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 Rsa1.0_02176.1_g00003.1
Organism
Raphanus sativus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family ARF
Protein Properties Length: 813aa    MW: 90528 Da    PI: 6.3819
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_02176.1_g00003.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B371.69.8e-23155256199
                              EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EE CS
                       B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfv 80 
                              f+k+lt sd++++g +++ +++a+e+      + + + +++l+ +d++ ++W++++i+r++++r++l++GW+ Fv++++L +gD +
  Rsa1.0_02176.1_g00003.1 155 FCKTLTASDTSTHGGFSVLRRHADEClppldmSRQ-PPTQELVAKDLHANEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAF 239
                              99*****************************7333.34459********************************************* PP

                              EEEE-SSSEE..EEEEE-S CS
                       B3  81 vFkldgrsefelvvkvfrk 99 
                              +F   + +++el+v+v+r+
  Rsa1.0_02176.1_g00003.1 240 IFL--RGENGELRVGVRRA 256
                              ***..449999*****996 PP
2Auxin_resp120.51.3e-39281363183
               Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                              a+ha+st+++F+v+Y+Pr+s+seF+v+++++++++k+++s+GmRfkm+fe+e+++e+r++Gt+vg++d+dp+rW +SkWrsLk
  Rsa1.0_02176.1_g00003.1 281 AWHAISTGTMFSVYYKPRTSPSEFIVPFDQYMESVKNNYSIGMRFKMRFEGEEAPEQRFTGTIVGIEDSDPTRWAKSKWRSLK 363
                              89*******************************************************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.96E-40150284IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.101.0E-40150270IPR015300DNA-binding pseudobarrel domain
CDDcd100171.32E-20153255No hitNo description
PfamPF023621.4E-20155256IPR003340B3 DNA binding domain
SMARTSM010194.1E-22155257IPR003340B3 DNA binding domain
PROSITE profilePS5086311.42155257IPR003340B3 DNA binding domain
PfamPF065071.2E-36281363IPR010525Auxin response factor
PfamPF023099.9E-11684775IPR033389AUX/IAA domain
SuperFamilySSF542773.43E-11689769No hitNo description
PROSITE profilePS5174524.61690772IPR000270PB1 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: 813 aa     Download sequence    Send to blast
MASSEVSMRG NRGGDNFNGD STTETRNVSV TGEGQKGHSN RVVDAEAALY RELWHACAGP  60
LVTVPKQDDR VFYFPQGHIE QVEASTNQAA EQQMPLYDLP SKLLCRVINV DLKAEVDSDE  120
VYAQITLLPE AIQDENAIEK ETPPPPPPKF QVHSFCKTLT ASDTSTHGGF SVLRRHADEC  180
LPPLDMSRQP PTQELVAKDL HANEWRFRHI FRGQPRRHLL QSGWSVFVSS KRLVAGDAFI  240
FLRGENGELR VGVRRAMRQQ GNVPSSVISS HSMHLGVLAT AWHAISTGTM FSVYYKPRTS  300
PSEFIVPFDQ YMESVKNNYS IGMRFKMRFE GEEAPEQRFT GTIVGIEDSD PTRWAKSKWR  360
SLKVRWDETS SIPRPDRVSP WKLEPALAPP ALSSSMASKD PLPASGLTRV FQGQEYPTLR  420
TKHSESVECD APESSVVWQS SADDDKVDVA SASKRYENWM SSGRHEPSYT DLLSGFGANI  480
DPSRGHQIPF YDHSSLPSVA ANKFLGDRDG KFDYFANQWQ MMQSGLSLKL HESPKVPAAS  540
DSSFQGRGSA KYGEYPVLHS LTTENAGGNW PIRPRALNYY EEAVHAQAQA QAQAREHVTQ  600
RPAMVEEETA KSRDGNCRLF GIALVNNVNG TDSPRNNFNG TAGLTQVASP KVQDLSDQSK  660
STTDHREQGR PFQVKNPHLK DVHTKSNSSR SCTKVHKQGI ALGRSVDLSK FQNYEELIAE  720
LDSMFEFNGE LMAPKKDWLI VYTDAEDDMM LVGDDPWQEF CGMVRKISIY TKEEVRKMNP  780
GTLSCRSEEE AVVGEGSDPK DAKSASNPSL SSA
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1804838518354Auxin response factor 1
4ldw_A1e-1804838518354Auxin response factor 1
4ldw_B1e-1804838518354Auxin response factor 1
4ldx_A1e-1804838518354Auxin response factor 1
