PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID SMil_00008328-RA_Salv
Organism
Salvia miltiorrhiza
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Lamiales; Lamiaceae; Nepetoideae; Mentheae; Salvia
Family C2H2
Protein Properties Length: 449aa    MW: 49214.4 Da    PI: 9.8888
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
SMil_00008328-RA_SalvgenomeNDCTCMView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H216.42.7e-055476123
                           EEETTTTEEESSHHHHHHHHHHT CS
                zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                           + C++C+k F r  nL+ H r H
  SMil_00008328-RA_Salv 54 FICEICNKGFQRDQNLQLHRRGH 76
                           89*******************88 PP
2zf-C2H212.90.00033131153123
                            EEETTTTEEESSHHHHHHHHHHT CS
                zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                            +kC++C+k +  +s+ k H +t+
  SMil_00008328-RA_Salv 131 WKCEKCSKKYAVQSDWKAHSKTC 153
                            58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576673.29E-75376No hitNo description
Gene3DG3DSA:3.30.160.601.2E-55376IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PfamPF121715.3E-55476IPR022755Zinc finger, double-stranded RNA binding
SMARTSM003550.0225476IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.8455476IPR007087Zinc finger, C2H2
PROSITE patternPS0002805676IPR007087Zinc finger, C2H2
SMARTSM0035514096126IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.1E-4119152IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576673.29E-7126151No hitNo description
SMARTSM00355140131151IPR015880Zinc 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: 449 aa     Download sequence    Send to blast
MMSGDVFSVP NSQTNPNSKP PSSAKKRRNL PGTPDPDAEV IALSPKTLMA TNRFICEICN  60
KGFQRDQNLQ LHRRGHNLPW KLKQRSNKDQ IKKKVYICPE KSCVHHEAAR ALGDLTGIKK  120
HFSRKHGEKK WKCEKCSKKY AVQSDWKAHS KTCGTREYKC DCGTLFSRKD SFITHRAFCD  180
ALAEETSRVT TNNLSFRNDL GGNIINPHFR PDFAGNSIMG DHQQQKPRLS LWLDQANSQL  240
NQIDHNSNMF MPNSSGLTDI IQMASNNLFG SNPSYANLSL SPQGMKEEPV SNKAADTTMA  300
DSLASLYSDT QKPSPMSATA LLQKAAQMGS SKSAPTFFGN TVGVMNSSSP TSSSTNTLPF  360
ATNRSELHQV FGRQQPENPA ANANAMINFN NNSLGANSVS LHSGLHGFTR DFLGMGGDGA  420
AAGPFLPQEL AKFASMNPAM GLTHFTSNH
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C5e-37127191367Zinc finger protein JACKDAW
5b3h_F5e-37127191367Zinc finger protein JACKDAW
Search in ModeBase
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}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_011094681.10.0protein indeterminate-domain 9
SwissprotQ700D21e-127IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBLA0A4D9AEY30.0A0A4D9AEY3_SALSN; Uncharacterized protein
STRINGMigut.J00556.1.p0.0(Erythranthe guttata)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA10324350
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G03150.11e-111C2H2-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-Avendaño 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]