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 RrC8653_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 C2H2
Protein Properties Length: 487aa    MW: 54232.6 Da    PI: 8.3906
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC8653_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H215.74.4e-057090323
                ETTTTEEESSHHHHHHHHHHT CS
     zf-C2H2  3 CpdCgksFsrksnLkrHirtH 23
                C++Cgk F r  nL+ H r H
  RrC8653_p1 70 CEICGKGFQRDQNLQLHRRGH 90
                *******************88 PP
2zf-C2H213.20.00026144166123
                 EEETTTTEEESSHHHHHHHHHHT CS
     zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                 +kC++C+k++  +s+ k H +t+
  RrC8653_p1 144 WKCGKCSKRYAVQSDWKAHSKTC 166
                 58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576671.07E-66790No hitNo description
Gene3DG3DSA:3.30.160.604.2E-56790IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.4896890IPR007087Zinc finger, C2H2
PROSITE patternPS0002807090IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.607.7E-4132165IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576671.07E-6139164No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 487 aa     Download sequence    Send to blast
MTAEEQTISS SGGYVQSLSA TDHVDHRHEP EPFNPPLAKK KRNLPGNPDP EAEVIALSPK  60
TLMATNRFLC EICGKGFQRD QNLQLHRRGH NLPWKLKQRT SKEIRKRVYV CPERSCVHHN  120
PTRALGDLTG IKKHFCRKHG EKKWKCGKCS KRYAVQSDWK AHSKTCGTRE YRCDCGTIFS  180
RRDSFITHRA FCDALAEETA RLNAASHLKS LTGNNLNYHY LMGTLIPSPQ SPPPSFPFGA  240
PQHHHHHFPI TTTTTFDQLH HQDAMKPASS LSLWMGGNVN HHQVSNEDCT QPQSPQEDYN  300
WVFGNANNSG ELSDSLITHE NINNFAHNEN ANAVTSLSVP SLFSNVDQIR QDANAAVAAA  360
ALLQKAAQMG ATSSTPTITN DQSAFLQNFT SKISDQRQIV EDGGSDKFFA LFGSNSVGLM  420
SNNGLDHETL NPRNSVTVVS RIDELQNYPL KRRRVENGDV LEGGQTRDFL GVGVQTMCRS  480
SSINGWI
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C1e-34140207370Zinc finger protein JACKDAW
5b3h_F1e-34140207370Zinc finger protein JACKDAW
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1450454KRRRV
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that regulates tissue boundaries and asymmetric cell division (PubMed:17785527, PubMed:25829440). Contributes to the sequestration of 'SHORT-ROOT' to the nucleus (PubMed:17785527, PubMed:25829440). Interacts with the SCR and MGP promoters (PubMed:21935722). Does not show transcription activity by itself, but regulates the transcription of downstream genes through interaction with other transcription factors (PubMed:21935722). Binds DNA via its zinc fingers (PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). Positively involved in gibberellic acid (GA) signaling (PubMed:24821766). {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:21935722, ECO:0000269|PubMed:24821766, ECO:0000269|PubMed:25829440}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Up-regulated by the transcription factor JKD, and down-regulated by SHR, SCR and itself. {ECO:0000269|PubMed:21935722}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC1895090.0AC189509.2 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrB089B13, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018490519.10.0PREDICTED: zinc finger protein MAGPIE-like
SwissprotQ9ZWA60.0IDD3_ARATH; Zinc finger protein MAGPIE
TrEMBLA0A0D3DZ450.0A0A0D3DZ45_BRAOL; Uncharacterized protein
STRINGBo8g115920.10.0(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM37102660
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G03840.10.0C2H2 family protein
Publications ? help Back to Top
  1. Muñoz-Strale D,León G
    Identification of two highly specific pollen promoters using transcriptomic data.
    Plant Physiol. Biochem., 2014. 83: p. 292-9
    [PMID:25208507]
  2. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]