PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Neem_4411_f_2
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Meliaceae; Azadirachta
Family YABBY
Protein Properties Length: 237aa    MW: 26317.3 Da    PI: 8.2298
Description YABBY family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Neem_4411_f_2genomeNGDView Nucleic Acid
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1YABBY103.44.7e-32111232117
          YABBY   2 dvfssseqvCyvqCnfCntilavsvPstslfkvvtvrCGhCtsllsvnlakasqllaaeshldeslkeelleelkveeenlksnvekeesastsvs 97 
                    d+ ssseq+Cyv+CnfC+t+lavsvP tslfk+vtvrCGhCt+llsvn++      a + hl++++  ++   ++ +++ +++ ++++ +++  ++
  Neem_4411_f_2  11 DHLSSSEQLCYVHCNFCDTVLAVSVPCTSLFKTVTVRCGHCTNLLSVNMRGLLLPAANQLHLGHAFFTPQNLLEEIRNTPTNMLMINQPNPT--EP 104
                    7899******************************************9988887777777788888776644333444444445555554444..44 PP

          YABBY  98 seklsenedeevprvppvir 117
                    ++   +  d+e+p++p v+r
  Neem_4411_f_2 105 VMP-VRGIDQEIPKPPVVNR 123
                    433.4678889998777776 PP

2YABBY121.31.5e-37146199117170
          YABBY 117 rPPekrqrvPsaynrfikeeiqrikasnPdishreafsaaaknWahfPkihfgl 170
                      PekrqrvPsaynrfik+eiqrika+nPdishreafsaaaknWahfP+ihfgl
  Neem_4411_f_2 146 ETPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL 199
                    67**************************************************97 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046905.4E-6515199IPR006780YABBY protein
SuperFamilySSF470951.31E-7144192IPR009071High mobility group box domain
Gene3DG3DSA:1.10.30.102.2E-4148191IPR009071High mobility group box domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
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
Sequence ? help Back to Top
Protein Sequence    Length: 237 aa     Download sequence    Send to blast
MSSSTSAFSP DHLSSSEQLC YVHCNFCDTV LAVSVPCTSL FKTVTVRCGH CTNLLSVNMR  60
GLLLPAANQL HLGHAFFTPQ NLLEEIRNTP TNMLMINQPN PTEPVMPVRG IDQEIPKPPV  120
VNRQKLAKAL ACCPPAFTVD IFAFKETPEK RQRVPSAYNR FIKDEIQRIK AGNPDISHRE  180
AFSAAAKNWA HFPHIHFGLM PSDQPVKKTS IRQQEGEDAM NMKDGFFAPA NVGVSPY
Functional Description ? help Back to Top
Source Description
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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00620PBMTransfer from AT2G45190Download
Motif logo
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAM4682964e-44AM468296.2 Vitis vinifera contig VV78X023826.39, whole genome shotgun sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006445302.11e-130axial regulator YABBY 1
RefseqXP_006490878.11e-130axial regulator YABBY 1
SwissprotO221521e-92YAB1_ARATH; Axial regulator YABBY 1
TrEMBLA0A067H4B31e-129A0A067H4B3_CITSI; Uncharacterized protein
TrEMBLA0A2H5NP361e-129A0A2H5NP36_CITUN; Uncharacterized protein
TrEMBLV4TY631e-129V4TY63_9ROSI; Uncharacterized protein
STRINGXP_006490878.11e-130(Citrus sinensis)
STRINGXP_006445302.11e-130(Citrus clementina)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM22172877
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G45190.16e-95YABBY family protein
Publications ? help Back to Top
  1. 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
    [PMID:16280546]
  2. 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
    [PMID:23918970]
  3. 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
    [PMID:23935517]
  4. 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
    [PMID:26530088]
  5. 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
    [PMID:28493925]
  6. 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
    [PMID:28556940]
  7. 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
    [PMID:29487187]