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 Thecc1EG021101t1
Common NameTCM_021101
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 SBP
Protein Properties Length: 808aa    MW: 90849.4 Da    PI: 6.6389
Description SBP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Thecc1EG021101t1genomeCGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SBP119.31.9e-37139214176
                       --SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S- CS
               SBP   1 lCqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkk 76 
                       +Cqv+gCead+se+k yhrrh+vC  ++++++vl++g+++r+CqqC++fh ls+fDe+krsCrr+L++hn+rrr+k
  Thecc1EG021101t1 139 RCQVPGCEADISELKGYHRRHRVCLRCANSSTVLIDGETKRYCQQCGKFHLLSDFDEGKRSCRRKLERHNNRRRRK 214
                       6************************************************************************997 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:4.10.1100.101.1E-28134201IPR004333Transcription factor, SBP-box
PROSITE profilePS5114129.735137214IPR004333Transcription factor, SBP-box
SuperFamilySSF1036122.35E-33138217IPR004333Transcription factor, SBP-box
PfamPF031101.8E-27140214IPR004333Transcription factor, SBP-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0055070Biological Processcopper ion homeostasis
GO:0005634Cellular Componentnucleus
GO:0016021Cellular Componentintegral component of membrane
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 808 aa     Download sequence    Send to blast
MERAPSSPTT QTPRGARRSK DPEMDVHVGV NEADPTSSVW DWGDLLDFTV DDHFSISFDD  60
ENLSPYPLEA PAPDSDPVPG PDRVRKRDPR LTCSNFLAGR IPCACPEIDE QIEKLEEEEA  120
GAPGKKRART GRIGSGTCRC QVPGCEADIS ELKGYHRRHR VCLRCANSST VLIDGETKRY  180
CQQCGKFHLL SDFDEGKRSC RRKLERHNNR RRRKPVGSKT VANNESQGAV QSEDVACDGE  240
AGKDGSSLSG QIAEEEAAFE SEDGRGSTHC SAPMLQSVNN DSVVTLIDTE MDGRKDDSKF  300
SLSTSSCDNK TAYSSMCPTG RISFKLYDWN PAEFPRRLRH QIFQWLANMP VELEGYIRPG  360
CIILTVFISM PKNMWNKLSE NPMTYMHDFV FTPGRMLYGR GFMTIYLNDM IFRTRKDGTS  420
MVKIDMEMQA PRLHYVYPAC FEAGKPMEFV ACGSNLLQPK FRFLVSFAGR YLAYDYCVAS  480
PHVQSKGDSP SCDHRLYKIH VPLTEPDLFG PAFIEVENQS GLSNFIPVLI GDKEVCSEMK  540
SIQKRFDASL FPGGSKMSAT GSLLEACEAS SLRQRTYSEL VLDIAWLLRE PKLENFQEMM  600
ASSQIQRFNC LLSFLIHNES TVILKKVLQN LKILVEKTGF NGANDSDIRL FEKHMDYARD  660
ILSIKLQKGE SLVLHSEYIE RERNWCLQSS FKDDELSVVP NAFQDLEERT NGKLRAMTAS  720
TSFTRSETVP LLNREIIMNV NLNKECPRKS CSPIFTATTL RSRPAVLILA TAAICLGMCA  780
VLFHPNKVGE FAVTIRRCLF DRVVDVE*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1ul5_A3e-42139222588squamosa promoter binding protein-like 7
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1200212RRKLERHNNRRRR
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that participates in reprogramming global gene expression during copper deficiency in order to improve the metal uptake and prioritize its distribution to copper proteins of major importance (Probable). Binds directly to 5'-GTAC-3' motifs in the microRNA (miRNA) promoter of the stress-responsive miRNAs miR398b and miR398c to activate their transcription. During copper deficiency, activates the copper transporters COPT1 and COPT2, and the copper chaperone CCH, directly or indirectly via miRNAs. Required for the expression of the miRNAs miR397, miR408 and miR857 (PubMed:19122104). Acts coordinately with HY5 to regulate miR408 and its target genes in response to changes in light and copper conditions (PubMed:25516599). Activates miR857 and its target genes in response to low copper conditions (PubMed:26511915). Involved in cadmium stress response by regulating miR397a, miR398b, miR398c and miR857 (PubMed:27352843). Required for iron homeostasis during copper deficiency (PubMed:22374396). {ECO:0000269|PubMed:19122104, ECO:0000269|PubMed:22374396, ECO:0000269|PubMed:25516599, ECO:0000269|PubMed:26511915, ECO:0000269|PubMed:27352843}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00604PBMTransfer from AT5G18830Download
Motif logo
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_007035425.20.0PREDICTED: squamosa promoter-binding-like protein 7
SwissprotQ8S9G80.0SPL7_ARATH; Squamosa promoter-binding-like protein 7
TrEMBLA0A061END10.0A0A061END1_THECC; Squamosa promoter binding protein-like 7, putative
STRINGEOY063510.0(Theobroma cacao)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM63582644
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G18830.10.0squamosa promoter binding protein-like 7
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. Zhang H, et al.
    MicroRNA408 is critical for the HY5-SPL7 gene network that mediates the coordinated response to light and copper.
    Plant Cell, 2014. 26(12): p. 4933-53
    [PMID:25516599]
  3. Zhao Y, et al.
    MicroRNA857 Is Involved in the Regulation of Secondary Growth of Vascular Tissues in Arabidopsis.
    Plant Physiol., 2015. 169(4): p. 2539-52
    [PMID:26511915]
  4. Perea-García A, et al.
    Modulation of copper deficiency responses by diurnal and circadian rhythms in Arabidopsis thaliana.
    J. Exp. Bot., 2016. 67(1): p. 391-403
    [PMID:26516126]
  5. Gielen H,Remans T,Vangronsveld J,Cuypers A
    Toxicity responses of Cu and Cd: the involvement of miRNAs and the transcription factor SPL7.
    BMC Plant Biol., 2016. 16(1): p. 145
    [PMID:27352843]
  6. Yan J, et al.
    Arabidopsis Pollen Fertility Requires the Transcription Factors CITF1 and SPL7 That Regulate Copper Delivery to Anthers and Jasmonic Acid Synthesis.
    Plant Cell, 2017. 29(12): p. 3012-3029
    [PMID:29114014]
  7. Araki R, et al.
    SPL7 locally regulates copper-homeostasis-related genes in Arabidopsis.
    J. Plant Physiol., 2018.
    [PMID:29635212]