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 RrC5222_p1
Organism
Raphanus raphanistrum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family bHLH
Protein Properties Length: 404aa    MW: 46080.1 Da    PI: 6.7421
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC5222_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH28.43e-09224253130
                 CHHHHHHHHHHHHHHHHHHHHHHHCTSCCC CS
         HLH   1 rrrahnerErrRRdriNsafeeLrellPka 30 
                 +r+ah ++Er+RR+++N+ +  Lr+l+P +
  RrC5222_p1 224 QRMAHIAVERNRRKQMNEHLRVLRSLMPGS 253
                 79**************************84 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd000831.01E-7222258No hitNo description
Gene3DG3DSA:4.10.280.109.6E-9222259IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474591.7E-8222260IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profilePS5088810.658223282IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000101.3E-6224253IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd048731.04E-4330394No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 404 aa     Download sequence    Send to blast
MYMFSTDSEA PGLLSLGRVE IKKLNLNKPP DVYNKYEEQW IKIIRYAPNF LSEYLCGNYD  60
NNSSMIDHMF NRNLQQRKQS MPQQQQLSPS GFGATSTSDK MSFADVMQFA DFCPMLPLNQ  120
TRSQNDQETW MDPFYILKFP VFNGDHNQAH HLMSQEGGGC EGNIGNVFLE EKDNQEDKND  180
NNSMQIRFIG GEECRENKND TKKEVKSKRK RARTSKTSEE VENQRMAHIA VERNRRKQMN  240
EHLRVLRSLM PGSYVQRKRR RILGETSDMH GGDMTTAMIT SSPITSIANP LIISGNVTDI  300
EGGGGFHEET AEKKSCLADV EVKLLGFDAI IKVLSRRRPG QLLMTIAALE DLHLSILHTN  360
ITTMEQTVLY SFNVKITSDT RFTAEDIASS IQEIFSFIHA YTTM
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1224235RMAHIAVERNRR
2256260RKRRR
3257261KRRRI
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
GenBankAB4936311e-106AB493631.1 Arabidopsis thaliana At3g24140 mRNA for hypothetical protein, partial cds, clone: RAAt3g24140.
GenBankAF4886241e-106AF488624.1 Arabidopsis thaliana clone bHLH097 putative bHLH transcription factor mRNA, partial sequence.
GenBankAK2213241e-106AK221324.1 Arabidopsis thaliana mRNA for putative bHLH transcription factor, complete cds, clone: RAFL25-14-O10.
GenBankBT0289611e-106BT028961.1 Arabidopsis thaliana At3g24140 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018489970.10.0PREDICTED: transcription factor FAMA-like
SwissprotQ56YJ81e-172FAMA_ARATH; Transcription factor FAMA
TrEMBLA0A3P6AZX70.0A0A3P6AZX7_BRACM; Uncharacterized protein
STRINGBo7g037540.10.0(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM55482649
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G24140.11e-160bHLH 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]