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 GSVIVT01025166001
Common NameVIT_06s0004g03070
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: 478aa    MW: 52536 Da    PI: 9.6539
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSVIVT01025166001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H216.22.9e-056284123
                       EEETTTTEEESSHHHHHHHHHHT CS
            zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                       + C++C+k F r  nL+ H r H
  GSVIVT01025166001 62 FICEICNKGFQRDQNLQLHRRGH 84
                       89*******************88 PP

2zf-C2H2120.00067138160123
                        EEETTTTEEESSHHHHHHHHHHT CS
            zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                        +kC++C+k +  +s+ k H + +
  GSVIVT01025166001 138 WKCEKCSKKYAVQSDWKAHSKIC 160
                        58*****************9876 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.601.3E-56184IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576674.82E-76184No hitNo description
PROSITE profilePS5015710.8456284IPR007087Zinc finger, C2H2
PfamPF121715.7E-56284IPR022755Zinc finger, double-stranded RNA binding
SMARTSM003550.0226284IPR015880Zinc finger, C2H2-like
PROSITE patternPS0002806484IPR007087Zinc finger, C2H2
SMARTSM0035591103133IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.605.0E-5126159IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576674.82E-7133158No hitNo description
SMARTSM00355140138158IPR015880Zinc 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: 478 aa     Download sequence    Send to blast
MAEDGLTLPS SIRGFVQEPN SNPNPNPSAN PVKKKRNLPG TPDPEAEVIA LSPKSLMATN  60
RFICEICNKG FQRDQNLQLH RRGHNLPWKL RQRTSKEVRK KVYICPEKSC VHHNPTRALG  120
DLTGIKKHYS RKHGEKKWKC EKCSKKYAVQ SDWKAHSKIC GTREYKCDCG TLFSRKDSFI  180
THRAFCDALA EESARLTSVS APNPIFRNEL MNGSISNPQA HIIPQFSSPR LPLWLDHANS  240
HLNNPIGVNT NGSFLAPTSA GLPEMVQTAP MSMYGSPASS QNQWLQRCSE ASFTSSTLPR  300
VLKEEEENKG NLSESITSLF SSNQNQQESS AHMSATALLQ KAAQMGSTKS NSAFFSTTGF  360
GSINSSLSNT TPFSSYPHGR SNNQVHKFLI RQSNQSDSMN QLINSTSPSS TMGDGLLMGD  420
MNSTPLFHAS SNEVERGLTR DFLGVGSDAS RPFLQQELAK FASMGSAMGM SQYSGNH*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C2e-38134203372Zinc finger protein JACKDAW
5b3h_F2e-38134203372Zinc finger protein JACKDAW
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
188100KLRQRTSKEVRKK
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Vvi.33600.0bud| fruit
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}.
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
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAM4519950.0AM451995.1 Vitis vinifera, whole genome shotgun sequence, contig VV78X227225.4, clone ENTAV 115.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002282251.20.0PREDICTED: protein indeterminate-domain 9
SwissprotQ700D21e-124IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBLF6GTZ50.0F6GTZ5_VITVI; Uncharacterized protein
STRINGVIT_06s0004g03070.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-113C2H2-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]