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 Tp57577_TGAC_v2_mRNA16054
Organism
Trifolium pratense
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium
Family C2H2
Protein Properties Length: 478aa    MW: 53753.8 Da    PI: 8.1909
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Tp57577_TGAC_v2_mRNA16054genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H214.10.000136888323
                               ETTTTEEESSHHHHHHHHHHT CS
                    zf-C2H2  3 CpdCgksFsrksnLkrHirtH 23
                               C++C+k F r  nL+ H r H
  Tp57577_TGAC_v2_mRNA16054 68 CEICNKGFQRDQNLQLHRRGH 88
                               *******************88 PP
2zf-C2H2120.00067143165123
                                EEETTTTEEESSHHHHHHHHHHT CS
                    zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                                +kC++C+k +  +s+ k H + +
  Tp57577_TGAC_v2_mRNA16054 143 WKCEKCSKKYAVQSDWKAHSKIC 165
                                58*****************9876 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576673.52E-76588No hitNo description
Gene3DG3DSA:3.30.160.602.2E-56588IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.116688IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.8246688IPR007087Zinc finger, C2H2
PROSITE patternPS0002806888IPR007087Zinc finger, C2H2
SMARTSM0035583108138IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.605.0E-5131164IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576673.52E-7138163No hitNo description
SMARTSM00355140143163IPR015880Zinc finger, C2H2-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0005634Cellular Componentnucleus
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 478 aa     Download sequence    Send to blast
MMSKQPFSVS CHSNTMKASS SNHVQQSNSN PNPNLPKKKR NLPGTPDPDS EVVAMSPKSL  60
MATNRFLCEI CNKGFQRDQN LQLHRRGHNL PWKLKQRANK DQIKKKVYVC PEKSCVHHEP  120
SRALGDLTGI KKHYSRKHGE KKWKCEKCSK KYAVQSDWKA HSKICGTREY KCDCGTIFSR  180
KDSFITHRAF CDALTEESGK ITTVPTALSN FRNHHLTNTH QTPRIPQIFP GFQFPSDFVN  240
SATSSIWQHH QNSDMMQTMD VFGSQTQTQN QQWLNNYSNN LSLPMLHGVM KQEQEQEENK  300
DLSHSVISSL YLSNSQNQQG GSNHMSATSL LQKASQIGST RTIISNDNNN VFNNVNNFNI  360
VHDVEKFYNK QDENGELNEL VNLGGSSGTN IEGGEYLFND SNSNNLFGIV NGTKDLDHVV  420
KEKNQMGLTR DFLGVGDDDD DDSMSRPFLQ HEVLGEFNGM GSLGNNLQSH YGGGNYC*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C7e-35139204368Zinc finger protein JACKDAW
5b3h_F7e-35139204368Zinc 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}.
UniProtTranscription factor that, together with JKD, regulates tissue boundaries and asymmetric cell division in roots by a rapid up-regulation of 'SCARECROW' (SCR), thus controlling the nuclear localization of 'SHORT-ROOT' (SHR) and restricting its action (PubMed:25829440). Confines CYCD6 expression to the cortex-endodermis initial/daughter (CEI/CEID) tissues (PubMed:25829440). 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). {ECO:0000269|PubMed:24821766, ECO:0000269|PubMed:25829440}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapTp57577_TGAC_v2_mRNA16054
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
GenBankAC1393441e-167AC139344.17 Medicago truncatula clone mth2-34b22, complete sequence.
GenBankAC1699791e-167AC169979.24 Medicago truncatula clone mth2-174m19, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_003606419.20.0protein indeterminate-domain 9
SwissprotQ700D21e-111IDD10_ARATH; Zinc finger protein JACKDAW
SwissprotQ944L31e-111IDD9_ARATH; Zinc finger protein BALDIBIS
TrEMBLG7JPG10.0G7JPG1_MEDTR; C2H2 and C2HC zinc finger protein, putative
STRINGAES886160.0(Medicago truncatula)
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
AT3G45260.11e-99C2H2-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]