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 AT3G45260.1
Common NameF18N11.20, IDD9, IDZ1
Organism
Arabidopsis thaliana
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family C2H2
Protein Properties Length: 446aa    MW: 49940.7 Da    PI: 9.8547
Description C2H2-like zinc finger protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT3G45260.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H219.13.6e-066890123
                 EEETTTTEEESSHHHHHHHHHHT CS
      zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                 + C+ C+k F+r  nL+ H r H
  AT3G45260.1 68 FICEVCNKGFKRDQNLQLHRRGH 90
                 89*******************88 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576671.01E-76790No hitNo description
Gene3DG3DSA:3.30.160.603.4E-66790IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PfamPF121711.9E-56890IPR022755Zinc finger, double-stranded RNA binding
PROSITE profilePS5015710.8876890IPR007087Zinc finger, C2H2
SMARTSM003550.0136890IPR015880Zinc finger, C2H2-like
PROSITE patternPS0002807090IPR007087Zinc finger, C2H2
SMARTSM00355110110140IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.604.3E-4133166IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576671.01E-7140165No hitNo description
SMARTSM00355200145165IPR015880Zinc finger, C2H2-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
GO:0008270Molecular Functionzinc ion binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009005anatomyroot
PO:0009006anatomyshoot system
PO:0009025anatomyvascular leaf
PO:0009029anatomystamen
PO:0009031anatomysepal
PO:0009047anatomystem
PO:0020030anatomycotyledon
PO:0020038anatomypetiole
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
PO:0001054developmental stagevascular leaf senescent stage
PO:0007064developmental stageLP.12 twelve leaves visible stage
PO:0007095developmental stageLP.08 eight leaves visible stage
PO:0007098developmental stageLP.02 two leaves visible stage
PO:0007103developmental stageLP.10 ten leaves visible stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 446 aa     Download sequence    Send to blast
MMMPDDHHPL SFPSYVLHQE HIAPNPNPNP NPTSSNSAKR KRNLPGNPDP DAEVIALSPN  60
SLMTTNRFIC EVCNKGFKRD QNLQLHRRGH NLPWKLKQRT NKEQVKKKVY ICPEKTCVHH  120
DPARALGDLT GIKKHFSRKH GEKKWKCDKC SKKYAVMSDW KAHSKICGTK EYRCDCGTLF  180
SRKDSFITHR AFCDALAEES ARFVSVPPAP AYLNNALDVE VNHGNINQNH QQRQLNTTSS  240
QLDQPGFNTN RNNIAFLGQT LPTNVFASSS SPSPRSASDS LQNLWHLQGQ SSHQWLLNEN  300
NNNNNNILQR GISKNQEEHE MKNVISNGSL FSSEARNNTN NYNQNGGQIA SMSATALLQK  360
AAQMGSKRSS SSSSNSKTFG LMTSIFNNKQ AENIKTKEVD ERGFTRDFLG VGSQHRSWPL  420
LMVNHNLPDS SPPASTDGTP TADMNQ
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C6e-35141206368Zinc finger protein JACKDAW
5b3h_F6e-35141206368Zinc finger protein JACKDAW
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.222830.0bud| leaf
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO425655650.0
Genevisible252573_at0.0
Expression AtlasAT3G45260-
AtGenExpressAT3G45260-
ATTED-IIAT3G45260-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in roots, especially in vascular initials, cortex, endodermis, and quiescent center (QC). {ECO:0000269|PubMed:25829440}.
Functional Description ? help Back to Top
Source Description
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
PlantRegMapAT3G45260.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Interaction ? help Back to Top
Source Intact With
BioGRIDAT1G50420
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT3G45260
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF4283020.0AF428302.1 Arabidopsis thaliana AT3g45260/F18N11_20 mRNA, complete cds.
GenBankAJ6214930.0AJ621493.1 Arabidopsis thaliana mRNA for ID1-like zinc finger protein 1 (idz1 gene).
GenBankAY1439360.0AY143936.1 Arabidopsis thaliana At3g45260/F18N11_20 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001327332.10.0C2H2-like zinc finger protein
RefseqNP_566877.10.0C2H2-like zinc finger protein
SwissprotQ944L30.0IDD9_ARATH; Zinc finger protein BALDIBIS
TrEMBLD7LNN70.0D7LNN7_ARALL; Zinc finger family protein
STRINGAT3G45260.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM15528306
Representative plantOGRP9516242
Publications ? help Back to Top
  1. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  2. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  3. Englbrecht CC,Schoof H,B
    Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome.
    BMC Genomics, 2004. 5(1): p. 39
    [PMID:15236668]
  4. Colasanti J, et al.
    The maize INDETERMINATE1 flowering time regulator defines a highly conserved zinc finger protein family in higher plants.
    BMC Genomics, 2006. 7: p. 158
    [PMID:16784536]
  5. Morita MT, et al.
    A C2H2-type zinc finger protein, SGR5, is involved in early events of gravitropism in Arabidopsis inflorescence stems.
    Plant J., 2006. 47(4): p. 619-28
    [PMID:16813575]
  6. Yoshida H, et al.
    DELLA protein functions as a transcriptional activator through the DNA binding of the indeterminate domain family proteins.
    Proc. Natl. Acad. Sci. U.S.A., 2014. 111(21): p. 7861-6
    [PMID:24821766]
  7. Long Y, et al.
    Arabidopsis BIRD Zinc Finger Proteins Jointly Stabilize Tissue Boundaries by Confining the Cell Fate Regulator SHORT-ROOT and Contributing to Fate Specification.
    Plant Cell, 2015. 27(4): p. 1185-99
    [PMID:25829440]
  8. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]