PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID evm_27.model.AmTr_v1.0_scaffold00049.17
Common NameAMTR_s00049p00034730, LOC18441831
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; basal Magnoliophyta; Amborellales; Amborellaceae; Amborella
Family B3
Protein Properties Length: 662aa    MW: 72704 Da    PI: 6.08
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
evm_27.model.AmTr_v1.0_scaffold00049.17genomeTAGPView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
                                              EEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEE.TTS-EEEEEE....EEETTEEEE-TTHH CS
                                       B3   2 fkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltled.esgrsWevkliy..rkksgryvltkGWk 66 
                                              +kvl++sdv+++gr+vlpkk ae+h  +++ + ++t+++ed  ++r+W++++++  ++ks++y+l+ ++ 
                                              79*************************99999*********7778*******99777777777777.*** PP

                                              HHHHHHT--TT-EEEEEE-SS.SEE..EEEE CS
                                       B3  67 eFvkangLkegDfvvFkldgr.sefelvvkv 96 
                                              +Fv++ngL+egDf+v++  ++ ++++++++ 
  evm_27.model.AmTr_v1.0_scaffold00049.17 583 DFVRSNGLQEGDFIVIY--SDtKCGKYMIRG 611
                                              *****************..444999888765 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.109.3E-29507614IPR015300DNA-binding pseudobarrel domain
CDDcd100153.78E-36511612No hitNo description
SuperFamilySSF1019364.58E-24512608IPR015300DNA-binding pseudobarrel domain
PROSITE profilePS5086311.025513615IPR003340B3 DNA binding domain
SMARTSM010198.3E-22513615IPR003340B3 DNA binding domain
PfamPF023621.8E-17514610IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006357Biological Processregulation of transcription from RNA polymerase II promoter
GO:0009657Biological Processplastid organization
GO:0009733Biological Processresponse to auxin
GO:0009737Biological Processresponse to abscisic acid
GO:0009793Biological Processembryo development ending in seed dormancy
GO:0031930Biological Processmitochondria-nucleus signaling pathway
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0005829Cellular Componentcytosol
GO:0001076Molecular Functiontranscription factor activity, RNA polymerase II transcription factor binding
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 662 aa     Download sequence    Send to blast
3D Structure ? help Back to Top
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9b_A3e-375096181110B3 domain-containing transcription factor FUS3
6j9b_D3e-375096181110B3 domain-containing transcription factor FUS3
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtParticipates in abscisic acid-regulated gene expression during seed development. Regulates the transcription of SGR1 and SGR2 that are involved in leaf and embryo degreening. {ECO:0000269|PubMed:19531597, ECO:0000269|PubMed:24043799}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00083PBMTransfer from AT3G24650Download
Motif logo
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Repressed by silencing mediated by polycomb group (PcG) protein complex containing EMF1 and EMF2. {ECO:0000269|PubMed:19783648}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006852120.20.0B3 domain-containing transcription factor ABI3 isoform X1
RefseqXP_020527576.10.0B3 domain-containing transcription factor ABI3 isoform X3
SwissprotQ015938e-79ABI3_ARATH; B3 domain-containing transcription factor ABI3
TrEMBLW1PU770.0W1PU77_AMBTC; Uncharacterized protein
STRINGERN135870.0(Amborella trichopoda)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP7881766
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G24650.14e-76B3 family protein
Publications ? help Back to Top
  1. Zeng Y,Kermode AR
    A gymnosperm ABI3 gene functions in a severe abscisic acid-insensitive mutant of Arabidopsis (abi3-6) to restore the wild-type phenotype and demonstrates a strong synergistic effect with sugar in the inhibition of post-germinative growth.
    Plant Mol. Biol., 2004. 56(5): p. 731-46
  2. Seifert M,Keilwagen J,Strickert M,Grosse I
    Utilizing gene pair orientations for HMM-based analysis of promoter array ChIP-chip data.
    Bioinformatics, 2009. 25(16): p. 2118-25
  3. Yang C, et al.
    VAL- and AtBMI1-mediated H2Aub initiate the switch from embryonic to postgerminative growth in Arabidopsis.
    Curr. Biol., 2013. 23(14): p. 1324-9
  4. Duarte GT, et al.
    Involvement of microRNA-related regulatory pathways in the glucose-mediated control of Arabidopsis early seedling development.
    J. Exp. Bot., 2013. 64(14): p. 4301-12
  5. Jia H,McCarty DR,Suzuki M
    Distinct roles of LAFL network genes in promoting the embryonic seedling fate in the absence of VAL repression.
    Plant Physiol., 2013. 163(3): p. 1293-305
  6. Bu Q, et al.
    Regulation of drought tolerance by the F-box protein MAX2 in Arabidopsis.
    Plant Physiol., 2014. 164(1): p. 424-39
  7. Gao DY, et al.
    Functional analyses of an E3 ligase gene AIP2 from wheat in Arabidopsis revealed its roles in seed germination and pre-harvest sprouting.
    J Integr Plant Biol, 2014. 56(5): p. 480-91
  8. Amborella Genome Project
    The Amborella genome and the evolution of flowering plants.
