PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT2G45190.1
Common NameAFO, AT, F4L23.30, FIL, YAB1
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: 229aa    MW: 25779.4 Da    PI: 7.274
Description YABBY family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT2G45190.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
        YABBY   2 dvfssseqvCyvqCnfCntilavsvPstslfkvvtvrCGhCtsllsvnlakasqllaaeshldeslkee.......lleelkveeenlksnvekeesa 92 
                  d+fs s+++CyvqCnfC+tilav+vP+tslfk+vtvrCG+Ct+lls  ++++s++l+a+++l+ +l ++       +leel+++ +n+++++++++ +
                  899*******************************************..66889********************************************* PP

        YABBY  93 stsvsseklsenedeevprvppvirPPekrqrvPsaynrfikeeiqrikasnPdishreafsaaaknWahfPkihfgl 170
                  +++++s+ ++ ++++e+p++ppv+rPPekrqrvPsaynrfikeeiqrika+nPdishreafsaaaknWahfP+ihfgl
                  ******6.5*******************************************************************97 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046901.4E-7021189IPR006780YABBY protein
SuperFamilySSF470957.46E-8135182IPR009071High 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:0009909Biological Processregulation of flower development
GO:0009933Biological Processmeristem structural organization
GO:0009944Biological Processpolarity specification of adaxial/abaxial axis
GO:0010093Biological Processspecification of floral organ identity
GO:0010154Biological Processfruit development
GO:0010158Biological Processabaxial cell fate specification
GO:0010159Biological Processspecification of organ position
GO:0010450Biological Processinflorescence meristem growth
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:0006019anatomyleaf abaxial epidermis
PO:0008019anatomyleaf lamina base
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009025anatomyvascular leaf
PO:0009052anatomyflower pedicel
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:0007098developmental stageLP.02 two leaves visible stage
PO:0007103developmental stageLP.10 ten leaves visible stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 229 aa     Download sequence    Send to blast
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT2G45190-
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 transition between globular and heart stages in the cotyledon anlagen. From the heart stage, 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 young lateral aerial organs, and in primordia leading to cotyledons, leaves, flower meristems, sepals, petals, stamen and carpels, but not in roots. {ECO:0000269|PubMed:10323860, ECO:0000269|PubMed:10457020, ECO:0000269|PubMed:14555697, ECO:0000269|Ref.3}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a member of the YABBY family of transcriptional regulators that is involved in abaxial cell type specification in leaves and fruits. YAB1 acts in a non-cell autonomous fashion within the meristem to affect phyllotactic patterning. The non-autonomous effect on the central region of the meristem is mediated through the activity if Lateral Suppressor (LAS).
UniProtInvolved in the abaxial cell fate determination during embryogenesis and organogenesis. Regulates the initiation of embryonic shoot apical meristem (SAM) development (PubMed:10323860, PubMed:10331982, PubMed:10457020, PubMed:11812777, PubMed:12417699, PubMed:9878633, Ref.3, Ref.6, PubMed:19837869). Required during flower formation and development, particularly for the patterning of floral organs. Positive regulator of class B (AP3 and PI) activity in whorls 2 and 3. Negative regulator of class B activity in whorl 1 and of SUP activity in whorl 3. Interacts with class A proteins (AP1, AP2 and LUG) to repress class C (AG) activity in whorls 1 and 2. Contributes to the repression of KNOX genes (STM, KNAT1/BP and KNAT2) to avoid ectopic meristems. Binds DNA without sequence specificity. In vitro, can compete and displace the AP1 protein binding to DNA containing CArG box (PubMed:10323860, PubMed:10331982, PubMed:10457020, PubMed:11812777, PubMed:12417699, PubMed:9878633, Ref.3, Ref.6). {ECO:0000269|PubMed:10323860, ECO:0000269|PubMed:10331982, ECO:0000269|PubMed:10457020, ECO:0000269|PubMed:11812777, ECO:0000269|PubMed:12417699, ECO:0000269|PubMed:19837869, ECO:0000269|PubMed:9878633, ECO:0000269|Ref.3, ECO:0000269|Ref.6}.
