PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Araha.8175s0022.1.p
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family ARF
Protein Properties Length: 793aa    MW: 87851.8 Da    PI: 6.5535
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Araha.8175s0022.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B376.92.3e-24172273199
                          EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE CS
                   B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkl 84 
                          f+k+lt sd++++g +++p++ ae++      + +++ s++l+ +d++g +W++++iyr++++r++lt+GW+ Fv++++L +gD v+F  
  Araha.8175s0022.1.p 172 FCKTLTASDTSTHGGFSVPRRAAEDCfapldyK-QQRPSQELIAKDLHGVEWKFRHIYRGQPRRHLLTTGWSIFVSQKNLASGDAVLFL- 259
                          99****************************963.3445679************************************************. PP

                          -SSSEE..EEEEE-S CS
                   B3  85 dgrsefelvvkvfrk 99 
                           +++++el+++++r+
  Araha.8175s0022.1.p 260 -RDEGGELRLGIRRA 273
                          .5699*******996 PP

2Auxin_resp122.92.3e-40297378182
           Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 
                          +a+a+stks+F+v+Y+Pra+++eFv+++ek+++++++++s+G+Rf+m+fe++ds+err++G+v+gv dldp+rWpnSkWr+L
  Araha.8175s0022.1.p 297 VANAVSTKSMFHVFYSPRATHAEFVIPYEKYVTSIRNPISIGTRFRMRFEMDDSPERRCAGVVTGVCDLDPYRWPNSKWRCL 378
                          689******************************************************************************9 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.106.4E-40163286IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019368.24E-42166281IPR015300DNA-binding pseudobarrel domain
CDDcd100172.59E-20170272No hitNo description
PfamPF023623.6E-22172273IPR003340B3 DNA binding domain
SMARTSM010191.1E-22172274IPR003340B3 DNA binding domain
PROSITE profilePS5086313.267172274IPR003340B3 DNA binding domain
PfamPF065074.8E-34297378IPR010525Auxin response factor
PfamPF023092.8E-5665748IPR033389AUX/IAA domain
SuperFamilySSF542772.26E-10666746No hitNo description
PROSITE profilePS5174523.609669751IPR000270PB1 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: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: 793 aa     Download sequence    Send to blast
MEFDLNTEIA EVEEEENDDV GVGGTRIKKG RLGISPSSSS SCSSGSSSSS TGPASSIYSE  60
LWHACAGPLT CLPKKGNVVV YFPQGHLEQD AMVSYSSPLE IPKFDLNPQI FCRVVHVQLL  120
ANKETDEVYT QVTLLPLQEF SMLNAEGKEV KELGGDEERN GSSSVKRTPH MFCKTLTASD  180
TSTHGGFSVP RRAAEDCFAP LDYKQQRPSQ ELIAKDLHGV EWKFRHIYRG QPRRHLLTTG  240
WSIFVSQKNL ASGDAVLFLR DEGGELRLGI RRAARPRNGL PDSIIEKNSC SNILSLVANA  300
VSTKSMFHVF YSPRATHAEF VIPYEKYVTS IRNPISIGTR FRMRFEMDDS PERRCAGVVT  360
GVCDLDPYRW PNSKWRCLLV RWDESFVSDH QERVSPWEID PSVSLPHLSI QSSPRPKRPW  420
AGLLDTTPPG NPITAERGGF LDFEESVRSS KVLQGQENLG SASPSQGFDV MNRQILDFAM  480
QSHASPVLLS SRVKDRFGEF VNATALNPAC SGVMDLDRFP RVLQGQEICS LKSFPQFAGF  540
SPAAASGKPN LGYTDPFAYQ ANKSSFYPLA LHGIRSTHVP YHNPYNAGNQ SSGRPSRAIN  600
VGEETRKFDA QKEGGLPNNV TADLPFKIDM MGKQKGSDFN MNASSGCKLF GFSLPVETPA  660
SNPQSSSKRI CTKVHKQGSQ VGRAIDLSRL NGYDDLLTEL ERLFNMEGLL RDPEKGWRIL  720
YTDSENDMMV VGDDPWHDFC NVVWKIHLYT KEEVENANDD NKSCLEQAAI MMEASKSSSV  780
SQPDSSPTIT RV*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-112454012354Auxin response factor 1
4ldw_A1e-112454012354Auxin response factor 1
4ldw_B1e-112454012354Auxin response factor 1
4ldx_A1e-112454012354Auxin response factor 1
4ldx_B1e-112454012354Auxin response factor 1
4ldy_A1e-112454012354Auxin response factor 1
4ldy_B1e-112454012354Auxin 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
PlantRegMapAraha.8175s0022.1.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
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_020889184.10.0auxin response factor 4
SwissprotQ9ZTX90.0ARFD_ARATH; Auxin response factor 4
TrEMBLD7MTU60.0D7MTU6_ARALL; Auxin response factor
STRINGfgenesh2_kg.8__2008__AT5G60450.10.0(Arabidopsis lyrata)
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]