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 Thecc1EG029792t6
Common NameTCM_029792
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: 544aa    MW: 60035.3 Da    PI: 9.3004
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Thecc1EG029792t6genomeCGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B346.37.6e-151534599
                      EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE-S CS
                B3 45 sWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvfrk 99
                      +W++++iyr++++r++lt+GW+ Fv+ ++L +gD v+F   + +++el+++++r+
  Thecc1EG029792t6  1 EWRFRHIYRGQPRRHLLTTGWSAFVNKKKLVSGDAVLFL--RGEDGELRLGIRRA 53
                      6**************************************..449999*****996 PP
2Auxin_resp126.32.1e-4178159182
        Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 
                       ++ha+s+ksvF+++YnPras+seF+++v+k+ k+l+++++vGmRfkm+feted++err++G+v+g+sd+dpvrWp+SkWr+L
  Thecc1EG029792t6  78 VVHAISMKSVFSIYYNPRASSSEFIIPVHKFWKSLDHSFAVGMRFKMRFETEDAAERRYTGLVTGISDMDPVRWPGSKWRCL 159
                       689******************************************************************************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019368.24E-14161IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.101.1E-17156IPR015300DNA-binding pseudobarrel domain
PROSITE profilePS5086312.351154IPR003340B3 DNA binding domain
CDDcd100175.70E-10152No hitNo description
PfamPF023623.7E-12153IPR003340B3 DNA binding domain
PfamPF065076.1E-3678159IPR010525Auxin 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:0010050Biological Processvegetative phase change
GO:0010158Biological Processabaxial cell fate specification
GO:0010582Biological Processfloral meristem determinacy
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 544 aa     Download sequence    Send to blast
EWRFRHIYRG QPRRHLLTTG WSAFVNKKKL VSGDAVLFLR GEDGELRLGI RRAAQIKNGT  60
SFPSLCSQQL NRSNFADVVH AISMKSVFSI YYNPRASSSE FIIPVHKFWK SLDHSFAVGM  120
RFKMRFETED AAERRYTGLV TGISDMDPVR WPGSKWRCLL VRWDDIDANR HSRVSPWEIE  180
LSGTISSSNN LLTPGVKRNR IGLPSGKPEF MVPDGIGASD FGEPLRFQKV LQGQEILGFN  240
TLYDGADGQN LHRSEIRRCF PGSNGSGIVA IGNVGRDPLG NSEISYRGVG FGESFRFHKV  300
LQGQEIYVSP PYIRGPTTND TQENDGLGVR DAGQFSGTRS GWSSLMQSYN THSHIRPSAP  360
SAQVSSPSSV LMFQQASNPI PNINPIYSVN NQEKEQGVDN RSSFRAPEMY GGKLLQSSTG  420
ECSSRGRHHG TFDSFGHSND SVQLGDSQPL AAQPTFRTSQ DIASSCKSSC RLFGFSLTEG  480
SQDANKEDNM VKATSSLGPR AFLPCIGEQF HPKPPAVTNT VGSNCTKVSN LYAVRDMLFD  540
IAL*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldy_A3e-561188173361Auxin response factor 1
4ldy_B3e-561188173361Auxin 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).
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00021PBMTransfer from AT2G33860Download
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_007025521.20.0PREDICTED: auxin response factor 3 isoform X2
SwissprotQ8S9851e-123ARFO_ORYSJ; Auxin response factor 15
TrEMBLA0A061GFF50.0A0A061GFF5_THECC; Auxin response factor
STRINGEOY281430.0(Theobroma cacao)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G33860.11e-118ARF family protein
Publications ? help Back to Top
  1. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]
  2. Cheng CH, et al.
    A fine physical map of the rice chromosome 5.
    Mol. Genet. Genomics, 2005. 274(4): p. 337-45
    [PMID:16261349]
  3. Khanday I,Yadav SR,Vijayraghavan U
    Rice LHS1/OsMADS1 controls floret meristem specification by coordinated regulation of transcription factors and hormone signaling pathways.
    Plant Physiol., 2013. 161(4): p. 1970-83
    [PMID:23449645]
  4. 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]