitaSTK genes of the orchid Orchis italica: a comparative analysis with other C- and D-class MADS-box genes.
    Mol. Biol. Rep., 2013. 40(5): p. 3523-35
  43. Chung KS,Lee JH,Lee JS,Ahn JH
    Fruit indehiscence caused by enhanced expression of NO TRANSMITTING TRACT in Arabidopsis thaliana.
    Mol. Cells, 2013. 35(6): p. 519-25
  44. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
  45. Debernardi JM, et al.
    Post-transcriptional control of GRF transcription factors by microRNA miR396 and GIF co-activator affects leaf size and longevity.
    Plant J., 2014. 79(3): p. 413-26
  46. Pabón-Mora N,Wong GK,Ambrose BA
    Evolution of fruit development genes in flowering plants.
    Front Plant Sci, 2014. 5: p. 300
  47. Marsch-Mart
    The NTT transcription factor promotes replum development in Arabidopsis fruits.
    Plant J., 2014. 80(1): p. 69-81
  48. 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
  49. Khan M, et al.
    Repression of Lateral Organ Boundary Genes by PENNYWISE and POUND-FOOLISH Is Essential for Meristem Maintenance and Flowering in Arabidopsis.
    Plant Physiol., 2015. 169(3): p. 2166-86
  50. Andrés F, et al.
    Floral Induction in Arabidopsis by FLOWERING LOCUS T Requires Direct Repression of BLADE-ON-PETIOLE Genes by the Homeodomain Protein PENNYWISE.
    Plant Physiol., 2015. 169(3): p. 2187-99
  51. Bencivenga S,Serrano-Mislata A,Bush M,Fox S,Sablowski R
    Control of Oriented Tissue Growth through Repression of Organ Boundary Genes Promotes Stem Morphogenesis.
    Dev. Cell, 2016. 39(2): p. 198-208
  52. Sehra B,Franks RG
    Redundant CArG Box Cis-motif Activity Mediates SHATTERPROOF2 Transcriptional Regulation during Arabidopsis thaliana Gynoecium Development.
    Front Plant Sci, 2017. 8: p. 1712
  53. Simonini S,Stephenson P,Østergaard L
    A molecular framework controlling style morphology in Brassicaceae.
    Development, 2018.