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 Thecc1EG022127t1
Common NameTCM_022127
Organism
Theobroma cacao
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma
Family C2H2
Protein Properties Length: 495aa    MW: 53620 Da    PI: 9.7437
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Thecc1EG022127t1genomeCGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H216.23e-056385123
                      EEETTTTEEESSHHHHHHHHHHT CS
           zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                      + C++C+k F r  nL+ H r H
  Thecc1EG022127t1 63 FICEICNKGFQRDQNLQLHRRGH 85
                      89*******************88 PP
2zf-C2H212.80.00037139161123
                       EEETTTTEEESSHHHHHHHHHHT CS
           zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                       +kC++C+k +  +s+ k H +t+
  Thecc1EG022127t1 139 WKCEKCSKKYAVQSDWKAHSKTC 161
                       58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576675.22E-76285No hitNo description
Gene3DG3DSA:3.30.160.601.3E-56285IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.0226385IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.8456385IPR007087Zinc finger, C2H2
PfamPF121715.9E-56385IPR022755Zinc finger, double-stranded RNA binding
PROSITE patternPS0002806585IPR007087Zinc finger, C2H2
SMARTSM0035579104134IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.603.7E-5127160IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576675.22E-7134159No hitNo description
SMARTSM00355140139159IPR015880Zinc 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: 495 aa     Download sequence    Send to blast
MSGDAFSMPV SRGGFVQDQN NANPNPKANP NPVKKKRNLP GTPDPDAEVI ALSPKTLMAT  60
NRFICEICNK GFQRDQNLQL HRRGHNLPWK LRQRTNKEVR KKVYICPEKT CVHHDPSRAL  120
GDLTGIKKHY SRKHGEKKWK CEKCSKKYAV QSDWKAHSKT CGTREYKCDC GTLFSRKDSF  180
ITHRAFCDAL AEESARLTSV AATNLNFRND TVNLPHGFAG RGVQDVAGIS QLGSGFGQDF  240
TGMPAAGLPE IVQMASGNLF GSSSLTNFDN HGHFPGFDKS GATSTNANLS LSPLPQGLKE  300
EGGSKGNLME SLSSLYSETQ NKQPKPAAPM SATALLQKAA QMGSTRSNPS FFGNSFGVMS  360
SSSSHTVSLS STQDRNDQLH QVYPNHVKEQ ETFMASSSVS MSTDAGLGSS NLNSVASATS  420
NNLEQLMLQT GAKHSNPSQL KMHHPGSNSI DQSLTRDFLG MSNDQSARPF LPQDLAKFAS  480
IGSTMGLSQF TSNH*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C1e-38135204372Zinc finger protein JACKDAW
5b3h_F1e-38135204372Zinc finger protein JACKDAW
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
189101KLRQRTNKEVRKK
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_007027297.20.0PREDICTED: zinc finger protein JACKDAW
SwissprotQ700D21e-150IDD10_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-126C2H2-like zinc finger protein
Publications ? help Back to Top
  1. Motamayor JC, et al.
    The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color.
    Genome Biol., 2013. 14(6): p. r53
    [PMID:23731509]
  2. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]
  3. 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]
  4. 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]
  5. 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]
  6. 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]