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 Cagra.0483s0062.1.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: 594aa    MW: 66850.8 Da    PI: 7.4198
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cagra.0483s0062.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B373.33e-23128228198
                          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.0483s0062.1.p 128 FVKILTASDTSTHGGFSVLRKHATEClpaldmtQ--ATPTQELVARDLHGFEWRFKHIFRGQPRRHLLTTGWSTFVSSKRLVAGDAFVFL 215
                          89****************************9543..445569************************************************ PP

                          E-SSSEE..EEEEE- CS
                   B3  84 ldgrsefelvvkvfr 98 
                            + +++ l+v+v+r
  Cagra.0483s0062.1.p 216 --RGENGDLRVGVRR 228
                          ..3488889***998 PP
2Auxin_resp94.31.9e-31254333183
           Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                          a+ha+ +k+ F v+Y+Pr   s+F+v v+k+++a+k+ +s+G+Rf+m+fe+e+s+er ++Gt+vg+ dl++ +Wp SkWrsL+
  Cagra.0483s0062.1.p 254 ASHAVGSKTLFVVFYKPRI--SQFIVGVNKYMEAIKHGFSLGTRFRMRFEGEESPERIFTGTIVGTGDLSS-QWPASKWRSLQ 333
                          68999*************8..9**********************************************777.*********97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019368.37E-41113257IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.101.4E-38121243IPR015300DNA-binding pseudobarrel domain
CDDcd100172.34E-20126228No hitNo description
PfamPF023622.6E-21128228IPR003340B3 DNA binding domain
SMARTSM010191.3E-21128230IPR003340B3 DNA binding domain
PROSITE profilePS5086312.097128230IPR003340B3 DNA binding domain
PfamPF065076.6E-29254333IPR010525Auxin response factor
PfamPF023099.4E-13479573IPR033389AUX/IAA domain
SuperFamilySSF542773.99E-13488565No hitNo description
PROSITE profilePS5174526.611489581IPR000270PB1 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:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 594 aa     Download sequence    Send to blast
MASVEGDGDF RTSLSSSYHD QLYTELWKAC AGPLVEVPRP EERVFYFPQG HMEQLVASTN  60
QGIKSEEIPK FNLPPKILCR VLGVTLKAEH ETDEVYAQIT LQPEEHQIEP TSLDPPLVEP  120
AKQMFHSFVK ILTASDTSTH GGFSVLRKHA TECLPALDMT QATPTQELVA RDLHGFEWRF  180
KHIFRGQPRR HLLTTGWSTF VSSKRLVAGD AFVFLRGENG DLRVGVRRLA RHQSTMPTSV  240
ISSQSMHLGV LATASHAVGS KTLFVVFYKP RISQFIVGVN KYMEAIKHGF SLGTRFRMRF  300
EGEESPERIF TGTIVGTGDL SSQWPASKWR SLQVQWDEPT TFQRPDKVSP WEIEPFLPTS  360
PDSSPTQQPQ SKCKRSRPIE PSVITPAPPS FLYSFPQSQD SINATIKVFQ DPPLERNSGG  420
YSSNNNFKAE TPPPPTNGCY RLFGFNLTSN PPAPILLDKQ PNETSGAAKC QESITPSSTN  480
EQRKQQTSRS RTKVQMQGIA VGRAVDLTLL KSYDELIKEL EKMFEIQGQL RPRDKWVVVF  540
TDDEGDMMLA GDDPWNEFCK MAKKIFIYSR DEVKKMTTKL KHYSSLENED GNE*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1612035617355Auxin response factor 1
4ldw_A1e-1612035617355Auxin response factor 1
4ldw_B1e-1612035617355Auxin 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.0483s0062.1.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
GenBankAF3347170.0AF334717.1 Arabidopsis thaliana auxin response factor ARF18 (At3g61830) mRNA, complete cds.
GenBankAY0597460.0AY059746.1 Arabidopsis thaliana auxin response factor ARF18 (At3g61830) mRNA, complete cds.
GenBankAY0704630.0AY070463.1 Arabidopsis thaliana AT3g61830/F15G16_220 mRNA, complete cds.
GenBankAY0913920.0AY091392.1 Arabidopsis thaliana putative auxin response factor protein (At3g61830) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006292708.10.0auxin response factor 18
SwissprotQ9C5W90.0ARFR_ARATH; Auxin response factor 18
TrEMBLR0FT390.0R0FT39_9BRAS; Auxin response factor
STRINGCagra.0483s0062.1.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
AT3G61830.10.0auxin response factor 18
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]