PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID RrC133_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: 456aa    MW: 51347.9 Da    PI: 8.7983
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC133_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H217.51.2e-0578100123
                EEETTTTEEESSHHHHHHHHHHT CS
    zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                y C++C++ F r  nL+ H r+H
  RrC133_p1  78 YICEICNQGFQRDQNLQMHRRRH 100
                89********************9 PP
2zf-C2H215.93.7e-05156178123
                EEETTTTEEESSHHHHHHHHHHT CS
    zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                ++C++C+k +  +s++k H++t+
  RrC133_p1 156 WTCEKCSKGYAVQSDYKAHLKTC 178
                58*******************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576676.17E-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
SMARTSM0035556156183IPR015880Zinc finger, C2H2-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009590Biological Processdetection of gravity
GO:0009959Biological Processnegative gravitropism
GO:0009965Biological Processleaf morphogenesis
GO:0010031Biological Processcircumnutation
GO:0010601Biological Processpositive regulation of auxin biosynthetic process
GO:0048444Biological Processfloral organ morphogenesis
GO:2000012Biological Processregulation of auxin polar transport
GO:2000904Biological Processregulation of starch metabolic process
GO:0005634Cellular Componentnucleus
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 456 aa     Download sequence    Send to blast
MRTDQGAVLM LDDDASNKNT SNPCCVVSSS SSDPFLTSSE NGVATTTTST QKRKRRPADP  60
DAEVVSLSPR TLLESDRYIC EICNQGFQRD QNLQMHRRRH KVPWKLLKRD NNIEVKKRVY  120
VCPEPTCLHH APCHALGDLV GIKKHFRRKH SNHKQWTCEK CSKGYAVQSD YKAHLKTCGT  180
RGHSCDCGRV FSRVESFIEH QDNCSVRKVN REPLPPKTAV IVQACSSRTA STASTPSSEA  240
NYRGAVAVAT PIPLEGRPIH MRNSSILTNS SSLNLELQLL PLTSNQNPNQ ENHQHRVNEP  300
SHYHHHDTTN LDLSIAPSSS SSSYHHHYNN FDRIKEIMAS EHMMKIALKE KAYAEEAKRE  360
AKRQREMAEN EFMNAKKIRQ QAQAELERAK LLKEQSMKKI SSTIMQVTCQ TCKGQFQAVD  420
IPAAVADETS LVVSYMSSAN TDGEGPTIEF EKGFKY
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C6e-18152204355Zinc finger protein JACKDAW
5b3h_F6e-18152204355Zinc 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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00254DAPTransfer from AT2G01940Download
Motif logo
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
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018456017.10.0PREDICTED: protein SHOOT GRAVITROPISM 5-like isoform X1
SwissprotF4IPE30.0IDD15_ARATH; Zinc finger protein SHOOT GRAVITROPISM 5
TrEMBLA0A3P5YCK90.0A0A3P5YCK9_BRACM; Uncharacterized protein
STRINGBra017432.1-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]