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 Glyma.03G179700.1.p
Common NameGLYMA_03G179700, LOC100812495
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Glycine; Soja
Family C2H2
Protein Properties Length: 515aa    MW: 55818.3 Da    PI: 9.5887
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Glyma.03G179700.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H216.13.1e-056789123
                         EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                         + C++C+k F r  nL+ H r H
  Glyma.03G179700.1.p 67 FICEICNKGFQRDQNLQLHRRGH 89
                         89*******************88 PP

2zf-C2H213.90.00016143165123
                          EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                          +kC++C+k +  +s+ k H +t+
  Glyma.03G179700.1.p 143 WKCEKCSKKYAVQSDWKAHTKTC 165
                          58*******************98 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576674.07E-76689No hitNo description
Gene3DG3DSA:3.30.160.601.4E-56689IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.8456789IPR007087Zinc finger, C2H2
SMARTSM003550.0226789IPR015880Zinc finger, C2H2-like
PfamPF121716.2E-56789IPR022755Zinc finger, double-stranded RNA binding
PROSITE patternPS0002806989IPR007087Zinc finger, C2H2
SMARTSM0035598108138IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.604.6E-5131164IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576674.07E-7138163No hitNo description
SMARTSM00355130143163IPR015880Zinc 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: 515 aa     Download sequence    Send to blast
MQMIPGDPFS LSTSLPAGLP NEQSTNTNPN PNPPPPNKKK RNLPGTPDPD AEVIALSPKT  60
LMATNRFICE ICNKGFQRDQ NLQLHRRGHN LPWKLRQRSN KEVRKKVYIC PEKTCVHHDA  120
ARALGDLTGI KKHYSRKHGE KKWKCEKCSK KYAVQSDWKA HTKTCGTREY KCDCGNLFSR  180
KDSFITHRAF CDALADESSR LTSVASTSLN FKSEDATMIN TQASLSTRGL ITDHGMQNVS  240
QFGPHGFRLM NMGTDQQRPN LSLWLNQGNH HINNPLDVAL SSSSSGLPEV VHMAQANINN  300
NALIGSSSVF SNFGMPASSN SSNPNLMGKK GDGGASDLAS MYSESQNKNS NSTSPMSATA  360
LLQKAAQMGS TRSTNPSIFS GSFGVMSSSS TQSTSLNSNI ANQSCDQLNQ AFQNFNATSS  420
SSATMLGSST NFSSLTHSSN GFDQFMMQNN VEPTQLKLHH PGSNSVEHNL TRDFLGVSGN  480
GGGQVHHAFL PQELAKFASL GSSMGLNQFT VGHQ*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C2e-35139208372Zinc finger protein JACKDAW
5b3h_F2e-35139208372Zinc finger protein JACKDAW
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
193105KLRQRSNKEVRKK
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
Cis-element ? help Back to Top
SourceLink
PlantRegMapGlyma.03G179700.1.p
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
GenBankAP0150371e-162AP015037.1 Vigna angularis var. angularis DNA, chromosome 4, almost complete sequence, cultivar: Shumari.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_014629360.10.0zinc finger protein JACKDAW
SwissprotQ700D21e-131IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBLI1JPL10.0I1JPL1_SOYBN; Uncharacterized protein
STRINGGLYMA03G33700.10.0(Glycine max)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF18134275
Representative plantOGRP9516242
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G03150.11e-112C2H2-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]