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 Niben101Ctg09569g00003.1
Organism
Nicotiana benthamiana
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; Nicotianeae; Nicotiana
Family C2H2
Protein Properties Length: 190aa    MW: 21820.1 Da    PI: 9.9985
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Niben101Ctg09569g00003.1genomeBTI-
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H217.98.6e-065779123
                              EEETTTTEEESSHHHHHHHHHHT CS
                   zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                              + C++C+k F r  nL+ H r H
  Niben101Ctg09569g00003.1 57 FICEICNKGFQRDQNLQLHRRGH 79
                              89*******************88 PP
2zf-C2H212.30.00052134156123
                               EEETTTTEEESSHHHHHHHHHHT CS
                   zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                               +kC++C+k +  +s+ k H + +
  Niben101Ctg09569g00003.1 134 WKCEKCSKKYAVHSDWKAHTKIC 156
                               58*****************9987 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576672.32E-75679No hitNo description
Gene3DG3DSA:3.30.160.603.7E-65679IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PfamPF121711.7E-55779IPR022755Zinc finger, double-stranded RNA binding
SMARTSM003550.0225779IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.8455779IPR007087Zinc finger, C2H2
PROSITE patternPS0002805979IPR007087Zinc finger, C2H2
SMARTSM0035510099129IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.608.7E-5122155IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.32E-7129154No hitNo description
SMARTSM00355140134154IPR015880Zinc 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: 190 aa     Download sequence    Send to blast
MMSEDGLSFI QDPNHSNIPN PNSNPSAKRK RNLPGKPDPD AEVIALSPKS LMATNRFICE  60
ICNKGFQRDQ NLQLHRRGHN LPWKLKQKNK NEVIKKKVYI CPEKTCIHHD TSRALGDLTG  120
IKKHYSRKHG EKKWKCEKCS KKYAVHSDWK AHTKICGTRE YKCDCGTLFS RKDSFITHRA  180
FCDALAEESA
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C2e-35130190363Zinc finger protein JACKDAW
5b3h_F2e-35130190363Zinc 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_009789501.11e-131PREDICTED: zinc finger protein JACKDAW-like
RefseqXP_016442367.11e-131PREDICTED: protein indeterminate-domain 9-like isoform X2
SwissprotQ700D21e-109IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBLA0A1S3XRQ41e-129A0A1S3XRQ4_TOBAC; protein indeterminate-domain 9-like isoform X2
TrEMBLA0A1U7XIP21e-129A0A1U7XIP2_NICSY; zinc finger protein JACKDAW-like
STRINGXP_009789501.11e-130(Nicotiana sylvestris)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA10324350
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G45260.12e-90C2H2-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]