    Science, 2013. 342(6165): p. 1241089
  9. Kim HU, et al.
    Ectopic overexpression of castor bean LEAFY COTYLEDON2 (LEC2) in Arabidopsis triggers the expression of genes that encode regulators of seed maturation and oil body proteins in vegetative tissues.
    FEBS Open Bio, 2013. 4: p. 25-32
  10. Molitor AM,Bu Z,Yu Y,Shen WH
    Arabidopsis AL PHD-PRC1 complexes promote seed germination through H3K4me3-to-H3K27me3 chromatin state switch in repression of seed developmental genes.
    PLoS Genet., 2014. 10(1): p. e1004091
  11. Suzuki M,Wu S,Li Q,McCarty DR
    Distinct functions of COAR and B3 domains of maize VP1 in induction of ectopic gene expression and plant developmental phenotypes in Arabidopsis.
    Plant Mol. Biol., 2014. 85(1-2): p. 179-91
  12. Xie M, et al.
    AtWNK9 is regulated by ABA and dehydration and is involved in drought tolerance in Arabidopsis.
    Plant Physiol. Biochem., 2014. 77: p. 73-83
  13. Chen C, et al.
    ASCORBATE PEROXIDASE6 protects Arabidopsis desiccating and germinating seeds from stress and mediates cross talk between reactive oxygen species, abscisic acid, and auxin.
    Plant Physiol., 2014. 166(1): p. 370-83
  14. Rikiishi K,Maekawa M
    Seed maturation regulators are related to the control of seed dormancy in wheat (Triticum aestivum L.).
    PLoS ONE, 2014. 9(9): p. e107618
  15. Yamamoto A, et al.
    Cell-by-cell developmental transition from embryo to post-germination phase revealed by heterochronic gene expression and ER-body formation in Arabidopsis leafy cotyledon mutants.
    Plant Cell Physiol., 2014. 55(12): p. 2112-25
  16. Bello B, et al.
    Cloning of Gossypium hirsutum sucrose non-fermenting 1-related protein kinase 2 gene (GhSnRK2) and its overexpression in transgenic Arabidopsis escalates drought and low temperature tolerance.
    PLoS ONE, 2014. 9(11): p. e112269
  17. Chen C,Twito S,Miller G
    New cross talk between ROS, ABA and auxin controlling seed maturation and germination unraveled in APX6 deficient Arabidopsis seeds.
    Plant Signal Behav, 2014. 9(12): p. e976489
  18. Shen Y,Devic M,Lepiniec L,Zhou DX
    Chromodomain, Helicase and DNA-binding CHD1 protein, CHR5, are involved in establishing active chromatin state of seed maturation genes.
    Plant Biotechnol. J., 2015. 13(6): p. 811-20
  19. Zhao M,Yang S,Liu X,Wu K
    Arabidopsis histone demethylases LDL1 and LDL2 control primary seed dormancy by regulating DELAY OF GERMINATION 1 and ABA signaling-related genes.
    Front Plant Sci, 2015. 6: p. 159
  20. Mukhopadhyay P,Tyagi AK
    OsTCP19 influences developmental and abiotic stress signaling by modulating ABI4-mediated pathways.
    Sci Rep, 2015. 5: p. 9998
  21. Ma X, et al.
    CYCLIN-DEPENDENT KINASE G2 regulates salinity stress response and salt mediated flowering in Arabidopsis thaliana.
    Plant Mol. Biol., 2015. 88(3): p. 287-99
  22. Zhang GZ, et al.
    Ectopic expression of UGT75D1, a glycosyltransferase preferring indole-3-butyric acid, modulates cotyledon development and stress tolerance in seed germination of Arabidopsis thaliana.
    Plant Mol. Biol., 2016. 90(1-2): p. 77-93
  23. Kim H, et al.
    ABA-HYPERSENSITIVE BTB/POZ PROTEIN 1 functions as a negative regulator in ABA-mediated inhibition of germination in Arabidopsis.
    Plant Mol. Biol., 2016. 90(3): p. 303-15
  24. Dekkers BJ, et al.
    The Arabidopsis DELAY OF GERMINATION 1 gene affects ABSCISIC ACID INSENSITIVE 5 (ABI5) expression and genetically interacts with ABI3 during Arabidopsis seed development.
    Plant J., 2016. 85(4): p. 451-65
  25. Huang Y,Feng CZ,Ye Q,Wu WH,Chen YF
    Arabidopsis WRKY6 Transcription Factor Acts as a Positive Regulator of Abscisic Acid Signaling during Seed Germination and Early Seedling Development.
    PLoS Genet., 2016. 12(2): p. e1005833
  26. Abraham Z, et al.
    A Developmental Switch of Gene Expression in the Barley Seed Mediated by HvVP1 (Viviparous-1) and HvGAMYB Interactions.
    Plant Physiol., 2016. 170(4): p. 2146-58
  27. Salas-Muñoz S,Rodríguez-Hernández AA,Ortega-Amaro MA,Salazar-Badillo FB,Jiménez-Bremont JF
    Arabidopsis AtDjA3 Null Mutant Shows Increased Sensitivity to Abscisic Acid, Salt, and Osmotic Stress in Germination and Post-germination Stages.
