PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT4G00180.1
Common NameF6N15.22, YAB3
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 YABBY
Protein Properties Length: 240aa    MW: 26338 Da    PI: 8.5262
Description YABBY family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT4G00180.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
        YABBY   2 dvfssseqvCyvqCnfCntilavsvPstslfkvvtvrCGhCtsllsvnlakasqllaaeshldeslkee........lleelkveeenlksnvekees 91 
                  d+fss++q+Cyv+C+fC+t+lavsvP +slfk+vtvrCGhC++llsv++++++ ll+++s+l++s+ ++        llee+++ ++n+++n++++++
                  89*****************************************************************9999*************************** PP

        YABBY  92 astsvssekl........senedeevprvppvirPPekrqrvPsaynrfikeeiqrikasnPdishreafsaaaknWahfPkihfgl 170
                  as+++++e+l        s ++ +e+pr+pp++rPPekrqrvPsaynrfikeeiqrika+nPdishreafsaaaknWahfP+ihfgl
                  *********99**************************************************************************97 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046902.4E-6821201IPR006780YABBY protein
SuperFamilySSF470957.99E-8146194IPR009071High mobility group box domain
Gene3DG3DSA: mobility group box domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009944Biological Processpolarity specification of adaxial/abaxial axis
GO:0010154Biological Processfruit development
GO:0010158Biological Processabaxial cell fate specification
GO:1902183Biological Processregulation of shoot apical meristem development
GO:2000024Biological Processregulation of leaf development
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
GO:0046872Molecular Functionmetal ion binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009025anatomyvascular leaf
PO:0009052anatomyflower pedicel
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
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: 240 aa     Download sequence    Send to blast
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.118670.0root| seed
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT4G00180-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in subepidermal cells of anlagen regions, then in abaxial part of primordia and finally in differentiating organs. Levels decrease in differentiated organs. In embryo the expression starts during the heart stage in the cotyledon anlagen. Later, expression expands to abaxial domain of the cotyledon primordia and decrease as the embryo matures. In stamen, expression restricted to the abaxial region differentiating into the connective. In gynoecium, expressed in the abaxial cell layers differentiating into the valves. {ECO:0000269|PubMed:10457020}.
UniprotTISSUE SPECIFICITY: Expressed in abaxial regions of lateral aerial organ primordia leading to cotyledons, leaves, flower meristems, sepals, petals, stamen and carpels, but not in roots. {ECO:0000269|PubMed:10457020, ECO:0000269|PubMed:12417699}.
Functional Description ? help Back to Top
Source Description
TAIRYABBY gene family member, likely has transcription factor activity, involved in specifying abaxial cell fate. Along with FIL, involved in patterning of the fruit. GUS reporter gene expression in seedlings is observed in the young leaves and as the leaf matures, expression is restricted to the abaxial tissues of leaves, expression is also observed on either side of the leaf margin in the younger tissues of leaf blades.
UniProtInvolved in the abaxial cell fate determination during embryogenesis and organogenesis. Regulates the initiation of embryonic shoot apical meristem (SAM) development (PubMed:10457020, PubMed:12417699, PubMed:19837869). Contributes to the repression of KNOX genes (STM, KNAT1/BP and KNAT2) to avoid ectopic meristems. Binds DNA without sequence specificity (PubMed:10457020, PubMed:12417699). {ECO:0000269|PubMed:10457020, ECO:0000269|PubMed:12417699, ECO:0000269|PubMed:19837869}.
Function -- GeneRIF ? help Back to Top
  1. Data show that mutations in the YABBY3 (YAB3) cause an array of defects, including aberrant phyllotaxis.
    [PMID: 18469164]
  2. YAB3 interact with LUG and LUH. Together these proteins maintain leaf polarity and meristem activity in Arabidopsis.
    [PMID: 19837869]
  3. Mutation of these YAB and KNOX1 genes together causes nearly complete suppression of bop1 bop2 ectopic organ outgrowth at the morphological and cellular levels.
    [PMID: 20610407]
Cis-element ? help Back to Top
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 AT1G65620 (R), AT2G28610 (R), AT4G37750 (A)
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT1G62360(R), AT1G65620(R), AT5G60910(A)
Interaction -- BIND ? help Back to Top
Source Intact With Description
BINDAT4G27330NZZ interacts with YAB3.
Interaction ? help Back to Top
Source Intact With
BioGRIDAT4G27330, AT1G18570
IntActSearch Q9XFB1
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: Leaves polarity and growth defects. {ECO:0000269|PubMed:19837869}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT4G00180
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF1365400.0AF136540.1 Arabidopsis thaliana YABBY3 (YABBY3) mRNA, complete cds.
GenBankAY0371860.0AY037186.1 Arabidopsis thaliana AT4g00180/F6N15_22 mRNA, complete cds.
GenBankBT0026620.0BT002662.1 Arabidopsis thaliana At4g00180/F6N15_22 gene, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_567154.11e-178Plant-specific transcription factor YABBY family protein
SwissprotQ9XFB11e-179YAB3_ARATH; Axial regulator YABBY 3
TrEMBLA0A178V3641e-176A0A178V364_ARATH; YAB3
STRINGAT4G00180.11e-177(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP46851123
Publications ? help Back to Top
  1. Siegfried KR, et al.
    Members of the YABBY gene family specify abaxial cell fate in Arabidopsis.
