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 LOC_Os05g50900.1
Organism
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; Oryza sativa
Family bHLH
Protein Properties Length: 493aa    MW: 52825.7 Da    PI: 7.6117
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os05g50900.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH40.55.1e-13256307155
                       CHHHHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
               HLH   1 rrrahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                       +r++h ++Er+RR+++N+ +  Lr+l+P +   + ++ + a+i   A+e+I++L+
  LOC_Os05g50900.1 256 QRMTHIAVERNRRRQMNEYLRVLRSLMPGS---YVQRGDQASIIGGAIEFIRELE 307
                       79****************************...9******************996 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd000836.22E-14254311No hitNo description
Gene3DG3DSA:4.10.280.101.5E-13254310IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474598.64E-17255324IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profilePS5088815.897255306IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000102.2E-10256307IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003531.0E-9261312IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd048730.00171418476No hitNo description
PROSITE profilePS5167110.103418492IPR002912ACT 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: 493 aa     Download sequence    Send to blast
MGQAGYFLCS EITASKLLTV TATRELKPPP PPRPSGRVLS RRARRRRSSV LAWRHRRCFG  60
GLILQTWKKN HTISAVQQRS HLERFAALDE APPPAPEETV VTGGEMVDYM LGQPPPTTPG  120
PQSQVSFDKL TFSDVLQFAD FGPKLALNQP AASDNGGGGG DDGDDDDDSY FLRFQSLPSL  180
PAVPPPRGGA AAAHQVVDEQ EGSKQTVDAG GVSESTTLVQ QADGGGGRAE KAGEQGKSGR  240
RKRPRTVKTS EEVESQRMTH IAVERNRRRQ MNEYLRVLRS LMPGSYVQRG DQASIIGGAI  300
EFIRELEQLI QCLESQKRRR LYGGDAPAPP ARPVADGAVL PAPMQQPPPA TPPFFPPSIP  360
FPASSGAGDG TGAGVAKVAL DLDASGGGEV GGGVREEMAE NKSCVADIEV RVVGVDAMIK  420
ILSRRRPGQL IKTVAALEEM HMSILHTNIT TIDQTVLYSF NVKIAGDARF SAEDIAGAVH  480
QILSFIDVNY TL*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1256267RMTHIAVERNRR
2316320KRRRL
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.466001e-31panicle| root| stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329688271e-31
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Not expressed in meristemoids, but strongly expressed in guard mother cells (GMCs) and in young guard cells (at protein level) (PubMed:17088607). Expressed at the transition to terminal stomatal differentiation, just before and after the symmetric division of stomatal differentiation, being confined to late-stage GMC and to young, still differentiating guard cells (PubMed:24571519). {ECO:0000269|PubMed:17088607, ECO:0000269|PubMed:24571519}.
UniprotTISSUE SPECIFICITY: Resctricted to stomatal cell lineages (at protein level). Expressed in roots, leaves, stems, and flowers. {ECO:0000269|PubMed:12679534, ECO:0000269|PubMed:17088607}.
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os05g50900.1
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-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs05g50900
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-108FAMA_ARATH; Transcription factor FAMA
TrEMBLA2Y8070.0A2Y807_ORYSI; Uncharacterized protein
STRINGOGLUM05G29000.10.0(Oryza glumipatula)
STRINGONIVA05G29540.10.0(Oryza nivara)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP95023340
Representative plantOGRP25315131
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G24140.14e-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]