    Front Plant Sci, 2016. 7: p. 220
  28. Kim SI,Kwak JS,Song JT,Seo HS
    The E3 SUMO ligase AtSIZ1 functions in seed germination in Arabidopsis.
    Physiol Plant, 2016. 158(3): p. 256-271
  29. Baud S, et al.
    Deciphering the Molecular Mechanisms Underpinning the Transcriptional Control of Gene Expression by Master Transcriptional Regulators in Arabidopsis Seed.
    Plant Physiol., 2016. 171(2): p. 1099-112
  30. Bedi S,Sengupta S,Ray A,Nag Chaudhuri R
    ABI3 mediates dehydration stress recovery response in Arabidopsis thaliana by regulating expression of downstream genes.
    Plant Sci., 2016. 250: p. 125-140
  31. Fatihi A, et al.
    Deciphering and modifying LAFL transcriptional regulatory network in seed for improving yield and quality of storage compounds.
    Plant Sci., 2016. 250: p. 198-204
  32. Zhu Z, et al.
    Overexpression of AtEDT1/HDG11 in Chinese Kale (Brassica oleracea var. alboglabra) Enhances Drought and Osmotic Stress Tolerance.
    Front Plant Sci, 2016. 7: p. 1285
  33. Feng J,Chen D,Berr A,Shen WH
    ZRF1 Chromatin Regulators Have Polycomb Silencing and Independent Roles in Development.
    Plant Physiol., 2016. 172(3): p. 1746-1759
  34. Wu JR, et al.
    The Arabidopsis heat-intolerant 5 (hit5)/enhanced response to aba 1 (era1) mutant reveals the crucial role of protein farnesylation in plant responses to heat stress.
    New Phytol., 2017. 213(3): p. 1181-1193
  35. Gu L, et al.
    An RRM-containing mei2-like MCT1 plays a negative role in the seed germination and seedling growth of Arabidopsis thaliana in the presence of ABA.
    Plant Physiol. Biochem., 2016. 109: p. 273-279
  36. Chen YS, et al.
    Two MYB-related transcription factors play opposite roles in sugar signaling in Arabidopsis.
    Plant Mol. Biol., 2017. 93(3): p. 299-311
  37. Xu J, et al.
    A Novel RNA-Binding Protein Involves ABA Signaling by Post-transcriptionally Repressing ABI2.
    Front Plant Sci, 2017. 8: p. 24
  38. Restovic F,Espinoza-Corral R,Gómez I,Vicente-Carbajosa J,Jordana X
    An active Mitochondrial Complex II Present in Mature Seeds Contains an Embryo-Specific Iron-Sulfur Subunit Regulated by ABA and bZIP53 and Is Involved in Germination and Seedling Establishment.
    Front Plant Sci, 2017. 8: p. 277
  39. Le Hir R, et al.
    AtbHLH68 transcription factor contributes to the regulation of ABA homeostasis and drought stress tolerance in Arabidopsis thaliana.
    Physiol Plant, 2017. 160(3): p. 312-327
  40. Han JD, et al.
    Evolutionary Analysis of the LAFL Genes Involved in the Land Plant Seed Maturation Program.
    Front Plant Sci, 2017. 8: p. 439
  41. Li K,Yang F,Miao Y,Song CP
    Abscisic acid signaling is involved in regulating the mitogen-activated protein kinase cascade module, AIK1-MKK5-MPK6.
    Plant Signal Behav, 2017. 12(5): p. e1321188
  42. Bi B,Tang J,Han S,Guo J,Miao Y
    Sinapic acid or its derivatives interfere with abscisic acid homeostasis during Arabidopsis thaliana seed germination.
    BMC Plant Biol., 2017. 17(1): p. 99
  43. Xiao X,Cheng X,Yin K,Li H,Qiu JL
    Abscisic acid negatively regulates post-penetration resistance of Arabidopsis to the biotrophic powdery mildew fungus.
    Sci China Life Sci, 2017. 60(8): p. 891-901
  44. Horstman A, et al.
    The BABY BOOM Transcription Factor Activates the LEC1-ABI3-FUS3-LEC2 Network to Induce Somatic Embryogenesis.
    Plant Physiol., 2017. 175(2): p. 848-857
  45. Hanano A,Almousally I,Shaban M,Murphy DJ
    Arabidopsis plants exposed to dioxin result in a WRINKLED seed phenotype due to 20S proteasomal degradation of WRI1.
    J. Exp. Bot., 2018. 69(7): p. 1781-1794
  46. Cheng Y,Zhang X,Sun T,Tian Q,Zhang WH
    Glutamate Receptor Homolog3.4 is Involved in Regulation of Seed Germination Under Salt Stress in Arabidopsis.
    Plant Cell Physiol., 2018. 59(5): p. 978-988
  47. Chen N,Veerappan V,Abdelmageed H,Kang M,Allen RD
    HSI2/VAL1 Silences AGL15 to Regulate the Developmental Transition from Seed Maturation to Vegetative Growth in Arabidopsis.
    Plant Cell, 2018. 30(3): p. 600-619