Function -- GeneRIF ? help Back to Top
  1. AINTEGUMENTA acts in combination with FILAMENTOUS FLOWER to promote organ polarity by up-regulating the expression of the adaxial-specifying HD-ZIP gene PHABULOSA.
    [PMID: 16714408]
  2. Results suggest that YAB1 activity stimulates signals from the organs to the meristem via a secondary message or signal cascade, a process essential for organized growth of the SAM.
    [PMID: 18469164]
  3. Analysis of FIL truncations revealed that the first 109 residues of the protein are required for LUG/LUH interactions
    [PMID: 19837869]
  4. FIL/YAB1 was exclusively expressed in trichome cells
    [PMID: 20101514]
  5. fil-9 allele mutant flowers show a wide range of organ morphological and identity defects.
    [PMID: 20584289]
  6. 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]
  7. FIL functions as a transcriptional activator in plants and that this activity is involved in leaf patterning.
    [PMID: 23025792]
  8. JAZ3 interacts with YABs to attenuate their transcriptional function.
    [PMID: 26530088]
  9. BREVIPEDICELLUS (BP) encodes a class-I KNOTTED1-like homeobox (KNOX) transcription factor. FIL acts to oppose KNOX1 gene function through a complex regulatory network that involves changes in secondary metabolites and auxin.
    [PMID: 28493925]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
Motif logo
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), AT2G33860 (A), AT2G34710 (A), AT2G37630 (R), AT3G44750 (A), AT4G37750 (A)
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT1G69120(A), AT2G34710(A), AT2G42830(A), AT4G18960(R), AT5G60910(A)
Interaction -- BIND ? help Back to Top
Source Intact With Description
BINDAT4G27330NZZ interacts with FIL.
Interaction ? help Back to Top
Source Intact With
IntActSearch O22152
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 ExpressAT2G45190
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF0749480.0AF074948.1 Arabidopsis thaliana FIL mRNA, complete cds.
GenBankAF0870150.0AF087015.1 Arabidopsis thaliana abnormal floral organs protein (AFO) mRNA, complete cds.
GenBankAF1365380.0AF136538.1 Arabidopsis thaliana YABBY1 (YABBY1) mRNA, complete cds.
GenBankBT0264090.0BT026409.1 Arabidopsis thaliana At2g45190 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_566037.11e-173Plant-specific transcription factor YABBY family protein
SwissprotO221521e-174YAB1_ARATH; Axial regulator YABBY 1
TrEMBLA0A384LM251e-172A0A384LM25_ARATH; YAB1
TrEMBLQ0V8111e-172Q0V811_ARATH; At2g45190
STRINGAT2G45190.11e-172(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP46851123
Publications ? help Back to Top
  1. Sawa S, et al.
    FILAMENTOUS FLOWER, a meristem and organ identity gene of Arabidopsis, encodes a protein with a zinc finger and HMG-related domains.
    Genes Dev., 1999. 13(9): p. 1079-88
  2. Chen Q, et al.
    The Arabidopsis FILAMENTOUS FLOWER gene is required for flower formation.
    Development, 1999. 126(12): p. 2715-26
  3. Siegfried KR, et al.
    Members of the YABBY gene family specify abaxial cell fate in Arabidopsis.
    Development, 1999. 126(18): p. 4117-28
  4. Yang WC,Ye D,Xu J,Sundaresan V
    The SPOROCYTELESS gene of Arabidopsis is required for initiation of sporogenesis and encodes a novel nuclear protein.
    Genes Dev., 1999. 13(16): p. 2108-17
  5. Bowman JL
    The YABBY gene family and abaxial cell fate.
    Curr. Opin. Plant Biol., 2000. 3(1): p. 17-22
  6. Kanaya E,Watanabe K,Nakajima N,Okada K,Shimura Y
    Zinc release from the CH2C6 zinc finger domain of FILAMENTOUS FLOWER protein from Arabidopsis thaliana induces self-assembly.
    J. Biol. Chem., 2001. 276(10): p. 7383-90
  7. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
  8. Eshed Y,Baum SF,Perea JV,Bowman JL
    Establishment of polarity in lateral organs of plants.
    Curr. Biol., 2001. 11(16): p. 1251-60
  9. Kanaya E,Nakajima N,Okada K
    Non-sequence-specific DNA binding by the FILAMENTOUS FLOWER protein from Arabidopsis thaliana is reduced by EDTA.
