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 Lsa013123
Organism
Lactuca sativa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; campanulids; Asterales; Asteraceae; Cichorioideae; Cichorieae; Lactucinae; Lactuca
Family C2H2
Protein Properties Length: 357aa    MW: 39574.5 Da    PI: 9.1633
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
PUT-187a-Lactuca_sativa-41621PU_refplantGDBView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H217.21.4e-056789123
               EEETTTTEEESSHHHHHHHHHHT CS
    zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
               ++C++C+k F r  nL+ H r H
  Lsa013123 67 FVCEICSKGFQRDQNLQLHRRGH 89
               89*******************88 PP
2zf-C2H212.50.00046144166123
                EEETTTTEEESSHHHHHHHHHHT CS
    zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                +kC++C+k +  +s+ k H + +
  Lsa013123 144 WKCEKCSKKYAVQSDWKAHSKIC 166
                58*****************9876 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576672.52E-76689No hitNo description
Gene3DG3DSA:3.30.160.603.9E-56689IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.8876789IPR007087Zinc finger, C2H2
SMARTSM003550.0366789IPR015880Zinc finger, C2H2-like
PROSITE patternPS0002806989IPR007087Zinc finger, C2H2
SMARTSM00355110109139IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.0E-4131165IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.52E-7139164No hitNo description
SMARTSM00355140144164IPR015880Zinc 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: 357 aa     Download sequence    Send to blast
MMSGDGFSSP PSSLSSFIHD PIPNPNPNPN PNSSVSGKRK RNQAGNPDPD AEVIALSPTS  60
LMATNRFVCE ICSKGFQRDQ NLQLHRRGHN LPWKLKQRNK NEVIKKKVYI CPEKSCVHHD  120
PSRALGDLTG VKKHFSRKHG EKKWKCEKCS KKYAVQSDWK AHSKICGTRE YKCDCGTLFS  180
RKDSFITHRA FCDALMEENS RMTSLTVLPS MPHLGFRNDL MIMNGGGPGG GSGGAGNTQF  240
HQGVFGGGLE SPLDVNGSKQ RLPIWLDHNA NNPHLENTNS STFLGSSSSN YNNGGMLQPE  300
MVNWLSRYNG LPQGLSLKEE EESQKEMQLN SMFNYGGSNT QNNLMCSSLP HHHHHGS
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C1e-38140206369Zinc finger protein JACKDAW
5b3h_F1e-38140206369Zinc 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}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Not regulated by SCR and SHR. {ECO:0000269|PubMed:21935722}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_023733243.10.0protein indeterminate-domain 9-like
SwissprotQ700D21e-112IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBLA0A2J6KGP80.0A0A2J6KGP8_LACSA; Uncharacterized protein
STRINGXP_009789501.11e-129(Nicotiana sylvestris)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G03150.11e-102C2H2-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]