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 Carubv10025912m
Common NameCARUB_v10025912mg
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: 791aa    MW: 88005 Da    PI: 6.1893
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Carubv10025912mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B376.82.5e-24171272199
                      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++      + +++ s++l+ +d++g +W++++iyr++++r++lt+GW+ Fv++++L +gD v+F   +++
  Carubv10025912m 171 FCKTLTASDTSTHGGFSVPRRAAEDCfapldyK-QQRPSQELIAKDLHGVEWKFRHIYRGQPRRHLLTTGWSIFVSQKNLVSGDAVLFL--RDE 261
                      99****************************963.3445679************************************************..569 PP

                      EE..EEEEE-S CS
               B3  89 efelvvkvfrk 99 
                      ++el+++++r+
  Carubv10025912m 262 DGELRLGIRRA 272
                      9999****996 PP
2Auxin_resp121.27.7e-40296377182
       Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 
                      +a+a+stks+F+v+Y+Pra+++eFv+++ek++++++++v++G+Rf+m+fe++ds+err++G+v+gv dldp+rWpnSkWr+ 
  Carubv10025912m 296 VANAVSTKSMFHVFYSPRATHAEFVIPYEKYVTTIRNPVCIGTRFRMRFEMDDSPERRCAGVVTGVCDLDPYRWPNSKWRCF 377
                      689*****************************************************************************95 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-40163285IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019361.03E-42164283IPR015300DNA-binding pseudobarrel domain
CDDcd100175.10E-21169271No hitNo description
PfamPF023622.5E-22171272IPR003340B3 DNA binding domain
PROSITE profilePS5086313.38171273IPR003340B3 DNA binding domain
SMARTSM010192.1E-23171273IPR003340B3 DNA binding domain
PfamPF065072.9E-33296377IPR010525Auxin response factor
SuperFamilySSF542772.31E-10664744No hitNo description
PfamPF023094.6E-5664746IPR033389AUX/IAA domain
PROSITE profilePS5174523.609667749IPR000270PB1 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:0010050Biological Processvegetative phase change
GO:0010158Biological Processabaxial cell fate specification
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 791 aa     Download sequence    Send to blast
MEFDLNTEIA EVEEEENDDV GVRIDKARLG ISPSSSSSCS SGSSSSSSST GSASSIYSEL  60
WHACAGPLTS LPIKGNVVVY FPQGHLEQDA MVSFPSPLEI PKFDLNPQIF CRVVNVQLLA  120
NKETDEVYTQ VTLLPLQEFS MLNPEGKEVR ELGGDEERNG SSTVKRTPHM FCKTLTASDT  180
STHGGFSVPR RAAEDCFAPL DYKQQRPSQE LIAKDLHGVE WKFRHIYRGQ PRRHLLTTGW  240
SIFVSQKNLV SGDAVLFLRD EDGELRLGIR RAARPRNGLP DSVIEKNSCS NILSPVANAV  300
STKSMFHVFY SPRATHAEFV IPYEKYVTTI RNPVCIGTRF RMRFEMDDSP ERRCAGVVTG  360
VCDLDPYRWP NSKWRCFLVR WDESFVSDHQ ERVSPWEIDP SVSLPHLSIQ SSPRPKRPWA  420
GVLDTTPPRK PITERGGFLD FEESVRPSKV LQGQENIGSA SPSQGFDVLN RRILDFAMQS  480
HANPVLLSSR VKDRFGEFVD ATAIDPACSG VMDLDRFPRV LQGQEICSLK SFPQFAGFTP  540
AATSGKPTLG YTDPFARQAN KSSFYPLALH GIRSTHVPYQ NPYNAGNQSS GRPSRAINFG  600
EETRKSDALN ESGLPNNVTA DLPFKIDMMG KQKGGEFNMN VSSGCKLFGF SLPVETPTPN  660
PQGSSKRICT KVHKQGSQVG RAIDLSRLNG YDDLLTELER LFNMEGLLRD PEKGWRILYT  720
DSENDMMVVG DDPWHDFCNV VWKIHLYTKE EVENANDDNK SCLEQAALMM EASKSSSVSQ  780
PDSSPTVTRV *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-112444002354Auxin response factor 1
4ldw_A1e-112444002354Auxin response factor 1
4ldw_B1e-112444002354Auxin response factor 1
4ldy_A1e-112444002354Auxin response factor 1
4ldy_B1e-112444002354Auxin 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
PlantRegMapCarubv10025912m
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY0808320.0AY080832.1 Arabidopsis thaliana auxin response factor ARF4 (At5g60450) mRNA, complete cds.
GenBankAY1139770.0AY113977.1 Arabidopsis thaliana auxin response factor ARF4 (At5g60450) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006280031.10.0auxin response factor 4
SwissprotQ9ZTX90.0ARFD_ARATH; Auxin response factor 4
TrEMBLR0G8Q00.0R0G8Q0_9BRAS; Auxin response factor
STRINGXP_006280031.10.0(Capsella rubella)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM95302636
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G60450.10.0auxin response factor 4
Publications ? help Back to Top
  1. 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]
  2. Machida C,Nakagawa A,Kojima S,Takahashi H,Machida Y
    The complex of ASYMMETRIC LEAVES (AS) proteins plays a central role in antagonistic interactions of genes for leaf polarity specification in Arabidopsis.
    Wiley Interdiscip Rev Dev Biol, 2015 Nov-Dec. 4(6): p. 655-71
    [PMID:26108442]
  3. 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]
  4. Matsumura Y, et al.
    A genetic link between epigenetic repressor AS1-AS2 and a putative small subunit processome in leaf polarity establishment of Arabidopsis.
    Biol Open, 2016. 5(7): p. 942-54
    [PMID:27334696]
  5. Guan C, et al.
    Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis.
    Curr. Biol., 2017. 27(19): p. 2940-2950.e4
    [PMID:28943086]
  6. 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]