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 XP_009112005.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family ARF
Protein Properties Length: 832aa    MW: 92670.6 Da    PI: 6.6324
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009112005.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B371.61e-22136237199
                     EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSE CS
              B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrse 89 
                     f+k+lt sd++++g +++ +++a+e+      + + + +++l+ +d++ ++W++++i+r++++r++l++GW+ Fv++++L +gD ++F   + ++
  XP_009112005.1 136 FCKTLTASDTSTHGGFSVLRRHADEClppldmSRQ-PPTQELVAKDLHANEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIFL--RGEN 227
                     99*****************************7333.34459************************************************..4499 PP

                     E..EEEEE-S CS
              B3  90 felvvkvfrk 99 
                     +el+v+v+r+
  XP_009112005.1 228 GELRVGVRRA 237
                     99*****996 PP
2Auxin_resp120.51.3e-39262344183
      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
  XP_009112005.1 262 AWHAISTGTMFSVYYKPRTSPSEFIVPFDQYMESVKNNYSIGMRFKMRFEGEEAPEQRFTGTIVGIEDSDPTRWAKSKWRSLK 344
                     89*******************************************************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.101.1E-40132251IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019366.02E-39133265IPR015300DNA-binding pseudobarrel domain
CDDcd100171.38E-20134236No hitNo description
PfamPF023621.4E-20136237IPR003340B3 DNA binding domain
SMARTSM010194.1E-22136238IPR003340B3 DNA binding domain
PROSITE profilePS5086311.42136238IPR003340B3 DNA binding domain
PfamPF065071.3E-36262344IPR010525Auxin response factor
PfamPF023096.2E-11695791IPR033389AUX/IAA domain
SuperFamilySSF542772.55E-12704785No hitNo description
PROSITE profilePS5174525.074706788IPR000270PB1 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: 832 aa     Download sequence    Send to blast
MTSSEALNVA VSGEGQKGHS SRVVDAEAAL YRELWHACAG PLVTVPRQDD RVFYFPQGHI  60
EQVEASTNQA AEQQMPLYDL PSKILCRVIN VDLKAEVDSD EVYAQITLLP EAIQDENAIE  120
KEAPPPPPPR FQVHSFCKTL TASDTSTHGG FSVLRRHADE CLPPLDMSRQ PPTQELVAKD  180
LHANEWRFRH IFRGQPRRHL LQSGWSVFVS SKRLVAGDAF IFLRGENGEL RVGVRRAMRQ  240
QGNVSSSVIS SHSMHLGVLA TAWHAISTGT MFSVYYKPRT SPSEFIVPFD QYMESVKNNY  300
SIGMRFKMRF EGEEAPEQRF TGTIVGIEDS DPTRWAKSKW RSLKVRWDET SSIPRPDRVS  360
PWKLEPALAP PALSPVPMPR PKRPRSNIAP SSPDSSVLIR EGSAMGNKDP LPASGLSRVL  420
QGQEHPTLRT KHTETVECDA PESSVVWQSS ADDDKVDVVS ASASRRYENW MSSGRHESAY  480
TDLLSGFGAN IDPSPGHQIP FYDHSSLPFV AANKFIGDRD GKFDYFANQW QMMHSGLSLT  540
LHESPKIPAA SDTSFQGGRG NAKYGEYPGL HSLTTENAGG NWPIRPRAVN YFEEAVQAHA  600
QAQAREHVTK RPEMVEDTAK SRDGNCRLFG IPLVNNVNVT ESTMSPRNNF NDTAGLTQMT  660
SPKVQDLSDQ SKGSKSTNDQ REQGRPFQAN HHPHPKDVHT KTHSSRSCTK VQKQGIALGR  720
SVDLSKFQNY EELIAELDRM FEFNGELMAP KKDWLIVYTD DENDMMLVGD DPWQEFCGMV  780
RKISIYTKEE VRKMNPGTLS CRSEEEAVVG EGSDPKDAKS ASNPSLSSAG HS
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1792936618354Auxin response factor 1
4ldw_A1e-1792936618354Auxin response factor 1
4ldw_B1e-1792936618354Auxin response factor 1
4ldx_A1e-1792936618354Auxin response factor 1
4ldx_B1e-1792936618354Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.91530.0bud| leaf| silique
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in the sepals and carpels of young flower buds. At stage 10 of flower development, expression in the carpels becomes restricted to the style. Also expressed in anthers and filaments. At stage 13, expressed in the region at the top of the pedicel, including the abscission zone. Expressed in developing siliques. {ECO:0000269|PubMed:15960614, ECO:0000269|PubMed:16176952}.
UniprotTISSUE SPECIFICITY: Expressed in the whole plant. {ECO:0000269|PubMed:10476078, ECO:0000269|PubMed:15960614}.
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
PlantRegMapXP_009112005.1
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_009112005.10.0PREDICTED: auxin response factor 2
SwissprotQ94JM30.0ARFB_ARATH; Auxin response factor 2
TrEMBLH9B4C20.0H9B4C2_BRARP; Auxin response factor
STRINGBra035910.1-P0.0(Brassica rapa)
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]