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 Thecc1EG015919t1
Common NameTCM_015919
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 HD-ZIP
Protein Properties Length: 301aa    MW: 33387.6 Da    PI: 7.969
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Thecc1EG015919t1genomeCGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox59.55.5e-19138192256
                       T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
          Homeobox   2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                       rk+ +++k+q  +Lee F+++++++ +++  LAk+lgL  rqV vWFqNrRa+ k
  Thecc1EG015919t1 138 RKKLRLSKDQSAILEESFKEHNTLNPKQKLALAKQLGLRPRQVEVWFQNRRARTK 192
                       788899***********************************************98 PP
2HD-ZIP_I/II129.61.2e-41138227191
       HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeveeLreel 91 
                       +kk+rlsk+q+++LEesF+e+++L+p++K +la++Lgl+prqv+vWFqnrRARtk+kq+E+d+e+Lkr++++l+een+rL+kev+eLr +l
  Thecc1EG015919t1 138 RKKLRLSKDQSAILEESFKEHNTLNPKQKLALAKQLGLRPRQVEVWFQNRRARTKLKQTEVDCEFLKRCCENLTEENRRLQKEVQELR-AL 227
                       69*************************************************************************************9.55 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046181.1E-322112IPR006712HD-ZIP protein, N-terminal
Gene3DG3DSA:1.10.10.604.7E-18120195IPR009057Homeodomain-like
SuperFamilySSF466891.0E-18129195IPR009057Homeodomain-like
PROSITE profilePS5007117.394134194IPR001356Homeobox domain
SMARTSM003891.2E-16136198IPR001356Homeobox domain
PfamPF000462.0E-16138192IPR001356Homeobox domain
CDDcd000864.35E-16138195No hitNo description
PRINTSPR000312.0E-5165174IPR000047Helix-turn-helix motif
PROSITE patternPS000270169192IPR017970Homeobox, conserved site
PRINTSPR000312.0E-5174190IPR000047Helix-turn-helix motif
SMARTSM003404.2E-27194237IPR003106Leucine zipper, homeobox-associated
PfamPF021832.3E-11194228IPR003106Leucine zipper, homeobox-associated
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0008283Biological Processcell proliferation
GO:0009641Biological Processshade avoidance
GO:0009733Biological Processresponse to auxin
GO:0009735Biological Processresponse to cytokinin
GO:0009826Biological Processunidimensional cell growth
GO:0010016Biological Processshoot system morphogenesis
GO:0010017Biological Processred or far-red light signaling pathway
GO:0010218Biological Processresponse to far red light
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:0048364Biological Processroot development
GO:0005634Cellular Componentnucleus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0042803Molecular Functionprotein homodimerization activity
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 301 aa     Download sequence    Send to blast
MMVGKEDLGL SLSLSFPQNH HSLQLNLRPS LVPSSANSCS SPSGLTLQKP SWNDASTPSD  60
PISESCRAET RSFLRGIDVN RLPSAVDCEE EAGVSSPNST ISSVSGKRSE REGNGDEHEI  120
ERACSRGISD EEDGDTSRKK LRLSKDQSAI LEESFKEHNT LNPKQKLALA KQLGLRPRQV  180
EVWFQNRRAR TKLKQTEVDC EFLKRCCENL TEENRRLQKE VQELRALKLS PQFYMQMTPP  240
TTLTMCPSCE RVAVPPNAAS TVDPRSHQLG QTHHRPIPIN PWAPAAPIPH GPLDALRPRS  300
*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1136142SRKKLRL
2186194RRARTKLKQ
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in the negative regulation of cell elongation and specific cell proliferation processes such as lateral root formation and secondary growth of the vascular system. Acts as mediator of the red/far-red light effects on leaf cell expansion in the shading response. Binds to the DNA sequence 5'-CAAT[GC]ATTG-3'. Negatively regulates its own expression. {ECO:0000269|PubMed:10477292, ECO:0000269|PubMed:11260495, ECO:0000269|PubMed:8449400}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Rapidly and strongly induced by lowering the ratio of red to far-red light. {ECO:0000269|PubMed:8106086}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankHM1347910.0HM134791.1 Gossypium hirsutum homeodomain-leucine zipper protein HD2 (HB2) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_007039762.20.0PREDICTED: homeobox-leucine zipper protein HAT4
SwissprotQ054661e-120HAT4_ARATH; Homeobox-leucine zipper protein HAT4
TrEMBLA0A061G4E40.0A0A061G4E4_THECC; Homeobox-leucine zipper protein 4 / HD-ZIP protein
STRINGEOY242630.0(Theobroma cacao)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM15632690
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G16780.11e-105homeobox protein 2
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. Carabelli M,Turchi L,Ruzza V,Morelli G,Ruberti I
    Homeodomain-Leucine Zipper II family of transcription factors to the limelight: central regulators of plant development.
    Plant Signal Behav, 2014.
    [PMID:23838958]
  3. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  4. Francisco M, et al.
    Genome Wide Association Mapping in Arabidopsis thaliana Identifies Novel Genes Involved in Linking Allyl Glucosinolate to Altered Biomass and Defense.
    Front Plant Sci, 2016. 7: p. 1010
    [PMID:27462337]
  5. Müller-Moulé P, et al.
    YUCCA auxin biosynthetic genes are required for Arabidopsis shade avoidance.
    PeerJ, 2016. 4: p. e2574
    [PMID:27761349]
  6. Ivarson E, et al.
    Effects of Overexpression of WRI1 and Hemoglobin Genes on the Seed Oil Content of Lepidium campestre.
    Front Plant Sci, 2016. 7: p. 2032
    [PMID:28119714]
  7. Kasulin L, et al.
    A single haplotype hyposensitive to light and requiring strong vernalization dominates Arabidopsis thaliana populations in Patagonia, Argentina.
    Mol. Ecol., 2017. 26(13): p. 3389-3404
    [PMID:28316114]
  8. Singh M,Gupta A,Singh D,Khurana JP,Laxmi A
    Arabidopsis RSS1 Mediates Cross-Talk Between Glucose and Light Signaling During Hypocotyl Elongation Growth.
    Sci Rep, 2017. 7(1): p. 16101
    [PMID:29170398]