    Development, 1999. 126(18): p. 4117-28
  2. Bowman JL
    The YABBY gene family and abaxial cell fate.
    Curr. Opin. Plant Biol., 2000. 3(1): p. 17-22
  3. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
  4. Kumaran MK,Bowman JL,Sundaresan V
    YABBY polarity genes mediate the repression of KNOX homeobox genes in Arabidopsis.
    Plant Cell, 2002. 14(11): p. 2761-70
  5. Lin WC,Shuai B,Springer PS
    The Arabidopsis LATERAL ORGAN BOUNDARIES-domain gene ASYMMETRIC LEAVES2 functions in the repression of KNOX gene expression and in adaxial-abaxial patterning.
    Plant Cell, 2003. 15(10): p. 2241-52
  6. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
  7. Engstrom EM,Izhaki A,Bowman JL
    Promoter bashing, microRNAs, and Knox genes. New insights, regulators, and targets-of-regulation in the establishment of lateral organ polarity in Arabidopsis.
    Plant Physiol., 2004. 135(2): p. 685-94
  8. Sieber P,Petrascheck M,Barberis A,Schneitz K
    Organ polarity in Arabidopsis. NOZZLE physically interacts with members of the YABBY family.
    Plant Physiol., 2004. 135(4): p. 2172-85
  9. Dinneny JR,Weigel D,Yanofsky MF
    A genetic framework for fruit patterning in Arabidopsis thaliana.
    Development, 2005. 132(21): p. 4687-96
  10. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
  11. Nole-Wilson S,Krizek BA
    AINTEGUMENTA contributes to organ polarity and regulates growth of lateral organs in combination with YABBY genes.
    Plant Physiol., 2006. 141(3): p. 977-87
  12. Dai M,Hu Y,Zhao Y,Liu H,Zhou DX
    A WUSCHEL-LIKE HOMEOBOX gene represses a YABBY gene expression required for rice leaf development.
    Plant Physiol., 2007. 144(1): p. 380-90
  13. 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
  14. Gallagher TL,Gasser CS
    Independence and interaction of regions of the INNER NO OUTER protein in growth control during ovule development.
    Plant Physiol., 2008. 147(1): p. 306-15
  15. Goldshmidt A,Alvarez JP,Bowman JL,Eshed Y
    Signals derived from YABBY gene activities in organ primordia regulate growth and partitioning of Arabidopsis shoot apical meristems.
    Plant Cell, 2008. 20(5): p. 1217-30
  16. Mummenhoff K,Polster A,M
    Lepidium as a model system for studying the evolution of fruit development in Brassicaceae.
    J. Exp. Bot., 2009. 60(5): p. 1503-13
  17. Dai M,Hu Y,Zhao Y,Zhou DX
    Regulatory Networks Involving YABBY Genes in Rice Shoot Development.
    Plant Signal Behav, 2007. 2(5): p. 399-400
  18. Stahle MI,Kuehlich J,Staron L,von Arnim AG,Golz JF
    YABBYs and the transcriptional corepressors LEUNIG and LEUNIG_HOMOLOG maintain leaf polarity and meristem activity in Arabidopsis.
    Plant Cell, 2009. 21(10): p. 3105-18
  19. Ha CM,Jun JH,Fletcher JC
    Control of Arabidopsis leaf morphogenesis through regulation of the YABBY and KNOX families of transcription factors.
    Genetics, 2010. 186(1): p. 197-206
  20. Hanada K, et al.
    Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana.
    Mol. Biol. Evol., 2011. 28(1): p. 377-82
  21. McKeown PC, et al.
    Identification of imprinted genes subject to parent-of-origin specific expression in Arabidopsis thaliana seeds.
    BMC Plant Biol., 2011. 11: p. 113
  22. Bonaccorso O,Lee JE,Puah L,Scutt CP,Golz JF
    FILAMENTOUS FLOWER controls lateral organ development by acting as both an activator and a repressor.
    BMC Plant Biol., 2012. 12: p. 176
  23. 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
  24. Yadav RK, et al.
    Plant stem cell maintenance involves direct transcriptional repression of differentiation program.
    Mol. Syst. Biol., 2013. 9: p. 654
  25. Xiang J, et al.
    Isolation and characterization of two VpYABBY genes from wild Chinese Vitis pseudoreticulata.
    Protoplasma, 2013. 250(6): p. 1315-25
  26. Frerigmann H,Berger B,Gigolashvili T
    bHLH05 is an interaction partner of MYB51 and a novel regulator of glucosinolate biosynthesis in Arabidopsis.
    Plant Physiol., 2014. 166(1): p. 349-69
  27. Chen GH,Sun JY,Liu M,Liu J,Yang WC
    SPOROCYTELESS is a novel embryophyte-specific transcription repressor that interacts with TPL and TCP proteins in Arabidopsis.
    J Genet Genomics, 2014. 41(12): p. 617-25
  28. 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