PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID ONIVA05G29540.1
Organism
Oryza nivara
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza
Family bHLH
Protein Properties Length: 421aa    MW: 44805.2 Da    PI: 4.7312
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
ONIVA05G29540.1genomeOGEView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH40.84.1e-13185236155
                      CHHHHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
              HLH   1 rrrahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                      +r++h ++Er+RR+++N+ +  Lr+l+P +   + ++ + a+i   A+e+I++L+
  ONIVA05G29540.1 185 QRMTHIAVERNRRRQMNEYLRVLRSLMPGS---YVQRGDQASIIGGAIEFIRELE 236
                      79****************************...9******************996 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:4.10.280.101.2E-13183239IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000834.28E-14183240No hitNo description
PROSITE profilePS5088815.897184235IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474596.67E-17184253IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000101.7E-10185236IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003531.0E-9190241IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd048730.00145347405No hitNo description
PROSITE profilePS5167110.103347421IPR002912ACT domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0010377Biological Processguard cell fate commitment
GO:0045597Biological Processpositive regulation of cell differentiation
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0051782Biological Processnegative regulation of cell division
GO:0005634Cellular Componentnucleus
GO:0016597Molecular Functionamino acid binding
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 421 aa     Download sequence    Send to blast
MDKEVQQRSH LERFAALDEA PPPAPEETVV TGGEMVDYML GQPPPTTPGP QSQVSFDKLT  60
FSDVLQFADF GPKLALNQPA ASDNGGGGGD DGDDDDDSYF LRFQSLPSLP AVPPPRGGAG  120
AAHQVVDEQE GSKQTVDAGG VSESTTLVQQ ADGGGGRAEK AGEQGKSGRR KRPRTVKTSE  180
EVESQRMTHI AVERNRRRQM NEYLRVLRSL MPGSYVQRGD QASIIGGAIE FIRELEQLIQ  240
CLESQKRRRL YGGDAPAPPA RPVADGAVLP APMQQPPPAT PPFFPPSIPF PASSGAGDGT  300
GAGVAKVALD LDASGGGEVG GGVREEMAEN KSCVADIEVR VVGVDAMIKI LSRRRPGQLI  360
KTVAALEEMH MSILHTNITT IDQTVLYSFN VKIAGDARFS AEDIAGAVHQ ILSFIDVNYT  420
L
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1185196RMTHIAVERNRR
2245249KRRRL
Functional Description ? help Back to Top
Source Description
UniProtTranscription activator (PubMed:17088607, PubMed:17183265, PubMed:17183267). Together with MYB88 and MYB124, ensures that stomata contain just two guard cells (GCs) by enforcing a single symmetric precursor cell division before stomatal maturity (PubMed:24571519). Together with SPCH and MUTE, regulates the stomata formation. Required to promote differentiation and morphogenesis of stomatal guard cells and to halt proliferative divisions in their immediate precursors. Mediates the formation of stomata (PubMed:17088607, PubMed:17183265, PubMed:17183267). Prevents histone H3K27me3 marks and derepresses stem cell gene expression (PubMed:24654956). {ECO:0000269|PubMed:17088607, ECO:0000269|PubMed:17183265, ECO:0000269|PubMed:17183267, ECO:0000269|PubMed:24571519, ECO:0000269|PubMed:24654956}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Inhibited by low relative humidity (LRH) via epigenetic CG methylation, thus leading to a reduced stomatal index. {ECO:0000269|PubMed:22442411}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC1376080.0AC137608.2 Oryza sativa Japonica Group cultivar Nipponbare chromosome 5 clone OSJNBa0009C07, complete sequence.
GenBankAP0149610.0AP014961.1 Oryza sativa Japonica Group DNA, chromosome 5, cultivar: Nipponbare, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015638786.10.0transcription factor FAMA
SwissprotQ56YJ81e-109FAMA_ARATH; Transcription factor FAMA
TrEMBLA0A0E0HJ390.0A0A0E0HJ39_ORYNI; Uncharacterized protein
STRINGONIVA05G29540.10.0(Oryza nivara)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP95023340
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G24140.11e-55bHLH family protein
Publications ? help Back to Top
  1. Skinner MK,Rawls A,Wilson-Rawls J,Roalson EH
    Basic helix-loop-helix transcription factor gene family phylogenetics and nomenclature.
    Differentiation, 2010. 80(1): p. 1-8
    [PMID:20219281]
  2. Matos JL, et al.
    Irreversible fate commitment in the Arabidopsis stomatal lineage requires a FAMA and RETINOBLASTOMA-RELATED module.
    Elife, 2015.
    [PMID:25303364]
  3. Chen L, et al.
    NRPB3, the third largest subunit of RNA polymerase II, is essential for stomatal patterning and differentiation in Arabidopsis.
    Development, 2016. 143(9): p. 1600-11
    [PMID:26989174]
  4. Lee JH,Jung JH,Park CM
    Light Inhibits COP1-Mediated Degradation of ICE Transcription Factors to Induce Stomatal Development in Arabidopsis.
    Plant Cell, 2017. 29(11): p. 2817-2830
    [PMID:29070509]
  5. Han X, et al.
    Jasmonate Negatively Regulates Stomatal Development in Arabidopsis Cotyledons.
    Plant Physiol., 2018. 176(4): p. 2871-2885
    [PMID:29496884]
  6. Li X,Yang R,Chen H
    The Arabidopsis thaliana Mediator subunit MED8 regulates plant immunity to Botrytis Cinerea through interacting with the basic helix-loop-helix (bHLH) transcription factor FAMA.
    PLoS ONE, 2018. 13(3): p. e0193458
    [PMID:29513733]