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 RrC5216_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: 494aa    MW: 53453.1 Da    PI: 9.5794
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC5216_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H214.97.5e-056587123
                EEETTTTEEESSHHHHHHHHHHT CS
     zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                + C  C+k F r  nL+ H r H
  RrC5216_p1 65 FICDVCKKGFQREQNLQLHRRGH 87
                89*******************88 PP
2zf-C2H212.80.00036141163123
                 EEETTTTEEESSHHHHHHHHHHT CS
     zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                 +kC +C+k++  +s+ k H +t+
  RrC5216_p1 141 WKCDKCSKRYAVQSDWKAHSKTC 163
                 58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM003550.0146587IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.6166587IPR007087Zinc finger, C2H2
PfamPF139121.6E-46587IPR007087Zinc finger, C2H2
SuperFamilySSF576672.89E-76587No hitNo description
Gene3DG3DSA:3.30.160.601.4E-46587IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS0002806787IPR007087Zinc finger, C2H2
SMARTSM0035560106136IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.603.0E-5128162IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.89E-7136161No hitNo description
SMARTSM00355140141161IPR015880Zinc finger, C2H2-like
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: 494 aa     Download sequence    Send to blast
MSSSSYNTSV VPSSPSTQPF FITGSGAGDN AFDRKDTFMS MIQQPNSSAP QPKKRRNQPG  60
NPSKFICDVC KKGFQREQNL QLHRRGHNLP WKLKQKSTKE VKRKVYICPE PTCVHHDPSR  120
ALGDLTGVKK HYYRKHGEKK WKCDKCSKRY AVQSDWKAHS KTCGTKEYRC DCGTIFSRRD  180
SYITHRAFCD ALIQETARNP TMTLTSITAA SSGAGFGGFH GRLEGGNALS HNHLSDHTNS  240
GFSSFSGYNL NFPSSGNSRD FAPQTSNPNF LIQYSSSQGI VTVPNNNNNN NDQSFMNQQG  300
LIHFDPVNNI NLKSSTTNNS LFNIGFFQEN TKNSETTLPS LYSTDALVHH GEGSLNVNSN  360
VSATALLQKA TQLGSITSND PSTLFRGLGS SSNSSSVVVN DFGGGHIMGN DNNGNLQGLM  420
NSVVAVNGGG TGGSGGNIFD VDFGNNNGNM SGSDNLTLDF LGVGGMVRNV NRGGAGRGRV  480
RGDVSLIGEL KFPE
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C3e-33137203369Zinc finger protein JACKDAW
5b3h_F3e-33137203369Zinc finger protein JACKDAW
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that may act a transcriptional activator of nuclear-encoded photosynthetic gene expression (Probable). 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). {ECO:0000269|PubMed:24821766, ECO:0000305|PubMed:19726569}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Down-regulated by gibberellin. {ECO:0000305|PubMed:17933900}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_013599228.10.0PREDICTED: protein indeterminate-domain 4, chloroplastic-like
RefseqXP_013599229.10.0PREDICTED: protein indeterminate-domain 4, chloroplastic-like
RefseqXP_013599230.10.0PREDICTED: protein indeterminate-domain 4, chloroplastic-like
RefseqXP_013599231.10.0PREDICTED: protein indeterminate-domain 4, chloroplastic-like
RefseqXP_013599232.10.0PREDICTED: protein indeterminate-domain 4, chloroplastic-like
RefseqXP_013599233.10.0PREDICTED: protein indeterminate-domain 4, chloroplastic-like
RefseqXP_013599234.10.0PREDICTED: protein indeterminate-domain 4, chloroplastic-like
RefseqXP_013736158.10.0protein indeterminate-domain 4, chloroplastic-like
RefseqXP_013736159.10.0protein indeterminate-domain 4, chloroplastic-like
RefseqXP_013736160.10.0protein indeterminate-domain 4, chloroplastic-like
RefseqXP_013736161.10.0protein indeterminate-domain 4, chloroplastic-like
RefseqXP_022560774.10.0protein indeterminate-domain 4, chloroplastic-like
RefseqXP_022560776.10.0protein indeterminate-domain 4, chloroplastic-like
SwissprotQ8GYC10.0IDD4_ARATH; Protein indeterminate-domain 4, chloroplastic
TrEMBLA0A0D3DAB20.0A0A0D3DAB2_BRAOL; Uncharacterized protein
STRINGBo7g080200.10.0(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM36781759
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G02080.10.0indeterminate(ID)-domain 4
Publications ? help Back to Top
  1. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]