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 Thecc1EG041071t1
Common NameTCM_041071
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 ARF
Protein Properties Length: 801aa    MW: 88190.4 Da    PI: 6.593
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Thecc1EG041071t1genomeCGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B375.94.6e-24166267199
                       EEEE-..-HHHHTT-EE--HHH.HTT.....---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSS CS
                B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.....ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrs 88 
                       f+k+lt sd++++g +++p++ ae++      ++++ s++l+ +d++g +W++++iyr++++r++lt+GW+ Fv++++L +gD v+F   + +
  Thecc1EG041071t1 166 FCKTLTASDTSTHGGFSVPRRAAEDCfppldYKQTRPSQELVAKDLHGVEWRFRHIYRGQPRRHLLTTGWSIFVSQKNLVAGDAVLFL--RGE 256
                       99****************************8444556789************************************************..449 PP

                       EE..EEEEE-S CS
                B3  89 efelvvkvfrk 99 
                       ++el+++++r+
  Thecc1EG041071t1 257 DGELRLGIRRA 267
                       999*****996 PP
2Auxin_resp120.31.5e-39292373182
        Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 
                       +a+a+stks+F+v+Y+Pras++eFvv+++k+ k ++++v+ G+Rfkm+fe++ds+ rr+sG+v+g+ d+dp+rWpnSkWr+L
  Thecc1EG041071t1 292 VANAISTKSMFHVFYSPRASHAEFVVPFQKYIKGITNPVCTGTRFKMRFEMDDSPDRRCSGVVTGIGDSDPYRWPNSKWRCL 373
                       689******************************************************************************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019362.62E-44158279IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.102.8E-41159278IPR015300DNA-binding pseudobarrel domain
CDDcd100175.95E-24164266No hitNo description
PfamPF023621.7E-22166267IPR003340B3 DNA binding domain
PROSITE profilePS5086313.014166268IPR003340B3 DNA binding domain
SMARTSM010197.2E-25166268IPR003340B3 DNA binding domain
PfamPF065071.0E-33292373IPR010525Auxin response factor
SuperFamilySSF542773.01E-10668752No hitNo description
PROSITE profilePS5174523.746672754IPR000270PB1 domain
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:0010050Biological Processvegetative phase change
GO:0010158Biological Processabaxial cell fate specification
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 801 aa     Download sequence    Send to blast
MEIDLNHAVN EVEKTALCNG DCDKSSACVY CLSSSSSSCS SNSASPPGSS SIYLELWHAC  60
AGPLASLPKK GNVVVYFPQG HLEQVSSASP FSPLEMATFD LPPQIFCKVV NVQLLANKEN  120
DEVYTQVTLL PQPELGGPNL ESKQLDELGV DEGGGGSPTK STPHMFCKTL TASDTSTHGG  180
FSVPRRAAED CFPPLDYKQT RPSQELVAKD LHGVEWRFRH IYRGQPRRHL LTTGWSIFVS  240
QKNLVAGDAV LFLRGEDGEL RLGIRRAVRP RNGLPDSVLA KQNSYPNVLS SVANAISTKS  300
MFHVFYSPRA SHAEFVVPFQ KYIKGITNPV CTGTRFKMRF EMDDSPDRRC SGVVTGIGDS  360
DPYRWPNSKW RCLMVRWDED IVSDHQERVS PWEIDPSVSL PPLSIQSSPR LKKLRTGLQA  420
APPDTPITGG GGFLDFEESV RSSKVLQGQE NVGFVSPLYG RDTVNCPLDF EMQSPAHQSL  480
ASTGIEKTNI SEFLRARATT YTGFAESNGF PKVLQGQEIC PLRSLTQKVD LNLGVWAKTN  540
LGCNSFNMHQ APKTNCYPLA SEGLRNMYFP YSDFYKAGQD PTMSSYTSTF LRGNVSFNPS  600
SIKTGVIVDS VRKPNPLNEH KPLENIASPA FRKNLRNQQD DCFKGNVAGC KLFGFSLTAE  660
SPTPNSQNSG KRSCTKVHKQ GSLVGRAIDL SRLNGYDDLM TELERLFSME GLLRDTDKGW  720
RVLYTDSEND VMVVGDDPWH EFCDVVSKIH IHTQEEVEKM TIGMASDDTQ SCLEQAPVIM  780
EASKSSSVGQ PDSSPTVIRV *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-125383962354Auxin response factor 1
4ldw_A1e-125383962354Auxin response factor 1
4ldw_B1e-125383962354Auxin response factor 1
4ldx_A1e-125383962354Auxin response factor 1
4ldx_B1e-125383962354Auxin response factor 1
4ldy_A1e-125383962354Auxin response factor 1
4ldy_B1e-125383962354Auxin 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). Could act as transcriptional activator or repressor. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. {ECO:0000269|PubMed:12036261}.
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_007015441.20.0PREDICTED: auxin response factor 4 isoform X1
SwissprotQ9ZTX90.0ARFD_ARATH; Auxin response factor 4
TrEMBLA0A061GT760.0A0A061GT76_THECC; Auxin response factor
STRINGEOY330600.0(Theobroma cacao)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM95302636
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G60450.10.0auxin response factor 4
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. Ozerova LV,Krasnikova MS,Troitsky AV,Solovyev AG,Morozov SY
    TAS3 Genes for small ta-siARF RNAs in plants belonging to subtribe Senecioninae: occurrence of prematurely terminated RNA precursors.
    Mol. Gen. Mikrobiol. Virusol., 2013.
    [PMID:24003511]
  3. Machida C,Nakagawa A,Kojima S,Takahashi H,Machida Y
    The complex of ASYMMETRIC LEAVES (AS) proteins plays a central role in antagonistic interactions of genes for leaf polarity specification in Arabidopsis.
    Wiley Interdiscip Rev Dev Biol, 2015 Nov-Dec. 4(6): p. 655-71
    [PMID:26108442]
  4. Pashkovskiy PP,Kartashov AV,Zlobin IE,Pogosyan SI,Kuznetsov VV
    Blue light alters miR167 expression and microRNA-targeted auxin response factor genes in Arabidopsis thaliana plants.
    Plant Physiol. Biochem., 2016. 104: p. 146-54
    [PMID:27031426]
  5. Matsumura Y, et al.
    A genetic link between epigenetic repressor AS1-AS2 and a putative small subunit processome in leaf polarity establishment of Arabidopsis.
    Biol Open, 2016. 5(7): p. 942-54
    [PMID:27334696]
  6. Guan C, et al.
    Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis.
    Curr. Biol., 2017. 27(19): p. 2940-2950.e4
    [PMID:28943086]
  7. Liu Z, et al.
    ARF2-ARF4 and ARF5 are Essential for Female and Male Gametophyte Development in Arabidopsis.
    Plant Cell Physiol., 2018. 59(1): p. 179-189
    [PMID:29145642]