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 Carubv10004139m
Common NameCARUB_v10004139mg
Organism
Capsella rubella
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: 825aa    MW: 91517.5 Da    PI: 6.3323
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Carubv10004139mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B373.23.2e-23126227199
                      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+        ++++  ++l+ +d++  +W++++i+r++++r++lt+GW+ Fv+a++L +gD+v+F   +++
  Carubv10004139m 126 FCKTLTASDTSTHGGFSVPRRAAEKVfppldyTLQPPA-QELIARDLHDVEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLVAGDSVIFI--RNE 216
                      99*****************************9666655.49************************************************..568 PP

                      EE..EEEEE-S CS
               B3  89 efelvvkvfrk 99 
                      + +l+++++r+
  Carubv10004139m 217 KNQLFLGIRRA 227
                      8889***9997 PP
2Auxin_resp1102.5e-36252335183
       Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                      aaha +t+s F+v+++Pras+seFv++++k+ ka+  +++svGmRf+m fete+ss rr++Gt++g+sdld+vrWpnS+Wrs+k
  Carubv10004139m 252 AAHASATNSCFTVFFHPRASPSEFVIQLSKYIKAVFhTRISVGMRFRMLFETEESSVRRYMGTITGISDLDTVRWPNSHWRSVK 335
                      799******************************986599******************************************985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.05E-47112255IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.104.2E-40119241IPR015300DNA-binding pseudobarrel domain
CDDcd100173.76E-21125221No hitNo description
PfamPF023624.7E-21126227IPR003340B3 DNA binding domain
SMARTSM010192.7E-23126228IPR003340B3 DNA binding domain
PROSITE profilePS5086312.308126228IPR003340B3 DNA binding domain
PfamPF065079.1E-32252335IPR010525Auxin response factor
SuperFamilySSF542773.47E-7712792No hitNo description
PfamPF023098.9E-8715803IPR033389AUX/IAA domain
PROSITE profilePS5174522.8718802IPR000270PB1 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:0009908Biological Processflower development
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 825 aa     Download sequence    Send to blast
MKLSTSGLGQ QGHEGEKCLN SELWHACAGP LVSLPSSGSR VVYFPQGHSE QVAATTNKEV  60
DGHIPNYPSL PPQLICQLHN VTMHADVETD EVYAQMTLQP LTPEEQKETF VPIELGIPSK  120
QPSNYFCKTL TASDTSTHGG FSVPRRAAEK VFPPLDYTLQ PPAQELIARD LHDVEWKFRH  180
IFRGQPKRHL LTTGWSVFVS AKRLVAGDSV IFIRNEKNQL FLGIRRATRP QTIVPSSVLS  240
SDSMHIGLLA AAAHASATNS CFTVFFHPRA SPSEFVIQLS KYIKAVFHTR ISVGMRFRML  300
FETEESSVRR YMGTITGISD LDTVRWPNSH WRSVKVGWDE STAGERQPRV SLWEIEPLTT  360
FPMYPSLFPL RLKRPWHAGT SSLPDGRGEL GSGLTWLRGG GGDQQGLLPL NYPSVGLFPW  420
MQQRLDLTQM GTDNNQQYQA MLAAGLQNIG GGDPLRQQFV QLQEPHHQYV QQSASHNSDL  480
MLQQQQQQQQ QQASRHAMHA QTQVMSENIP QQNMRQEVSN HPTGQQLQQP DQNAYLNAFK  540
MQNGHLQQWQ HQEMASPSFM KSDFTDSSNK FATSATPMQQ NAASPASNDG SNLLNFSITG  600
QSVLPEQLTT EGWSPKASNT FSEPLSLPQA YPGKSLALEP GNPNLNPQNP SLFGVDPDSG  660
LFLPSTVPRF ASSSGDAEAS PMSLTDSGFQ NSLYGCMQDT THELLHGAGQ INPSNQTKNF  720
VKVYKSGSVG RSLDISRFSS YHELREELGK MFAIEGLLED PLRSGWQLVF VDKENDILLL  780
GDDPWESFVN NVWYIKILSP EDVQQMGDQG EGSAGSFPQN PTHL*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A1e-155835640388Auxin response factor 5
