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 Thecc1EG004526t1
Common NameTCM_004526
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: 756aa    MW: 85514.9 Da    PI: 7.971
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Thecc1EG004526t1genomeCGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B376.53e-24187289199
                       EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SS CS
                B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgr 87 
                       f k+ltpsd++++g +++pk++a++       +++++ +++l+  d++g +W++++i+r++++r++lt+GW+ Fv +++L +gD+++F   + 
  Thecc1EG004526t1 187 FSKKLTPSDTNTHGGFSVPKRHADDGclppldMSQHTPQQDLVAIDLHGSEWRFRHIFRGQPKRHLLTSGWSTFVTSKKLVAGDTFIFL--RG 277
                       88*********************888*****9556666679************************************************..34 PP

                       SEE..EEEEE-S CS
                B3  88 sefelvvkvfrk 99 
                       +++el+v+v+r+
  Thecc1EG004526t1 278 DNGELHVGVHRA 289
                       89999****997 PP
2Auxin_resp100.72e-33314396183
        Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                       a ha+st+s+F+++Y+P++s+seF++++++++k+ ++ +s+G+Rf+m+ e++++ e+r  Gt++g++d+d +rWpnS+Wr+Lk
  Thecc1EG004526t1 314 AFHAFSTRSMFTIYYRPWTSSSEFIIPLDQYMKSAEIVYSIGTRFRMQSEGKECGEQRALGTIIGTEDVDHIRWPNSEWRCLK 396
                       679******************************************************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.01E-30181316IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.103.2E-36183301IPR015300DNA-binding pseudobarrel domain
CDDcd100177.70E-21185288No hitNo description
SMARTSM010193.2E-19187290IPR003340B3 DNA binding domain
PROSITE profilePS5086313.084187290IPR003340B3 DNA binding domain
PfamPF023629.5E-21187289IPR003340B3 DNA binding domain
PfamPF065073.0E-30314396IPR010525Auxin response factor
SuperFamilySSF542771.47E-9654734No hitNo description
PROSITE profilePS5174518.925657741IPR000270PB1 domain
PfamPF023093.3E-7697736IPR033389AUX/IAA 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:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 756 aa     Download sequence    Send to blast
MPFLFSLSLL LLICCIFLIL GKKVSFFYSV SSFWIYRKER KREMYGERNG VKAKVTSKSR  60
KHIDVDGLRR PPNNQGEKDD LYVKLWHACA GPSVYAPRAG EKVFYFPQGH MEQVEAYMNK  120
DGTMEMPIYN LPSKILCRVA HVQLKAETGT DEVFAQITLL PEAEQDELSM EHRNYQALPR  180
EAHPRIFSKK LTPSDTNTHG GFSVPKRHAD DGCLPPLDMS QHTPQQDLVA IDLHGSEWRF  240
RHIFRGQPKR HLLTSGWSTF VTSKKLVAGD TFIFLRGDNG ELHVGVHRAT TLMNNTSTSV  300
ISGHSMRHGI LASAFHAFST RSMFTIYYRP WTSSSEFIIP LDQYMKSAEI VYSIGTRFRM  360
QSEGKECGEQ RALGTIIGTE DVDHIRWPNS EWRCLKVKLD PTSDANFRPE RVCPWNIEPI  420
ESTNRKKPFI LRQQKRARTD DASSPGFSSL LMDGMWCGSV KYESQSSSGV LQGQEDDTDV  480
NQSSALRQPL PHLVLPLHPD CASMQPQMEN QLEIQVPICN SFYQYTSSRA LYSGGKVACL  540
GLHNNWSPTF SSYGVDDDAL ARRKFSVPYV NSQESRTLEL RNENETSLCE PTGGHRCMIF  600
GVNLVNGPPE LPSRQLLTSS ELKRLCSIPP TSQSSVSEPS KVTSSKQCNN SCSVSNRSCT  660
KVLKYGTALG RSVDLTRFNG YENLISELDR MFDFKGRLIN GSSGWHVTYT DDEGDMMLLG  720
DYPWQKFQYE VRRIVICPME EIDRLNQSSP NSTSQ*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1327942217357Auxin response factor 1
4ldw_A1e-1327942217357Auxin response factor 1
4ldw_B1e-1327942217357Auxin response factor 1
4ldx_A1e-1317942217357Auxin response factor 1
4ldx_B1e-1317942217357Auxin 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. Promotes flowering, stamen development, floral organ abscission and fruit dehiscence. Functions independently of ethylene and cytokinin response pathways. May act as a repressor of cell division and organ growth. {ECO:0000269|PubMed:12036261, ECO:0000269|PubMed:15960614, ECO:0000269|PubMed:16176952, ECO:0000269|PubMed:16339187}.
