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 RrC5218_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: 438aa    MW: 49558.1 Da    PI: 9.2199
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC5218_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H217.61.1e-0578100123
                 EEETTTTEEESSHHHHHHHHHHT CS
     zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                 y C++C++ F r  nL+ H r+H
  RrC5218_p1  78 YICEICNQGFQRDQNLQMHRRRH 100
                 89********************9 PP
2zf-C2H213.70.00019157178223
                 EETTTTEEESSHHHHHHHHHHT CS
     zf-C2H2   2 kCpdCgksFsrksnLkrHirtH 23 
                  C+ C+k +  +s++k H++t+
  RrC5218_p1 157 ICERCSKGYAVQSDYKAHLKTC 178
                 7*******************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576675.88E-575101No hitNo description
Gene3DG3DSA:3.30.160.601.3E-577100IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.006578100IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.86678100IPR007087Zinc finger, C2H2
PROSITE patternPS00028080100IPR007087Zinc finger, C2H2
SMARTSM00355160120150IPR015880Zinc finger, C2H2-like
SMARTSM00355110156183IPR015880Zinc 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: 438 aa     Download sequence    Send to blast
MMRTDQGAVV MLNAASNKNT TNTCCVVSSS SSDPFLSSSE NGVTTTNTSN QKRKRRPADP  60
DAEVVSLSPR TLLESDRYIC EICNQGFQRD QNLQMHRRRH KVPWKLLKRD NNIEVKKRVY  120
VCPEPTCLHH DPCHALGDLV GIKKHFRRKH SNHKQWICER CSKGYAVQSD YKAHLKTCGT  180
RGHSCDCGRV FSRVESFIEH QDKCSVRKVH REPPPRPQPT VTVPTCFSRT ASTTSTPSTE  240
TNYGGALATP LPLEGRPIPI RNFSSNNVNL ELQLLPLTPN QNPHQENQQH KVKEPSHHRN  300
HHDTTNLNLS IAPSAPSLSH QYNNFDRIKE IMASEHIMKI AMKEKTYAEE AKREAKKQRE  360
IAENEFVNAK KIRQQAQVEL ERAKILKEES MKKINSTIMQ VTCQTCKGQF QAIAVPAADE  420
TSLVVSYMSS ANTDEEGS
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C2e-17152206357Zinc finger protein JACKDAW
5b3h_F2e-17152206357Zinc finger protein JACKDAW
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor involved in inflorescence stems gravitropism, probably by regulating starch accumulation in amyloplasts of graviperceptive cells. Required for stem circumnutation movements. Regulates lateral organ morphogenesis and gravitropic responses (PubMed:24039602). Acts cooperatively with IDD16 to control silique and branche orientation (PubMed:24039602). Involved in the establishment of auxin gradients through the regulation of auxin biosynthesis and transport (PubMed:24039602). {ECO:0000269|PubMed:16813575, ECO:0000269|PubMed:18259878, ECO:0000269|PubMed:24039602, ECO:0000269|PubMed:9210330}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Not regulated by auxin. {ECO:0000269|PubMed:24039602}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankHM2229240.0HM222924.1 Thellungiella parvula phosphatase, cyclin J18, clathrin assembly protein-related protein, BPC1, SGR5/ATIDD15, leucine-rich receptor kinase, endomemebrane protein 70, salt overly sensitive 1, glutamate decarboxylae 4, oligopeptide transport protein, peptide transporter, and NADH-ubiquinone oxidoreductase B18 genes, complete cds; and unknown genes.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018439399.10.0PREDICTED: protein SHOOT GRAVITROPISM 5-like
SwissprotF4IPE30.0IDD15_ARATH; Zinc finger protein SHOOT GRAVITROPISM 5
TrEMBLA0A3P6AWF40.0A0A3P6AWF4_BRACM; Uncharacterized protein
STRINGBra026624.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM69328131
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G01940.10.0C2H2-like zinc finger protein
Publications ? help Back to Top
  1. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  2. Kim JY,Ryu JY,Baek K,Park CM
    High temperature attenuates the gravitropism of inflorescence stems by inducing SHOOT GRAVITROPISM 5 alternative splicing in Arabidopsis.
    New Phytol., 2016. 209(1): p. 265-79
    [PMID:26256266]
  3. Ryu JY,Kim JY,Park CM
    Adaptive thermal control of stem gravitropism through alternative RNA splicing in Arabidopsis.
    Plant Signal Behav, 2015. 10(11): p. e1093715
    [PMID:26452406]
  4. Qu Y, et al.
    Peroxisomal CuAOζ and its product H2O2 regulate the distribution of auxin and IBA-dependent lateral root development in Arabidopsis.
    J. Exp. Bot., 2017. 68(17): p. 4851-4867
    [PMID:28992128]
  5. Shi H, et al.
    Zinc finger of Arabidopsis thaliana 6 is involved in melatonin-mediated auxin signaling through interacting INDETERMINATE DOMAIN15 and INDOLE-3-ACETIC ACID 17.
    J. Pineal Res., 2018. 65(2): p. e12494
    [PMID:29607541]