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_mRNA18897
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: 439aa    MW: 49513.7 Da    PI: 9.0821
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Tp57577_TGAC_v2_mRNA18897genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H217.41.2e-0583105123
                                EEETTTTEEESSHHHHHHHHHHT CS
                    zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                                ++C++C+k F r  nL+ H r H
  Tp57577_TGAC_v2_mRNA18897  83 FVCEICNKGFQRDQNLQLHRRGH 105
                                89*******************88 PP
2zf-C2H213.50.00021159181123
                                EEETTTTEEESSHHHHHHHHHHT CS
                    zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                                +kC +C+k +  +s+ k H +t+
  Tp57577_TGAC_v2_mRNA18897 159 WKCDKCSKKYAVQSDWKAHTKTC 181
                                58*******************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576671.63E-782105No hitNo description
Gene3DG3DSA:3.30.160.601.4E-582105IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PfamPF121716.8E-583105IPR022755Zinc finger, double-stranded RNA binding
SMARTSM003550.01783105IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.94983105IPR007087Zinc finger, C2H2
PROSITE patternPS00028085105IPR007087Zinc finger, C2H2
SMARTSM00355120124154IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.8E-4147180IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576671.63E-7154179No hitNo description
SMARTSM00355140159179IPR015880Zinc 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: 439 aa     Download sequence    Send to blast
LYFLKTFHIV ICFLLLTTFL TQMNILGDPF SLSSSTSGFD KIQNPNPNPP QTNKKKRNLP  60
GTPDPDAEVI ALSPKTLMAT NRFVCEICNK GFQRDQNLQL HRRGHNLPWK LKQRSNKEPR  120
KKVYICPEKT CVHHDAARAL GDLTGIKKHF SRKHGEKKWK CDKCSKKYAV QSDWKAHTKT  180
CGTREYKCDC GTLFSRKDSF ITHRAFCDAL AEESARQTSL PPPTTLNFKN EESNMMNNQT  240
SLSHNGLLSC QGLQNLPQFN TPHNALFHHE QRPNLSLWLN QENQQMNHQH HHQIQHDSLE  300
DHASSSFCDV MQMTQTSTAP MSATALLQKA AQMGSTRSST NPSIFNGSFG LMSSSSTQTN  360
NSTLNQNHDE VNMVINQNMK QHENYNNAAM VGNGNSSNGF RDFLGVSNDH PHHSFLPQEL  420
AKFASMTSSM MSFNQFNA*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C9e-38155220368Zinc finger protein JACKDAW
5b3h_F9e-38155220368Zinc finger protein JACKDAW
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1109121KLKQRSNKEPRKK
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
PlantRegMapTp57577_TGAC_v2_mRNA18897
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_024625671.10.0zinc finger protein JACKDAW
SwissprotQ700D21e-129IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBLA0A396H6Q60.0A0A396H6Q6_MEDTR; Putative transcription factor C2H2 family
STRINGAES818270.0(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
AT5G03150.11e-103C2H2-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]