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 Lj5g3v1664160.1
Organism
Lotus japonicus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus
Family C2H2
Protein Properties Length: 181aa    MW: 20783.5 Da    PI: 9.3886
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Lj5g3v1664160.1genomeKazusaView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H218.55.6e-06628123
                     EEETTTTEEESSHHHHHHHHHHT CS
          zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                     ++C++C+k F r  nL+ H r H
  Lj5g3v1664160.1  6 FVCEICSKGFQRDQNLQLHRRGH 28
                     89*******************88 PP
2zf-C2H218.17.6e-0683105123
                      EEETTTTEEESSHHHHHHHHHHT CS
          zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                      +kC +C+k++  +s+ k H++t+
  Lj5g3v1664160.1  83 WKCDKCSKRYAVQSDWKAHQKTC 105
                      58*******************98 PP
3zf-C2H211.50.00091113131523
                      TTTEEESSHHHHHHHHHHT CS
          zf-C2H2   5 dCgksFsrksnLkrHirtH 23 
                      dCg+ Fsr++++ +H   +
  Lj5g3v1664160.1 113 DCGTIFSRRDSFITHRAFC 131
                      8**************8765 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576675.96E-9528No hitNo description
Gene3DG3DSA:3.30.160.601.6E-5528IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.887628IPR007087Zinc finger, C2H2
SMARTSM003550.036628IPR015880Zinc finger, C2H2-like
PfamPF121718.6E-5628IPR022755Zinc finger, double-stranded RNA binding
PROSITE patternPS000280828IPR007087Zinc finger, C2H2
SMARTSM00355754878IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.602.3E-671104IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576675.96E-978104No hitNo description
SMARTSM003558983103IPR015880Zinc 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: 181 aa     Download sequence    Send to blast
MATNRFVCEI CSKGFQRDQN LQLHRRGHNL PWKLKQRTSS EVVKKRVYVC PEPSCVHHNP  60
ARALGDLTGI KKHYSRKHGE KKWKCDKCSK RYAVQSDWKA HQKTCGTKEY KCDCGTIFSR  120
RDSFITHRAF CDALTEENNR VNQGLTSGME PNSQNEVPDL IATMPLSTSS NTVSEFNNHE  180
P
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C5e-3679142366Zinc finger protein JACKDAW
5b3h_F5e-3679142366Zinc finger protein JACKDAW
Search in ModeBase
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
UniProtProbable transcription factor. {ECO:0000305}.
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLj5g3v1664160.1
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
GenBankAC2353491e-123AC235349.1 Glycine max strain Williams 82 clone GM_WBb0092H01, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_027364196.11e-121zinc finger protein GAI-ASSOCIATED FACTOR 1-like
SwissprotQ700D27e-90IDD10_ARATH; Zinc finger protein JACKDAW
SwissprotQ8H1F53e-90IDD7_ARATH; Protein indeterminate-domain 7
TrEMBLA0A151TW901e-119A0A151TW90_CAJCA; Zinc finger protein MAGPIE
STRINGGLYMA19G39640.21e-118(Glycine max)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF21923085
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G55110.11e-92indeterminate(ID)-domain 7
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]