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 RrC2202_p4
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: 351aa    MW: 37292.4 Da    PI: 6.7885
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC2202_p4genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH38.91.6e-121922311155
                 HHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
         HLH  11 rRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                 rRR+riN+++  L++l+P++      K +Ka++L +A+eY+k+Lq
  RrC2202_p4 192 RRRSRINEKMKALQSLIPNS-----NKTDKASMLDEAIEYLKQLQ 231
                 8******************7.....5******************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF474596.15E-16174241IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000831.84E-15177235No hitNo description
Gene3DG3DSA:4.10.280.101.4E-15177241IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003531.8E-12180236IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profilePS5088814.805181230IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000107.5E-10192231IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0007623Biological Processcircadian rhythm
GO:0009409Biological Processresponse to cold
GO:0010114Biological Processresponse to red light
GO:0010154Biological Processfruit development
GO:0010187Biological Processnegative regulation of seed germination
GO:0048440Biological Processcarpel development
GO:0005634Cellular Componentnucleus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 351 aa     Download sequence    Send to blast
MADKKLISSP SSTTSIYDTR SSNSNHHHYP PSSSDEISLF LRHIIDRSSP LPSYYSPATM  60
TTAVHGEPHA GNSICFVSPQ TSKRSADFSE VLVGSGVGSS SAAACYGFSG GGGGGNNIAQ  120
GNSSGTRVSS SSVGASGNET DEYDCESEEG VEAVVDDELP SKSGPSRSSS KRCRAAEVHN  180
LSEKTQANIL LRRRSRINEK MKALQSLIPN SNKTDKASML DEAIEYLKQL QLQVQMLSMR  240
NGINLHPLCL PGTALHPLQL SQLRPGVPPE ATNDSLLNAP AMINTGASSY ALEPSIRSHF  300
GPFPLLTSPV EMSCEGGLTH PRLNIGHSNT NLNGGQAAFN GQQPDIKDRL T
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that plays a role in floral organogenesis. Promotes the growth of carpel margins and of pollen tract tissues derived from them. {ECO:0000269|PubMed:10225997, ECO:0000269|Ref.8}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00035PBMTransfer from AT4G36930Download
Motif logo
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Down-regulated by the A class gene AP2 in the first whorl and by ARF3/ETT in gynoecium. {ECO:0000269|PubMed:11245574}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankKF9210901e-129KF921090.1 Brassica oleracea var. capitata bHLH transcription factor SPT mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018449018.10.0PREDICTED: transcription factor SPATULA-like
RefseqXP_018449689.10.0PREDICTED: transcription factor SPATULA-like
SwissprotQ9FUA41e-142SPT_ARATH; Transcription factor SPATULA
TrEMBLA0A078GCN80.0A0A078GCN8_BRANA; BnaC03g61610D protein
STRINGBra010591.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM41992754
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G36930.11e-123bHLH 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. Pabón-Mora N,Wong GK,Ambrose BA
    Evolution of fruit development genes in flowering plants.
    Front Plant Sci, 2014. 5: p. 300
    [PMID:25018763]
  3. Moubayidin L,Ostergaard L
    Dynamic control of auxin distribution imposes a bilateral-to-radial symmetry switch during gynoecium development.
    Curr. Biol., 2014. 24(22): p. 2743-8
    [PMID:25455035]
  4. Pfannebecker KC,Lange M,Rupp O,Becker A
    Seed Plant-Specific Gene Lineages Involved in Carpel Development.
    Mol. Biol. Evol., 2017. 34(4): p. 925-942
    [PMID:28087776]
  5. Zumajo-Cardona C,Ambrose BA,Pabón-Mora N
    Evolution of the SPATULA/ALCATRAZ gene lineage and expression analyses in the basal eudicot, Bocconia frutescens L. (Papaveraceae).
    Evodevo, 2017. 8: p. 5
    [PMID:28331573]
  6. Reyes-Olalde JI, et al.
    The bHLH transcription factor SPATULA enables cytokinin signaling, and both activate auxin biosynthesis and transport genes at the medial domain of the gynoecium.
    PLoS Genet., 2017. 13(4): p. e1006726
    [PMID:28388635]
  7. Wu M, et al.
    SPATULA regulates floral transition and photomorphogenesis in a PHYTOCHROME B-dependent manner in Arabidopsis.
    Biochem. Biophys. Res. Commun., 2018. 503(4): p. 2380-2385
    [PMID:29966653]