    J. Biol. Chem., 2002. 277(14): p. 11957-64
  10. 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
  11. 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
  12. Watanabe K,Okada K
    Two discrete cis elements control the Abaxial side-specific expression of the FILAMENTOUS FLOWER gene in Arabidopsis.
    Plant Cell, 2003. 15(11): p. 2592-602
  13. 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
  14. Meister RJ,Oldenhof H,Bowman JL,Gasser CS
    Multiple protein regions contribute to differential activities of YABBY proteins in reproductive development.
    Plant Physiol., 2005. 137(2): p. 651-62
  15. Dinneny JR,Weigel D,Yanofsky MF
    A genetic framework for fruit patterning in Arabidopsis thaliana.
    Development, 2005. 132(21): p. 4687-96
  16. 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
  17. Franks RG,Liu Z,Fischer RL
    SEUSS and LEUNIG regulate cell proliferation, vascular development and organ polarity in Arabidopsis petals.
    Planta, 2006. 224(4): p. 801-11
  18. Garcia D,Collier SA,Byrne ME,Martienssen RA
    Specification of leaf polarity in Arabidopsis via the trans-acting siRNA pathway.
    Curr. Biol., 2006. 16(9): p. 933-8
  19. Xu L, et al.
    Genetic interaction between the AS1-AS2 and RDR6-SGS3-AGO7 pathways for leaf morphogenesis.
    Plant Cell Physiol., 2006. 47(7): p. 853-63
  20. 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
  21. Balanz
    Patterning the female side of Arabidopsis: the importance of hormones.
    J. Exp. Bot., 2006. 57(13): p. 3457-69
  22. Huang W, et al.
    The proteolytic function of the Arabidopsis 26S proteasome is required for specifying leaf adaxial identity.
    Plant Cell, 2006. 18(10): p. 2479-92
  23. Ueno Y, et al.
    Histone deacetylases and ASYMMETRIC LEAVES2 are involved in the establishment of polarity in leaves of Arabidopsis.
    Plant Cell, 2007. 19(2): p. 445-57
  24. 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
  25. 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
  26. Ha CM,Jun JH,Nam HG,Fletcher JC
    BLADE-ON-PETIOLE 1 and 2 control Arabidopsis lateral organ fate through regulation of LOB domain and adaxial-abaxial polarity genes.
    Plant Cell, 2007. 19(6): p. 1809-25
  27. Gordon SP, et al.
    Pattern formation during de novo assembly of the Arabidopsis shoot meristem.
    Development, 2007. 134(19): p. 3539-48
  28. Azhakanandam S,Nole-Wilson S,Bao F,Franks RG
    SEUSS and AINTEGUMENTA mediate patterning and ovule initiation during gynoecium medial domain development.
    Plant Physiol., 2008. 146(3): p. 1165-81
  29. 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
  30. 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
  31. Meng C,Chen J,Ding SW,Peng J,Wong SM
    Hibiscus chlorotic ringspot virus coat protein inhibits trans-acting small interfering RNA biogenesis in Arabidopsis.
    J. Gen. Virol., 2008. 89(Pt 9): p. 2349-58
  32. 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
  33. Girin T,Sorefan K,Ostergaard L
    Meristematic sculpting in fruit development.
    J. Exp. Bot., 2009. 60(5): p. 1493-502
  34. Alvarez JP,Goldshmidt A,Efroni I,Bowman JL,Eshed Y
    The NGATHA distal organ development genes are essential for style specification in Arabidopsis.
    Plant Cell, 2009. 21(5): p. 1373-93
  35. 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
  36. Colombo M, et al.
    A new role for the SHATTERPROOF genes during Arabidopsis gynoecium development.
    Dev. Biol., 2010. 337(2): p. 294-302
  37. Schliep M,Ebert B,Simon-Rosin U,Zoeller D,Fisahn J
    Quantitative expression analysis of selected transcription factors in pavement, basal and trichome cells of mature leaves from Arabidopsis thaliana.
