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 Lus10019927
Organism
Linum usitatissimum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Linaceae; Linum
Family C2H2
Protein Properties Length: 484aa    MW: 53047.3 Da    PI: 9.57
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Lus10019927genomeBGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H214.10.0001483103323
                  ETTTTEEESSHHHHHHHHHHT CS
      zf-C2H2   3 CpdCgksFsrksnLkrHirtH 23 
                  C++C+k F r  nL+ H r H
  Lus10019927  83 CEICNKGFQRDQNLQLHRRGH 103
                  *******************88 PP
2zf-C2H2110.0013158180123
                  EEETTTTEEESSHHHHHHHHHHT CS
      zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                  +kC++C+k +   s+ k H +t+
  Lus10019927 158 WKCEKCSKKYAVLSDWKAHSKTC 180
                  58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576675.39E-780103No hitNo description
Gene3DG3DSA:3.30.160.602.2E-580103IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.82481103IPR007087Zinc finger, C2H2
SMARTSM003550.1181103IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028083103IPR007087Zinc finger, C2H2
SMARTSM00355100123153IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.0E-4146179IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576675.39E-7153178No hitNo description
SMARTSM00355180158178IPR015880Zinc 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: 484 aa     Download sequence    Send to blast
MSSGGGDPFS LTLPPFFPPL QHEQTHQLPP LPPPPPASAN PNPNLTSSNN NRKKRNLPGT  60
PDPDAEVMAL SPKSLMATNR FLCEICNKGF QRDQNLQLHR RGHNLPWKLK QRNTKEPIRK  120
KVYICPEKTC VHHDPSRALG DLTGIKKHFS RKHGEKKWKC EKCSKKYAVL SDWKAHSKTC  180
GTREYKCDCG TLFSRKDSFI THRAFCDALA DDSLRFNSAN AAAAASATNL NFESIGNNTQ  240
NDNNPSQLPR HHQGFHNQDM NSQFGNFINS LAAGNHNGMN MMMTMMPNNN STSTNGSYLT  300
DEMVQMGRSS SSTGSGMKEE ALPSLYSSQM MSHENKQQQS NGGRSPMSAT ALLQKAAQIG  360
STRSSSSGGG TIVNNTQQSS LFGMTNMPPP MDQNSFEQLM MMQGSGKLQG VGIMESIINN  420
NDNHQNNNNN NYTSDSMESR LTRDFLGMSG GRPFLQQEIA RFANSMNSSS SLGFAATASG  480
NPL*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C4e-34154218367Zinc finger protein JACKDAW
5b3h_F4e-34154218367Zinc finger protein JACKDAW
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1107120KLKQRNTKEPIRKK
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
PlantRegMapLus10019927
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 -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_021674002.11e-141zinc finger protein JACKDAW-like isoform X1
SwissprotQ700D21e-129IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBLA0A2C9VC911e-139A0A2C9VC91_MANES; Uncharacterized protein
STRINGLus100199270.0(Linum usitatissimum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF18134275
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G03150.11e-100C2H2-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]