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 Ciclev10004533m
Common NameCICLE_v10004533mg
Organism
Citrus clementina
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus
Family C2H2
Protein Properties Length: 642aa    MW: 69355 Da    PI: 9.2862
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Ciclev10004533mgenomeICGCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H2163.4e-057294123
                     EEETTTTEEESSHHHHHHHHHHT CS
          zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                     + C+ C+k F r  nL+ H r H
  Ciclev10004533m 72 FICEVCNKGFQREQNLQLHRRGH 94
                     89*******************88 PP
2zf-C2H2130.00031148170123
                      EEETTTTEEESSHHHHHHHHHHT CS
          zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                      +kC++C+k++  +s+ k H +t+
  Ciclev10004533m 148 WKCEKCSKRYAVQSDWKAHSKTC 170
                      58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576673.17E-77194No hitNo description
Gene3DG3DSA:3.30.160.607.3E-67194IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.997294IPR007087Zinc finger, C2H2
PfamPF121713.2E-57294IPR022755Zinc finger, double-stranded RNA binding
SMARTSM003550.00527294IPR015880Zinc finger, C2H2-like
PROSITE patternPS0002807494IPR007087Zinc finger, C2H2
SMARTSM00355130113143IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.602.4E-5136169IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576673.17E-7143168No hitNo description
SMARTSM00355130148168IPR015880Zinc 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: 642 aa     Download sequence    Send to blast
MNMSASSSAP FFEIREDQNQ MKQQHSSTPT SSSAPPPVPP PQKKKRNQPG TPNPDAEVIA  60
LSPKTLMATN RFICEVCNKG FQREQNLQLH RRGHNLPWKL KQKTTKEVKR KVYLCPEPTC  120
VHHDPSRALG DLTGIKKHYS RKHGEKKWKC EKCSKRYAVQ SDWKAHSKTC GTREYRCDCG  180
TLFSRRDSFI THRAFCDALA QESARHQPSL SAIGSHLYAS TNNMALGLSQ VGPQLSSIKD  240
HHQPNQSGDI LCLGGSGSRS TPFDHLLSPS MGSSSSSFRP PQSLASTPFF MQESNQNYHE  300
EQQQHQQGLL PNKPPPFHGL MQFADLQNNP NNSNPVTNSA AAANNLFNLS FLSNSSSTNS  360
LSNSNSNNNN NNASNLMLSA AGGHHHHFNN NEQNGTASTG TGGVDHHQGT NNNLFTNNLI  420
SDHQISSGAV PSLFSTSSVH QNETMVPHMS ATALLQKAAQ MGSTSSNNNT ASLLRSFGGS  480
SSSSGSKPNN NNNNFGGVGN VFGGPGSSEN DNSSSIHDLM NPFAATNSSI FGTGSNDQVN  540
AFSGQDQNHH RRHHHHHPNY EAKLHHNMNA GMGGSDRMTR DFLGVGQIVR SVSGGFQQRE  600
KQQQQHGGVI DVSSLDSERN ITAPTSQSFG GGGGGGGGSF H*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C5e-34144205364Zinc finger protein JACKDAW
5b3h_F5e-34144205364Zinc finger protein JACKDAW
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Highly expressed in leaf tissues. {ECO:0000305|PubMed:22898356}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor acting as a positive regulator of the starch synthase SS4. Controls chloroplast development and starch granule formation (PubMed:22898356). 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:22898356, ECO:0000269|PubMed:24821766}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00255DAPTransfer from AT2G02070Download
Motif logo
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2084941e-134AC208494.1 Populus trichocarpa clone JGIACSB265-L05, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006420703.10.0protein indeterminate-domain 5, chloroplastic
SwissprotQ9ZUL31e-143IDD5_ARATH; Protein indeterminate-domain 5, chloroplastic
TrEMBLV4RIS40.0V4RIS4_9ROSI; Uncharacterized protein
STRINGXP_006420703.10.0(Citrus clementina)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM43732654
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G02070.11e-119indeterminate(ID)-domain 5
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]