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_007050773.20.0PREDICTED: auxin response factor 4 isoform X1
SwissprotQ94JM31e-147ARFB_ARATH; Auxin response factor 2
TrEMBLA0A061DQD70.0A0A061DQD7_THECC; Auxin response factor
STRINGEOX949300.0(Theobroma cacao)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM157971016
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G62000.31e-149auxin response factor 2
Publications ? help Back to Top
  1. Chao WS,Doğramaci M,Foley ME,Horvath DP,Anderson JV
    Selection and validation of endogenous reference genes for qRT-PCR analysis in leafy spurge (Euphorbia esula).
    PLoS ONE, 2012. 7(8): p. e42839
    [PMID:22916167]
  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. 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]
  4. Li C, et al.
    Ectopic expression of a maize hybrid down-regulated gene ZmARF25 decreases organ size by affecting cellular proliferation in Arabidopsis.
    PLoS ONE, 2014. 9(4): p. e94830
    [PMID:24756087]
  5. Lyons R, et al.
    Fusarium oxysporum triggers tissue-specific transcriptional reprogramming in Arabidopsis thaliana.
    PLoS ONE, 2015. 10(4): p. e0121902
    [PMID:25849296]
  6. Roodbarkelari F,Du F,Truernit E,Laux T
    ZLL/AGO10 maintains shoot meristem stem cells during Arabidopsis embryogenesis by down-regulating ARF2-mediated auxin response.
    BMC Biol., 2015. 13: p. 74
    [PMID:26358077]
  7. Meng LS,Wang ZB,Yao SQ,Liu A
    The ARF2-ANT-COR15A gene cascade regulates ABA-signaling-mediated resistance of large seeds to drought in Arabidopsis.
    J. Cell. Sci., 2015. 128(21): p. 3922-32
    [PMID:26395398]
  8. Zhao S,Zhang ML,Ma TL,Wang Y
    Phosphorylation of ARF2 Relieves Its Repression of Transcription of the K+ Transporter Gene HAK5 in Response to Low Potassium Stress.
    Plant Cell, 2016. 28(12): p. 3005-3019
    [PMID:27895227]
  9. Promchuea S,Zhu Y,Chen Z,Zhang J,Gong Z
    ARF2 coordinates with PLETHORAs and PINs to orchestrate ABA-mediated root meristem activity in Arabidopsis .
    J Integr Plant Biol, 2017. 59(1): p. 30-43
    [PMID:28074634]
  10. Wójcikowska B,Gaj MD
    Expression profiling of AUXIN RESPONSE FACTOR genes during somatic embryogenesis induction in Arabidopsis.
    Plant Cell Rep., 2017. 36(6): p. 843-858
    [PMID:28255787]
  11. Sanz-Fernández M, et al.
    Screening Arabidopsis mutants in genes useful for phytoremediation.
    J. Hazard. Mater., 2017. 335: p. 143-151
    [PMID:28441590]
  12. Zhang M,Hu X,Zhu M,Xu M,Wang L
    Transcription factors NF-YA2 and NF-YA10 regulate leaf growth via auxin signaling in Arabidopsis.
    Sci Rep, 2017. 7(1): p. 1395
    [PMID:28469131]
  13. Guan C, et al.
    Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis.
    Curr. Biol., 2017. 27(19): p. 2940-2950.e4
    [PMID:28943086]
  14. 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]
  15. Sarkar Das S, et al.
    Expression dynamics of miRNAs and their targets in seed germination conditions reveals miRNA-ta-siRNA crosstalk as regulator of seed germination.
    Sci Rep, 2018. 8(1): p. 1233
    [PMID:29352229]