PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID GSVIVT01025658001
Common NameLOC100243175, VIT_08s0040g02100
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; rosids incertae sedis; Vitales; Vitaceae; Vitis
Family C2H2
Protein Properties Length: 470aa    MW: 50880.3 Da    PI: 9.476
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSVIVT01025658001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H216.32.8e-056385123
                       EEETTTTEEESSHHHHHHHHHHT CS
            zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                       + C++C+k F r  nL+ H r H
  GSVIVT01025658001 63 FICEICNKGFQRDQNLQLHRRGH 85
                       89*******************88 PP

2zf-C2H212.90.00034139161123
                        EEETTTTEEESSHHHHHHHHHHT CS
            zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                        +kC++C+k +  +s+ k H +t+
  GSVIVT01025658001 139 WKCEKCSKKYAVQSDWKAHSKTC 161
                        58*****************9998 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.601.2E-56285IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576673.95E-76285No hitNo description
PfamPF121715.5E-56385IPR022755Zinc finger, double-stranded RNA binding
PROSITE profilePS5015710.8456385IPR007087Zinc finger, C2H2
SMARTSM003550.0226385IPR015880Zinc finger, C2H2-like
PROSITE patternPS0002806585IPR007087Zinc finger, C2H2
SMARTSM00355100104134IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.1E-4127160IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576673.95E-7134159No hitNo description
SMARTSM00355140139159IPR015880Zinc finger, C2H2-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0010075Biological Processregulation of meristem growth
GO:0045604Biological Processregulation of epidermal cell differentiation
GO:0048364Biological Processroot development
GO:0051302Biological Processregulation of cell division
GO:0003676Molecular Functionnucleic acid binding
GO:0042803Molecular Functionprotein homodimerization activity
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 470 aa     Download sequence    Send to blast
MQMMSGDMFS IPSSIRTFAQ DPDANPNNLK PPPKKKRNLP GTPDPDAEVI ALSPKTLMAT  60
NRFICEICNK GFQRDQNLQL HRRGHNLPWK LKQRSNKEVR KKVYICPEKT CVHHDPSRAL  120
GDLTGIKKHF SRKHGEKKWK CEKCSKKYAV QSDWKAHSKT CGTREYKCDC GTLFSRKDSF  180
ITHRAFCDAL AEERARITSV AATNLNFRND SMNETVINPQ PGLLNGFSGR GGPDAAGISQ  240
FCPGFGPDLT GLPEMVQVAA SNLFGSSSVG NFGSCNESPW LDKSSATSNG ANLSLASLPH  300
ALKEEEGNKG SMVETLTSLY SGNHSQQSSP AAPMSATALL QKAAQMGSTR SNPSFFGNSF  360
GVMNSSGSHS TTLNTLTHNR NELHQVFGTG KQHENLMATA SLSEGTSGKQ TEPVPLKLHL  420
GSNSVENSLT RDFLGMGGGE SGRPFLPQEL AKFASMGSAM GLSHFTSNH*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C5e-38135204372Zinc finger protein JACKDAW
5b3h_F5e-38135204372Zinc finger protein JACKDAW
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
189101KLKQRSNKEVRKK
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Vvi.153450.0inflorescence
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Start to accumulate during the 16- to 32-cell stage of embryogenesis. {ECO:0000269|PubMed:17785527}.
UniprotTISSUE SPECIFICITY: Expressed in the quiescent center, the ground tissue stem cells and to a lesser extent in mature cortex and endodermis cells. {ECO:0000269|PubMed:17785527}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that, together with BIB, regulates tissue boundaries and asymmetric cell division by a rapid up-regulation of 'SCARECROW' (SCR), thus controlling the nuclear localization of 'SHORT-ROOT' (SHR) and restricting its action (PubMed:17785527, PubMed:25829440). Binds DNA via its zinc fingers (PubMed:28211915, PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). Confines CYCD6 expression to the cortex-endodermis initial/daughter (CEI/CEID) tissues (PubMed:25829440). Required for radial patterning and stem cell maintenance (PubMed:17785527). Counteracted by 'MAGPIE' (MGP) (PubMed:17785527). Binds to the SCR and MGP promoter sequences (PubMed:21935722). Controls position-dependent signals that regulate epidermal-cell-type patterning (PubMed:20356954). {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:20356954, ECO:0000269|PubMed:21935722, ECO:0000269|PubMed:24821766, ECO:0000269|PubMed:25829440, ECO:0000269|PubMed:28211915}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00485DAPTransfer from AT5G03150Download
Motif logo
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Not regulated by SCR and SHR. {ECO:0000269|PubMed:21935722}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAM4576790.0AM457679.2 Vitis vinifera contig VV78X050744.10, whole genome shotgun sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002275477.30.0PREDICTED: zinc finger protein JACKDAW
RefseqXP_010653553.10.0PREDICTED: zinc finger protein JACKDAW
SwissprotQ700D21e-124IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBLF6HR110.0F6HR11_VITVI; Uncharacterized protein
STRINGVIT_08s0040g02100.t010.0(Vitis vinifera)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP9516242
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G03150.11e-108C2H2-like zinc finger protein
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]
  2. Hirano Y, et al.
    Structure of the SHR-SCR heterodimer bound to the BIRD/IDD transcriptional factor JKD.
    Nat Plants, 2017. 3: p. 17010
    [PMID:28211915]
  3. Kobayashi A,Miura S,Kozaki A
    INDETERMINATE DOMAIN PROTEIN binding sequences in the 5'-untranslated region and promoter of the SCARECROW gene play crucial and distinct roles in regulating SCARECROW expression in roots and leaves.
    Plant Mol. Biol., 2017. 94(1-2): p. 1-13
    [PMID:28324206]
  4. Long Y, et al.
    In vivo FRET-FLIM reveals cell-type-specific protein interactions in Arabidopsis roots.
    Nature, 2017. 548(7665): p. 97-102
    [PMID:28746306]
  5. Bustillo-AvendaƱo E, et al.
    Regulation of Hormonal Control, Cell Reprogramming, and Patterning during De Novo Root Organogenesis.
    Plant Physiol., 2018. 176(2): p. 1709-1727
    [PMID:29233938]