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). Seems to act as transcriptional activator. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Regulates both stamen and gynoecium maturation. Promotes jasmonic acid production. Partially redundant with ARF6. Involved in fruit initiation. Acts as an inhibitor to stop further carpel development in the absence of fertilization and the generation of signals required to initiate fruit and seed development. {ECO:0000269|PubMed:12036261, ECO:0000269|PubMed:16107481, ECO:0000269|PubMed:16829592}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00033PBMTransfer from AT5G37020Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapCarubv10004139m
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Repressed by miR167. {ECO:0000269|PubMed:17021043}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF0421960.0AF042196.1 Arabidopsis thaliana auxin response factor 8 (ARF8) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006282446.10.0auxin response factor 8
SwissprotQ9FGV10.0ARFH_ARATH; Auxin response factor 8
TrEMBLR0GF160.0R0GF16_9BRAS; Auxin response factor
STRINGXP_006282446.10.0(Capsella rubella)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM13442894
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G37020.10.0auxin response factor 8
Publications ? help Back to Top
  1. Liu N, et al.
    Down-regulation of AUXIN RESPONSE FACTORS 6 and 8 by microRNA 167 leads to floral development defects and female sterility in tomato.
    J. Exp. Bot., 2014. 65(9): p. 2507-20
    [PMID:24723401]
  2. Minato N, et al.
    The phytoplasmal virulence factor TENGU causes plant sterility by downregulating of the jasmonic acid and auxin pathways.
    Sci Rep, 2014. 4: p. 7399
    [PMID:25492247]
  3. Ortega-Amaro MA, et al.
    Overexpression of AtGRDP2, a novel glycine-rich domain protein, accelerates plant growth and improves stress tolerance.
    Front Plant Sci, 2014. 5: p. 782
    [PMID:25653657]
  4. Wang Y, et al.
    MicroRNA167-Directed Regulation of the Auxin Response Factors GmARF8a and GmARF8b Is Required for Soybean Nodulation and Lateral Root Development.
    Plant Physiol., 2015. 168(3): p. 984-99
    [PMID:25941314]
  5. Barik S, et al.
    Coevolution Pattern and Functional Conservation or Divergence of miR167s and their targets across Diverse Plant Species.
    Sci Rep, 2015. 5: p. 14611
    [PMID:26459056]
  6. 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]
  7. Mlotshwa S,Pruss GJ,MacArthur JL,Reed JW,Vance V
    Developmental Defects Mediated by the P1/HC-Pro Potyviral Silencing Suppressor Are Not Due to Misregulation of AUXIN RESPONSE FACTOR 8.
    Plant Physiol., 2016. 172(3): p. 1853-1861
    [PMID:27688620]
  8. 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]
  9. Zhang GZ, et al.
    Ectopic expression of UGT84A2 delayed flowering by indole-3-butyric acid-mediated transcriptional repression of ARF6 and ARF8 genes in Arabidopsis.
    Plant Cell Rep., 2017. 36(12): p. 1995-2006
    [PMID:29027578]
  10. Zheng K, et al.
    Involvement of PACLOBUTRAZOL RESISTANCE6/KIDARI, an Atypical bHLH Transcription Factor, in Auxin Responses in Arabidopsis.
    Front Plant Sci, 2017. 8: p. 1813
    [PMID:29114256]
  11. 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]
  12. Ghelli R, et al.
    A Newly Identified Flower-Specific Splice Variant of AUXIN RESPONSE FACTOR8 Regulates Stamen Elongation and Endothecium Lignification in Arabidopsis.
    Plant Cell, 2018. 30(3): p. 620-637
    [PMID:29514943]