    Protoplasma, 2010. 241(1-4): p. 29-36
  38. Tononi P,M
    GRAMINIFOLIA homolog expression in Streptocarpus rexii is associated with the basal meristems in phyllomorphs, a morphological novelty in Gesneriaceae.
    Evol. Dev., 2010 Jan-Feb. 12(1): p. 61-73
  39. Lugassi N,Nakayama N,Bochnik R,Zik M
    A novel allele of FILAMENTOUS FLOWER reveals new insights on the link between inflorescence and floral meristem organization and flower morphogenesis.
    BMC Plant Biol., 2010. 10: p. 131
  40. 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
  41. Szakonyi D,Byrne ME
    Ribosomal protein L27a is required for growth and patterning in Arabidopsis thaliana.
    Plant J., 2011. 65(2): p. 269-81
  42. Szakonyi D,Byrne ME
    Involvement of ribosomal protein RPL27a in meristem activity and organ development.
    Plant Signal Behav, 2011. 6(5): p. 712-4
  43. Liu Z,Jia L,Wang H,He Y
    HYL1 regulates the balance between adaxial and abaxial identity for leaf flattening via miRNA-mediated pathways.
    J. Exp. Bot., 2011. 62(12): p. 4367-81
  44. Toyokura K, et al.
    Succinic semialdehyde dehydrogenase is involved in the robust patterning of Arabidopsis leaves along the adaxial-abaxial axis.
    Plant Cell Physiol., 2011. 52(8): p. 1340-53
  45. Arabidopsis Interactome Mapping Consortium
    Evidence for network evolution in an Arabidopsis interactome map.
    Science, 2011. 333(6042): p. 601-7
  46. Bartholmes C,Hidalgo O,Gleissberg S
    Evolution of the YABBY gene family with emphasis on the basal eudicot Eschscholzia californica (Papaveraceae).
    Plant Biol (Stuttg), 2012. 14(1): p. 11-23
  47. Toyokura K,Hayashi M,Nishimura M,Okada K
    Adaxial-abaxial patterning: a novel function of the GABA shunt.
    Plant Signal Behav, 2012. 7(7): p. 705-7
  48. Vosnakis N, et al.
    A FILAMENTOUS FLOWER orthologue plays a key role in leaf patterning in opium poppy.
    Plant J., 2012. 72(4): p. 662-73
  49. 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
  50. 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
  51. Xiang J, et al.
    Isolation and characterization of two VpYABBY genes from wild Chinese Vitis pseudoreticulata.
    Protoplasma, 2013. 250(6): p. 1315-25
  52. Lian H,Li X,Liu Z,He Y
    HYL1 is required for establishment of stamen architecture with four microsporangia in Arabidopsis.
    J. Exp. Bot., 2013. 64(11): p. 3397-410
  53. Tameshige T, et al.
    Pattern dynamics in adaxial-abaxial specific gene expression are modulated by a plastid retrograde signal during Arabidopsis thaliana leaf development.
    PLoS Genet., 2013. 9(7): p. e1003655
  54. 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
  55. 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
  56. Boter M, et al.
    FILAMENTOUS FLOWER Is a Direct Target of JAZ3 and Modulates Responses to Jasmonate.
    Plant Cell, 2015. 27(11): p. 3160-74
  57. Douglas SJ,Li B,Kliebenstein DJ,Nambara E,Riggs CD
    A novel Filamentous Flower mutant suppresses brevipedicellus developmental defects and modulates glucosinolate and auxin levels.
    PLoS ONE, 2017. 12(5): p. e0177045
  58. Tanaka W,Toriba T,Hirano HY
    Three TOB1-related YABBY genes are required to maintain proper function of the spikelet and branch meristems in rice.
    New Phytol., 2017. 215(2): p. 825-839
  59. Silverblatt-Buser EW,Frick MA,Rabeler C,Kaplinsky NJ
    Genetic Interactions Between BOB1 and Multiple 26S Proteasome Subunits Suggest a Role for Proteostasis in Regulating Arabidopsis Development.
    G3 (Bethesda), 2018. 8(4): p. 1379-1390
  60. Sawa S,Ito T,Shimura Y,Okada K
    FILAMENTOUS FLOWER controls the formation and development of arabidopsis inflorescences and floral meristems.
    Plant Cell, 1999. 11(1): p. 69-86