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 Thecc1EG018404t1
Common NameTCM_018404
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 B3
Protein Properties Length: 342aa    MW: 38150.3 Da    PI: 8.2188
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Thecc1EG018404t1genomeCGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B335.81.4e-1167134183
                       EEEE-..-HHHHTT-EE--HHH.HTT---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEE CS
                B3   1 ffkvltpsdvlksgrlvlpkkfaeehggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFk 83 
                       f+k+lt+ d++ +g +++p +fa+++  +  +   l+         +++    ++++r++lt+GWk+Fv++++L +gD +vF 
  Thecc1EG018404t1  67 FCKTLTTLDASLHGGFSVPMSFADQCL-P--Q---LV-------HVNLRG--LRQPRRHLLTSGWKDFVNSKRLGAGDAFVFL 134
                       899999999999999999999998883.2..2...33.......233444..899***************************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.104.9E-1563170IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019362.35E-1464136IPR015300DNA-binding pseudobarrel domain
CDDcd100172.76E-1365159No hitNo description
SMARTSM010190.001967150IPR003340B3 DNA binding domain
PfamPF023624.9E-1067134IPR003340B3 DNA binding domain
PROSITE profilePS508638.79799161IPR003340B3 DNA binding domain
PfamPF065071.3E-4213238IPR010525Auxin response factor
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009734Biological Processauxin-activated signaling pathway
GO:0005634Cellular Componentnucleus
GO:0016021Cellular Componentintegral component of membrane
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 342 aa     Download sequence    Send to blast
MPVSLSLLKH LQALHSTINV QLKADPETDE VLAQVTLLPE INISQEENDA EMEPPFPPLP  60
EFRVHSFCKT LTTLDASLHG GFSVPMSFAD QCLPQLVHVN LRGLRQPRRH LLTSGWKDFV  120
NSKRLGAGDA FVFLGFAFVL NLMIMMRGEN GELCVGVRRA MKPRSNVSAS ISIFGMYLSV  180
LATTWEALAR RTMFAISYKP SFSIYFFTIC YCEFSGTIVG IEDADPIKWP GSKRRCLKVF  240
RLCEMGWNLY HNSSGKVSPW KIELALTYTI LSPLPMPWPE PNMVPLSPNS SVLTQEGILK  300
SQVYHLGSLR VTIQPSQGSG FSRVSQCHEI STFGDNFAKM N*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldy_A9e-491826978359Auxin response factor 1
4ldy_B9e-491826978359Auxin response factor 1
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtAuxin response factors (ARFs) are transcriptional factors that bind specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs) (By similarity). Could act as transcriptional activator or repressor (PubMed:26959229, PubMed:26716451, PubMed:27645097, PubMed:28167023). Involved in the control of fruit ripening process (PubMed:26959229, PubMed:26716451, PubMed:28167023). Regulates expression of a number of ripening regulators, transcription factors, and ethylene biosynthesis and signaling components (PubMed:26959229, PubMed:26716451). May act as a transcriptional repressor of auxin-responsive genes (PubMed:26716451). Regulates vegetative growth, lateral root formation and flower organ senescence, possibly partially by regulating gene expression of auxin and ethylene response factor (ERF) genes (PubMed:28167023). Plays a negative role in axillary shoot meristem formation (PubMed:27645097). {ECO:0000255|RuleBase:RU004561, ECO:0000269|PubMed:26716451, ECO:0000269|PubMed:26959229, ECO:0000269|PubMed:27645097, ECO:0000269|PubMed:28167023}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By tomato fruit ripening. Expression in tomato fruits is up-regulated by exogenous application of ethylene and down-regulated by inhibition of ethylene receptors with 1-methylcyclopropene (1-MCP) (PubMed:26959229, PubMed:26716451). Up-regulated by plant hormone abscisic acid (ABA) in tomato fruits (PubMed:26959229). Expression is not up-regulated by plant hormone auxin in tomato fruits (PubMed:26716451). Up-regulated by auxin and gibberellic acid (GA), and down-regulated by ethylene in seedlings (PubMed:28167023). Down-regulated during decapitation-induced axillary shoot development and by excision of immature leaves. Down-regulation is inhibited by the application of auxin on the cut surface (PubMed:27645097). {ECO:0000269|PubMed:26716451, ECO:0000269|PubMed:26959229, ECO:0000269|PubMed:27645097, ECO:0000269|PubMed:28167023}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_021297666.11e-143auxin response factor 2-like
SwissprotQ2LAJ32e-81ARF2A_SOLLC; Auxin response factor 2A
TrEMBLA0A061EEH20.0A0A061EEH2_THECC; Auxin response factor
STRINGEOY033950.0(Theobroma cacao)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G62000.32e-75auxin response factor 2
Publications ? help Back to Top
  1. Tomato Genome Consortium
    The tomato genome sequence provides insights into fleshy fruit evolution.
    Nature, 2012. 485(7400): p. 635-41
    [PMID:22660326]
  2. 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]
  3. Breitel DA, et al.
    AUXIN RESPONSE FACTOR 2 Intersects Hormonal Signals in the Regulation of Tomato Fruit Ripening.
    PLoS Genet., 2016. 12(3): p. e1005903
    [PMID:26959229]
  4. Xu T, et al.
    SlARF2a plays a negative role in mediating axillary shoot formation.
    Sci Rep, 2016. 6: p. 33728
    [PMID:27645097]
  5. Ren Z,Liu R,Gu W,Dong X
    The Solanum lycopersicum auxin response factor SlARF2 participates in regulating lateral root formation and flower organ senescence.
    Plant Sci., 2017. 256: p. 103-111
    [PMID:28167023]