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 Rsa1.0_04270.1_g00001.1
Organism
Raphanus sativus
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: 459aa    MW: 51603.1 Da    PI: 8.7983
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_04270.1_g00001.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H217.51.2e-0581103123
                              EEETTTTEEESSHHHHHHHHHHT CS
                  zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                              y C++C++ F r  nL+ H r+H
  Rsa1.0_04270.1_g00001.1  81 YICEICNQGFQRDQNLQMHRRRH 103
                              89********************9 PP
2zf-C2H215.93.8e-05159181123
                              EEETTTTEEESSHHHHHHHHHHT CS
                  zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                              ++C++C+k +  +s++k H++t+
  Rsa1.0_04270.1_g00001.1 159 WTCEKCSKGYAVQSDYKAHLKTC 181
                              58*******************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576676.37E-578104No hitNo description
Gene3DG3DSA:3.30.160.601.3E-580103IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.006581103IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.86681103IPR007087Zinc finger, C2H2
PROSITE patternPS00028083103IPR007087Zinc finger, C2H2
SMARTSM00355160123153IPR015880Zinc finger, C2H2-like
SMARTSM0035556159186IPR015880Zinc 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: 459 aa     Download sequence    Send to blast
MRTDQGAVLM LDDDASNKNT SNPCCVVSSS SSDPFLTSSE NGVATTTTST QKRKRRPAGT  60
PDPDAEVVSL SPRTLLESDR YICEICNQGF QRDQNLQMHR RRHKVPWKLL KRDNNIEVKK  120
RVYVCPEPTC LHHAPCHALG DLVGIKKHFR RKHSNHKQWT CEKCSKGYAV QSDYKAHLKT  180
CGTRGHSCDC GRVFSRVESF IEHQDNCSVR KVNREPLPPK TAVIVQACSS RTASTASTPS  240
SEANYRGAVA VATPIPLEGR PIHMRNSSIL TNSSSLNLEL QLLPLTSNQN PNQENHQHRV  300
NEPSHYHHHD TTNLDLSIAP SSSSSSYHHH YNNFDRIKEI MASEHMMKIA LKEKAYAEEA  360
KREAKRQREM AENEFMNAKK IRQQAQAELE RAKLLKEQSM KKISSTIMQV TCQTCKGQFQ  420
AVDIPAAVAD ETSLVVSYMS SANTDGEGPT IEFEKGFKY
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C6e-18155207355Zinc finger protein JACKDAW
5b3h_F6e-18155207355Zinc 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
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_04270.1_g00001.1
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]