PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Cagra.4553s0009.1.p
Organism
Capsella grandiflora
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella
Family ARF
Protein Properties Length: 874aa    MW: 96909.2 Da    PI: 6.4805
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cagra.4553s0009.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B371.51.1e-22164265199
                          EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE CS
                   B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkl 84 
                          f+k+lt sd++++g +++ +++a+e+      + + + +++l+ +d++ ++W++++i+r++++r++l++GW+ Fv++++L +gD ++F  
  Cagra.4553s0009.1.p 164 FCKTLTASDTSTHGGFSVLRRHADEClppldmSRQ-PPTQELVAKDLHANEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIFL- 251
                          99*****************************7333.34459************************************************. PP

                          -SSSEE..EEEEE-S CS
                   B3  85 dgrsefelvvkvfrk 99 
                           + +++el+v+v+r+
  Cagra.4553s0009.1.p 252 -RGENGELRVGVRRA 265
                          .449999*****996 PP
2Auxin_resp120.31.5e-39290372183
           Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                          a+ha+st+++F+v+Y+Pr+s+seF+v+++++++++k+++s+GmRfkm+fe+e+++e+r++Gt+vg++++dp+rWp+SkWrsLk
  Cagra.4553s0009.1.p 290 AWHAISTGTMFTVYYKPRTSPSEFIVPFDQYMESVKNNYSIGMRFKMRFEGEEAPEQRFTGTIVGTEESDPTRWPKSKWRSLK 372
                          89*******************************************************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.101.2E-40160279IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019363.27E-40161293IPR015300DNA-binding pseudobarrel domain
CDDcd100171.51E-20162264No hitNo description
PfamPF023621.5E-20164265IPR003340B3 DNA binding domain
PROSITE profilePS5086311.42164266IPR003340B3 DNA binding domain
SMARTSM010194.1E-22164266IPR003340B3 DNA binding domain
PfamPF065078.8E-37290372IPR010525Auxin response factor
PfamPF023091.9E-5635783IPR033389AUX/IAA domain
PROSITE profilePS5174525.174747831IPR000270PB1 domain
SuperFamilySSF542771.28E-11748824No hitNo description
PfamPF023097.3E-6793832IPR033389AUX/IAA domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0008285Biological Processnegative regulation of cell proliferation
GO:0009737Biological Processresponse to abscisic acid
GO:0009911Biological Processpositive regulation of flower development
GO:0010047Biological Processfruit dehiscence
GO:0010150Biological Processleaf senescence
GO:0010227Biological Processfloral organ abscission
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:0048481Biological Processplant ovule development
GO:0005634Cellular Componentnucleus
GO:0005515Molecular Functionprotein binding
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 874 aa     Download sequence    Send to blast
MASSEVSMKG NRGGDNFSSS GYTDPKETRN VSVAGDGQIT HSNRSVAAER AVDPEAALYR  60
ELWHACAGPL VTVPRQDDRV FYFPQGHIEQ VEASTNQAAE QQMPLYDLPS KLLCRVINVD  120
LKAEADTDEV YAQITLLPEA NQDENAIEKE APPPPPPRFQ VHSFCKTLTA SDTSTHGGFS  180
VLRRHADECL PPLDMSRQPP TQELVAKDLH ANEWRFRHIF RGQPRRHLLQ SGWSVFVSSK  240
RLVAGDAFIF LRGENGELRV GVRRAMRQQG NVPSSVISSH SMHLGVLATA WHAISTGTMF  300
TVYYKPRTSP SEFIVPFDQY MESVKNNYSI GMRFKMRFEG EEAPEQRFTG TIVGTEESDP  360
TRWPKSKWRS LKVRWDETSS IPRPDRVSPW KIEPALAPPA LSPVPMPRPK RPRSNIAPSS  420
PDSSMLTKDG TAKANMDPLP ASGLSRVLQG QEYSTLRTKH IENVECDAPE NSVVWQSTTD  480
DDKVDVVSAS KRYGSENWMS SARHEPTYTD LLSGFGNNID PPHGQRIPFY DHSSSPSMPA  540
KKILSDPEGK FDYLANQWQM MHSGLSLKLH ESPKAPAASD SSFQGLGNGK YSEYPVLNGL  600
STENGGGNWP IRPRALNYFE EVVQAQAQAQ AQAQAQAQAQ AQAQARDQVT KQPMTIQEEG  660
AKSRDGNCRL FGIPLINNMN GTDSSMSQRN NLNDAVGFTQ VASAKVQDLS DQSKGSKTTN  720
DHREQGRPLP TSNPHPKDAQ TKTNSSRSCT KVHKQGIALG RSVDLSKFQN YEELIAELDR  780
LFEFNGELMA PKKDWLIVYT DDENDMMLVG DDPWQEFCCM VRKIFIYTKE EVRKMNPGTL  840
SCRSEEEVVV GEGSDAKDAK SASNPSLSSA GNS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A0.05739418354Auxin response factor 1
4ldw_A0.05739418354Auxin response factor 1
4ldw_B0.05739418354Auxin response factor 1
4ldx_A0.05739418354Auxin response factor 1
4ldx_B0.05739418354Auxin 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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00574DAPTransfer from AT5G62000Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapCagra.4553s0009.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF3788620.0AF378862.1 Arabidopsis thaliana AT5g62000/mtg10_20 mRNA, complete cds.
GenBankAK2212520.0AK221252.1 Arabidopsis thaliana mRNA for ARF1-binding protein, complete cds, clone: RAFL24-07-O11.
GenBankAK2212540.0AK221254.1 Arabidopsis thaliana mRNA for ARF1-binding protein, complete cds, clone: RAFL24-09-L23.
GenBankAK2212740.0AK221274.1 Arabidopsis thaliana mRNA for ARF1-binding protein, complete cds, clone: RAFL24-16-M02.
GenBankAK2212820.0AK221282.1 Arabidopsis thaliana mRNA for ARF1-binding protein, complete cds, clone: RAFL24-19-K22.
GenBankAK2213050.0AK221305.1 Arabidopsis thaliana mRNA for ARF1-binding protein, complete cds, clone: RAFL24-31-F22.
GenBankAY6697870.0AY669787.1 Arabidopsis thaliana clone C105342 ARF2 (At5g62000) mRNA, complete cds.
GenBankBT0007840.0BT000784.1 Arabidopsis thaliana clone RAFL07-10-G12 (R10939) auxin response factor (At5g62000) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_023633601.10.0auxin response factor 2 isoform X1
SwissprotQ94JM30.0ARFB_ARATH; Auxin response factor 2
TrEMBLR0EUS70.0R0EUS7_9BRAS; Auxin response factor
STRINGCagra.4553s0009.1.p0.0(Capsella grandiflora)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM53482647
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G62000.30.0auxin 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. 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. 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]
  4. Lyons R, et al.
    Fusarium oxysporum triggers tissue-specific transcriptional reprogramming in Arabidopsis thaliana.
    PLoS ONE, 2015. 10(4): p. e0121902
    [PMID:25849296]
  5. 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]
  6. 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]
  7. 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]
  8. 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]
  9. 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]
  10. Sanz-Fernández M, et al.
    Screening Arabidopsis mutants in genes useful for phytoremediation.
    J. Hazard. Mater., 2017. 335: p. 143-151
    [PMID:28441590]
  11. 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]
  12. Guan C, et al.
    Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis.
    Curr. Biol., 2017. 27(19): p. 2940-2950.e4
    [PMID:28943086]
  13. 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]
  14. 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]