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 Neem_5428_f_1
Organism
Azadirachta indica
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Meliaceae; Azadirachta
Family C2H2
Protein Properties Length: 544aa    MW: 60330.8 Da    PI: 9.1918
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Neem_5428_f_1genomeNGDView Nucleic Acid
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H2163.3e-05115137123
                    EEETTTTEEESSHHHHHHHHHHT CS
        zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                    + C++C+k F r  nL+ H r H
  Neem_5428_f_1 115 FICEICNKGFQRDQNLQLHRRGH 137
                    89*******************88 PP
2zf-C2H212.60.00041191213123
                    EEETTTTEEESSHHHHHHHHHHT CS
        zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                    +kC++C+k +  +s+ k H +t+
  Neem_5428_f_1 191 WKCEKCSKKYAVQSDWKAHSKTC 213
                    58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576675.51E-7114137No hitNo description
Gene3DG3DSA:3.30.160.601.5E-5114137IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.845115137IPR007087Zinc finger, C2H2
SMARTSM003550.022115137IPR015880Zinc finger, C2H2-like
PfamPF121716.6E-5115137IPR022755Zinc finger, double-stranded RNA binding
PROSITE patternPS000280117137IPR007087Zinc finger, C2H2
SMARTSM00355100156186IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.4E-4179212IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576675.51E-7186211No hitNo description
SMARTSM00355140191211IPR015880Zinc 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: 544 aa     Download sequence    Send to blast
MYLCISKHML RSTRSMHADT YSQYSSSVVV DETCLEVRWG REDEAKQSNF LKGWSIDPAN  60
LVPLSRQSTR SVRRQYLFDT GVDHRVINDI CVENAYPDAE VIALSPKTLM ATNRFICEIC  120
NKGFQRDQNL QLHRRGHNLP WKLRQRTNKE IKKKVYICPE KTCVHHDPSR ALGDLTGIKK  180
HFSRKHGEKK WKCEKCSKKY AVQSDWKAHS KTCGTREYKC DCGTLFSRKD SFITHRAFCD  240
ALAEESARLT SVAAANLNFR NDTVNLPHGF PNQGLQDVSG VPQFGSGFRP DLAAAEFTVS  300
LPEMVQMASG NLLGSSSNMA NFGSHNQFQG FDRSVTTSSK CANLSLSATP QGLKEESSSL  360
YSDTQNKKSK PATPMSATAL LQKAAQMGST RSNPSIFGNS FNVMSSSSSN TSNFNSLHQN  420
RNELHQVFQN VRQQENFAGT VTLAMSDGVM GGSNLSSMNT TTTATATTSS TLNQLIMQTR  480
GEQNDQVQLK LHPCSNSIEH SLTRDFLGMS GDQSGRLFLP QELAKFASIG SVSTMGLSQF  540
TSNH
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C7e-38187256372Zinc finger protein JACKDAW
5b3h_F7e-38187256372Zinc 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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00485DAPTransfer from AT5G03150Download
Motif logo
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_007027297.20.0PREDICTED: zinc finger protein JACKDAW
SwissprotQ700D21e-133IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBLA0A061EZX00.0A0A061EZX0_THECC; C2H2-like zinc finger protein, putative
STRINGEOY077990.0(Theobroma cacao)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM15528306
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G03150.11e-119C2H2-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]