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 RrC152_p3
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 MIKC_MADS
Protein Properties Length: 295aa    MW: 33747.1 Da    PI: 9.9476
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC152_p3genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF99.41.4e-3165115151
                S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
     SRF-TF   1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 
                krien++nrqvtf+kRrng+lKKA+ELSvLCdaeva+i+fss+g+lyeys+
  RrC152_p3  65 KRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVALIVFSSRGRLYEYSN 115
                79***********************************************95 PP
2K-box97.52e-321322323100
      K-box   3 kssgksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkk...ekelqeenkaLrkkle 99 
                ++++ s++e +a+++qqe+akL+++i ++q+++R+l+Ge ++s+s keL++Le +L++s+++iRskKnell+++i+++qk+   e +l+++n+ Lr+k++
  RrC152_p3 132 NTNTGSVAEINAQYYQQESAKLRQQIISIQNSNRQLMGETIGSMSPKELRNLEGRLDRSVNRIRSKKNELLFAEIDYMQKRsvqEVDLHNDNQLLRAKIA 231
                445556999***********************************************************************85556789**********98 PP

      K-box 100 e 100
                e
  RrC152_p3 232 E 232
                6 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006633.31957117IPR002100Transcription factor, MADS-box
SMARTSM004328.1E-4157116IPR002100Transcription factor, MADS-box
SuperFamilySSF554553.66E-3358132IPR002100Transcription factor, MADS-box
CDDcd002652.72E-4558131No hitNo description
PRINTSPR004049.9E-335979IPR002100Transcription factor, MADS-box
PROSITE patternPS00350059113IPR002100Transcription factor, MADS-box
PfamPF003191.2E-2666113IPR002100Transcription factor, MADS-box
PRINTSPR004049.9E-337994IPR002100Transcription factor, MADS-box
PRINTSPR004049.9E-3394115IPR002100Transcription factor, MADS-box
PfamPF014866.5E-25142230IPR002487Transcription factor, K-box
PROSITE profilePS5129714.943143236IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0048366Biological Processleaf development
GO:0048440Biological Processcarpel development
GO:0048443Biological Processstamen development
GO:0048497Biological Processmaintenance of floral organ identity
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 295 aa     Download sequence    Send to blast
NLTFHFLQLL QISYFPENHF PKRNKTFLFV HLSPPTGAAN MAYQMEVGGD SSPQRKAGRG  60
KIEIKRIENT TNRQVTFCKR RNGLLKKAYE LSVLCDAEVA LIVFSSRGRL YEYSNNSVKG  120
TIERYKKAIS DNTNTGSVAE INAQYYQQES AKLRQQIISI QNSNRQLMGE TIGSMSPKEL  180
RNLEGRLDRS VNRIRSKKNE LLFAEIDYMQ KRSVQEVDLH NDNQLLRAKI AENERNNPSM  240
SLMPGGSNYE QIMPPPQTQP QPFDSRNYFQ VAALQPNNHH YSSAGREDQT ALQLV
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1egw_A1e-1958125168MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
1egw_B1e-1958125168MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
1egw_C1e-1958125168MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
1egw_D1e-1958125168MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
3kov_A2e-1958125168Myocyte-specific enhancer factor 2A
3kov_B2e-1958125168Myocyte-specific enhancer factor 2A
3kov_I2e-1958125168Myocyte-specific enhancer factor 2A
3kov_J2e-1958125168Myocyte-specific enhancer factor 2A
3p57_A2e-1958125168Myocyte-specific enhancer factor 2A
3p57_B2e-1958125168Myocyte-specific enhancer factor 2A
3p57_C2e-1958125168Myocyte-specific enhancer factor 2A
3p57_D2e-1958125168Myocyte-specific enhancer factor 2A
3p57_I2e-1958125168Myocyte-specific enhancer factor 2A
3p57_J2e-1958125168Myocyte-specific enhancer factor 2A
6c9l_A2e-1958125269Myocyte-specific enhancer factor 2B
6c9l_B2e-1958125269Myocyte-specific enhancer factor 2B
6c9l_C2e-1958125269Myocyte-specific enhancer factor 2B
6c9l_D2e-1958125269Myocyte-specific enhancer factor 2B
6c9l_E2e-1958125269Myocyte-specific enhancer factor 2B
6c9l_F2e-1958125269Myocyte-specific enhancer factor 2B
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in the control of organ identity during the early development of flowers. Is required for normal development of stamens and carpels in the wild-type flower. Plays a role in maintaining the determinacy of the floral meristem. Acts as C class cadastral protein by repressing the A class floral homeotic genes like APETALA1. Forms a heterodimer via the K-box domain with either SEPALATTA1/AGL2, SEPALATTA2/AGL4, SEPALLATA3/AGL9 or AGL6 that could be involved in genes regulation during floral meristem development. Controls AHL21/GIK, a multifunctional chromatin modifier in reproductive organ patterning and differentiation (PubMed:19956801). Induces microsporogenesis through the activation of SPL/NZZ (PubMed:15254538). {ECO:0000269|PubMed:15254538, ECO:0000269|PubMed:19956801}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00609ChIP-seqTransfer from AT4G18960Download
Motif logo
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Negatively regulated by the A class floral homeotic protein APETALA2 and by other repressors like LEUNIG, SEUSS, SAP or CURLY LEAF. Positively regulated by both LEAFY and APETALA1. Repressed by silencing mediated by polycomb group (PcG) protein complex containing EMF1 and EMF2. Up-regulated by HUA2. {ECO:0000269|PubMed:10198637, ECO:0000269|PubMed:11058164, ECO:0000269|PubMed:1675158, ECO:0000269|PubMed:17794879, ECO:0000269|PubMed:18281509, ECO:0000269|PubMed:19783648, ECO:0000269|PubMed:9783581}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankKC9843000.0KC984300.2 Brassica oleracea var. viridis AG mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_010445284.10.0PREDICTED: floral homeotic protein AGAMOUS
SwissprotP178391e-177AG_ARATH; Floral homeotic protein AGAMOUS
TrEMBLD7M9D00.0D7M9D0_ARALL; Uncharacterized protein
STRINGscaffold_702516.10.0(Arabidopsis lyrata)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM61812237
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G18960.11e-156MIKC_MADS family protein
Publications ? help Back to Top
  1. Huang Z, et al.
    APETALA2 antagonizes the transcriptional activity of AGAMOUS in regulating floral stem cells in Arabidopsis thaliana.
    New Phytol., 2017. 215(3): p. 1197-1209
    [PMID:27604611]
  2. Rong XF, et al.
    Type-B ARRs Control Carpel Regeneration Through Mediating AGAMOUS Expression in Arabidopsis.
    Plant Cell Physiol., 2018. 59(4): p. 756-764
    [PMID:29186581]
  3. Uemura A, et al.
    Regulation of floral meristem activity through the interaction of AGAMOUS, SUPERMAN, and CLAVATA3 in Arabidopsis.
    Plant Reprod, 2018. 31(1): p. 89-105
    [PMID:29218596]