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 Ciclev10011592m
Common NameCICLE_v10011592mg
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: 489aa    MW: 52804.2 Da    PI: 9.9781
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Ciclev10011592mgenomeICGCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H216.22.9e-056486123
                     EEETTTTEEESSHHHHHHHHHHT CS
          zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                     + C++C+k F r  nL+ H r H
  Ciclev10011592m 64 FICEICNKGFQRDQNLQLHRRGH 86
                     89*******************88 PP
2zf-C2H212.80.00036141163123
                      EEETTTTEEESSHHHHHHHHHHT CS
          zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                      +kC++C+k +  +s+ k H +t+
  Ciclev10011592m 141 WKCEKCSKKYAVQSDWKAHSKTC 163
                      58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.601.3E-56386IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576675.56E-76386No hitNo description
PROSITE profilePS5015710.8456486IPR007087Zinc finger, C2H2
SMARTSM003550.0226486IPR015880Zinc finger, C2H2-like
PfamPF121715.8E-56486IPR022755Zinc finger, double-stranded RNA binding
PROSITE patternPS0002806686IPR007087Zinc finger, C2H2
SMARTSM00355110106136IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.2E-4129162IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576675.56E-7136161No hitNo description
SMARTSM00355140141161IPR015880Zinc 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: 489 aa     Download sequence    Send to blast
MMSGNAFTIP SSLGGFVHQE QNPNPNPKPN QAASKKKRNL PGTPDPDAEV IALSPKTLMA  60
TNRFICEICN KGFQRDQNLQ LHRRGHNLPW KLRQRTNKDV IKKKVYICPE KTCVHHEPSR  120
ALGDLTGIKK HFSRKHGEKK WKCEKCSKKY AVQSDWKAHS KTCGTREYKC DCGTLFSRKD  180
SFITHRAFCD ALAEESTRLA SSVVAAASNL NFRTDHTVNL PQGVPQDVAG SISQFGSGFA  240
GLAEMVQIGS VSNNLFGSSS SNMGNFGHQF QGFHKSMAGA TTNSKSANLT LLSELKEETS  300
CLYNSDSTHE NKQLKPVAVG PMSATALLQK AAQMGSTRSN NNPITSIFGN GSGFNNVMSS  360
SSSSSNATSY NNNTSLHNTN LSGSAVTLAT SDGVMGSSNL RSMNTTATAA AVATSDTLNQ  420
LMMMQTRGDQ QNEQQQQVQL KLTRDFLGMT SGNQGQSVRP FLPQELANFA SNIGSVSPIG  480
LSQFTSNN*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C1e-37137201367Zinc finger protein JACKDAW
5b3h_F1e-37137201367Zinc finger protein JACKDAW
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Start to accumulate during the 16- to 32-cell stage of embryogenesis. {ECO:0000269|PubMed:17785527}.
UniprotTISSUE SPECIFICITY: Expressed in the quiescent center, the ground tissue stem cells and to a lesser extent in mature cortex and endodermis cells. {ECO:0000269|PubMed:17785527}.
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}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006428811.10.0zinc finger protein JACKDAW
SwissprotQ700D21e-145IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBLV4SXX20.0V4SXX2_9ROSI; Uncharacterized protein
STRINGXP_006428811.10.0(Citrus clementina)
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]