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.0050s0046.1.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: 607aa    MW: 67321.9 Da    PI: 6.0179
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cagra.0050s0046.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B370.81.8e-22125224197
                          EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEE CS
                   B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFk 83 
                          f+k+lt sd++++g +++ +k+a+e+       +   + +++l+ +d++g +W++k+i+r++++r++lt+GW+ Fv +++L +gD +vF 
  Cagra.0050s0046.1.p 125 FVKILTASDTSTHGGFSVLRKHATEClplldmtQ--ATPTQELVARDLHGYEWRFKHIFRGQPRRHLLTTGWSTFVTSKKLVAGDAFVFL 212
                          89****************************9543..445569************************************************ PP

                          E-SSSEE..EEEEE CS
                   B3  84 ldgrsefelvvkvf 97 
                            + +++ l+v+v+
  Cagra.0050s0046.1.p 213 --RGETGDLRVGVR 224
                          ..348888899987 PP
2Auxin_resp96.63.7e-32251330183
           Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                          a+ha++tks+F v+Y+Pr   s+F+++v+k++ a+k+ +s GmRf+m+fe+e+s+er ++Gt++g  dl++ +Wp SkWrsL+
  Cagra.0050s0046.1.p 251 ASHAVNTKSIFIVLYKPRI--SQFIISVNKYMVAMKNGLSFGMRFRMRFEGEESPERIFTGTIIGSGDLSS-QWPASKWRSLQ 330
                          789***************8..9**********************************************777.*********97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.07E-38110254IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.106.9E-38118240IPR015300DNA-binding pseudobarrel domain
CDDcd100173.43E-19124224No hitNo description
PfamPF023621.2E-20125224IPR003340B3 DNA binding domain
PROSITE profilePS5086311.744125227IPR003340B3 DNA binding domain
SMARTSM010192.1E-20125227IPR003340B3 DNA binding domain
PfamPF065074.9E-29251330IPR010525Auxin response factor
PfamPF023091.1E-8477531IPR033389AUX/IAA domain
SuperFamilySSF542774.38E-13492571No hitNo description
PROSITE profilePS5174526.347495587IPR000270PB1 domain
PfamPF023091.9E-5541580IPR033389AUX/IAA domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009725Biological Processresponse to hormone
GO:0005634Cellular Componentnucleus
GO:0009506Cellular Componentplasmodesma
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 607 aa     Download sequence    Send to blast
MANVVDADFG RSGSNDGQLY TELWKACAGP LVEVPRSGER VFYFPQGHME QLVASSNQGV  60
VDQEIPVFNL PPKILCRVLS VMLKAEHETD EVYAQITLHP EEDQSEPTSL DPPLVEPAKP  120
KVDSFVKILT ASDTSTHGGF SVLRKHATEC LPLLDMTQAT PTQELVARDL HGYEWRFKHI  180
FRGQPRRHLL TTGWSTFVTS KKLVAGDAFV FLRGETGDLR VGVRHLARQQ STMPASVISS  240
QSMRLGVLAT ASHAVNTKSI FIVLYKPRIS QFIISVNKYM VAMKNGLSFG MRFRMRFEGE  300
ESPERIFTGT IIGSGDLSSQ WPASKWRSLQ IQWDESSSIQ RPNKVSPWEI EPLSPSALTP  360
SPTQPQSKSK RSRPIDSSVS EITGSPVASN FLSSFSQSNE SNPSGKLLFH DPATERNVDK  420
TVLSSGLQGN NSEAPGTSCC RLFGFDLTSK PASAPVPPDR QLISVNSNNS DSTTKCQDPN  480
SSNSTREQKQ QTSTRSRTKV QMQGTAVGRA VDLTLLRSYD ELIKELEKMF EIEGELNPKD  540
KWAVVFTDDE DDIMLVGDDP WDEFCKMAKK LFIYSSDEVK KMSSKSLLDD EATIVNLESE  600
QRTVQD*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1631935419356Auxin response factor 1
4ldw_A1e-1631935419356Auxin response factor 1
4ldw_B1e-1631935419356Auxin 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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapCagra.0050s0046.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2299240.0AK229924.1 Arabidopsis thaliana mRNA for ARF1 family auxin responsive transcription factor like protein, complete cds, clone: RAFL22-28-H22.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006293856.10.0auxin response factor 11
SwissprotQ9ZPY60.0ARFK_ARATH; Auxin response factor 11
TrEMBLR0HBF00.0R0HBF0_9BRAS; Auxin response factor
STRINGCagra.0050s0046.1.p0.0(Capsella grandiflora)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM74351841
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G46530.10.0auxin response factor 11
Publications ? help Back to Top
  1. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
    [PMID:16280546]
  2. 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]