4ldx_B1e-1804838518354Auxin 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. Promotes flowering, stamen development, floral organ abscission and fruit dehiscence. Functions independently of ethylene and cytokinin response pathways. May act as a repressor of cell division and organ growth. {ECO:0000269|PubMed:12036261, ECO:0000269|PubMed:15960614, ECO:0000269|PubMed:16176952, ECO:0000269|PubMed:16339187}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_02176.1_g00003.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankJN9794610.0JN979461.1 Brassica rapa subsp. pekinensis auxin response factor 2-3 (ARF2-3) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018456407.10.0PREDICTED: auxin response factor 2
RefseqXP_018456408.10.0PREDICTED: auxin response factor 2
SwissprotQ94JM30.0ARFB_ARATH; Auxin response factor 2
TrEMBLA0A1J3EGZ40.0A0A1J3EGZ4_NOCCA; Auxin response factor
STRINGAT5G62000.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM53482647
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G62000.30.0auxin response factor 2
Publications ? help Back to Top
  1. Chao WS,Doğramaci M,Foley ME,Horvath DP,Anderson JV
    Selection and validation of endogenous reference genes for qRT-PCR analysis in leafy spurge (Euphorbia esula).
    PLoS ONE, 2012. 7(8): p. e42839
    [PMID:22916167]
  2. 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]
  3. Li C, et al.
    Ectopic expression of a maize hybrid down-regulated gene ZmARF25 decreases organ size by affecting cellular proliferation in Arabidopsis.
    PLoS ONE, 2014. 9(4): p. e94830
    [PMID:24756087]
  4. Lyons R, et al.
    Fusarium oxysporum triggers tissue-specific transcriptional reprogramming in Arabidopsis thaliana.
    PLoS ONE, 2015. 10(4): p. e0121902
    [PMID:25849296]
  5. Roodbarkelari F,Du F,Truernit E,Laux T
    ZLL/AGO10 maintains shoot meristem stem cells during Arabidopsis embryogenesis by down-regulating ARF2-mediated auxin response.
    BMC Biol., 2015. 13: p. 74
    [PMID:26358077]
  6. Meng LS,Wang ZB,Yao SQ,Liu A
    The ARF2-ANT-COR15A gene cascade regulates ABA-signaling-mediated resistance of large seeds to drought in Arabidopsis.
    J. Cell. Sci., 2015. 128(21): p. 3922-32
    [PMID:26395398]
  7. Zhao S,Zhang ML,Ma TL,Wang Y
    Phosphorylation of ARF2 Relieves Its Repression of Transcription of the K+ Transporter Gene HAK5 in Response to Low Potassium Stress.
    Plant Cell, 2016. 28(12): p. 3005-3019
    [PMID:27895227]
  8. Promchuea S,Zhu Y,Chen Z,Zhang J,Gong Z
    ARF2 coordinates with PLETHORAs and PINs to orchestrate ABA-mediated root meristem activity in Arabidopsis .
    J Integr Plant Biol, 2017. 59(1): p. 30-43
    [PMID:28074634]
  9. 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]
  10. Sanz-Fernández M, et al.
    Screening Arabidopsis mutants in genes useful for phytoremediation.
    J. Hazard. Mater., 2017. 335: p. 143-151
    [PMID:28441590]
  11. Zhang M,Hu X,Zhu M,Xu M,Wang L
    Transcription factors NF-YA2 and NF-YA10 regulate leaf growth via auxin signaling in Arabidopsis.
    Sci Rep, 2017. 7(1): p. 1395
    [PMID:28469131]
  12. Guan C, et al.
    Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis.
    Curr. Biol., 2017. 27(19): p. 2940-2950.e4
    [PMID:28943086]
  13. 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]
  14. Sarkar Das S, et al.
    Expression dynamics of miRNAs and their targets in seed germination conditions reveals miRNA-ta-siRNA crosstalk as regulator of seed germination.
    Sci Rep, 2018. 8(1): p. 1233
    [PMID:29352229]