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 GSVIVT01020612001
Common NameVIT_12s0028g03030
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: 428aa    MW: 47173.2 Da    PI: 9.4518
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSVIVT01020612001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H215.93.7e-055979323
                       ETTTTEEESSHHHHHHHHHHT CS
            zf-C2H2  3 CpdCgksFsrksnLkrHirtH 23
                       C++Cgk F r  nL+ H r H
  GSVIVT01020612001 59 CEICGKGFQRDQNLQLHRRGH 79
                       *******************88 PP

2zf-C2H214.88.1e-05133155123
                        EEETTTTEEESSHHHHHHHHHHT CS
            zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                        +kC++C+k++  +s+ k H +t+
  GSVIVT01020612001 133 WKCEKCSKRYAVQSDWKAHTKTC 155
                        58*******************98 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.603.6E-55679IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576671.9E-65679No hitNo description
PROSITE profilePS5015711.4895779IPR007087Zinc finger, C2H2
SMARTSM003550.0765779IPR015880Zinc finger, C2H2-like
PROSITE patternPS0002805979IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.6E-4121154IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576671.9E-6128153No hitNo description
SMARTSM00355120133153IPR015880Zinc finger, C2H2-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0005634Cellular Componentnucleus
GO:0044212Molecular Functiontranscription regulatory region DNA binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 428 aa     Download sequence    Send to blast
MLQKMAAEAI PNGFIQNPIG GSNPPTIKKK RNLPGTPDPE AEVIALSPKT LMATNRFLCE  60
ICGKGFQRDQ NLQLHRRGHN LPWKLKQRSS KEPRKRVYVC PEKTCVHHHP SRALGDLTGI  120
KKHFCRKHGE KKWKCEKCSK RYAVQSDWKA HTKTCGTREY KCDCGTLFSR RDSFITHRAF  180
CDALAEETAR VTAASNINNG TINYHFMGTS LAPSMPQHFS SIFKPISSND EATDQTRRGL  240
SLWMGQGSQG HETMGTNLQE IHQLRSSMSP GSSSNNTEDQ LTSSTSLPLS NVKEAAGSQI  300
VSVPSLYSSQ HHSHQTPLGN MSATALLQKA AQMGATSADP FLGSFGLKCD SSLVQDGNKF  360
CGLYTANQLP TNDMENPKDL STFNQLQMYP AKRRNTQNDD STGGQTRDFL GVGVQTICHP  420
SSINGWM*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C1e-37129198372Zinc finger protein JACKDAW
5b3h_F1e-37129198372Zinc finger protein JACKDAW
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in the ground tissue and stele cells of embryos and 2-days post-germination roots but not in the quiescent center (PubMed:17785527). Detected only in cells that perform asymmetric cell divisions (PubMed:17785527). In roots, present in cortex, endodermis, and pericycle layer (PubMed:25829440). {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:25829440}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that regulates tissue boundaries and asymmetric cell division (PubMed:17785527, PubMed:25829440). Contributes to the sequestration of 'SHORT-ROOT' to the nucleus (PubMed:17785527, PubMed:25829440). Interacts with the SCR and MGP promoters (PubMed:21935722). Does not show transcription activity by itself, but regulates the transcription of downstream genes through interaction with other transcription factors (PubMed:21935722). Binds DNA via its zinc fingers (PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). Positively involved in gibberellic acid (GA) signaling (PubMed:24821766). {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:21935722, ECO:0000269|PubMed:24821766, ECO:0000269|PubMed:25829440}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00125DAPTransfer from AT1G03840Download
Motif logo
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Up-regulated by the transcription factor JKD, and down-regulated by SHR, SCR and itself. {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
GenBankAM4252920.0AM425292.2 Vitis vinifera contig VV78X015037.17, whole genome shotgun sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002275400.30.0PREDICTED: zinc finger protein MAGPIE
SwissprotQ9ZWA61e-152IDD3_ARATH; Zinc finger protein MAGPIE
TrEMBLE0CTJ20.0E0CTJ2_VITVI; Uncharacterized protein
STRINGVIT_12s0028g03030.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
AT1G03840.11e-153C2H2 family protein
Publications ? help Back to Top
  1. Muñoz-Strale D,León G
    Identification of two highly specific pollen promoters using transcriptomic data.
    Plant Physiol. Biochem., 2014. 83: p. 292-9
    [PMID:25208507]
  2. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]