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_009103121.1
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: 665aa    MW: 73797 Da    PI: 6.5121
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009103121.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B368.87.6e-22124225199
                     EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSS CS
              B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrs 88 
                     f+k+lt sd++++g +++ +++a+++       +++    ++l+ +d+++++W +++i+r++++r++lt+GW+ Fv++++L +gD ++F   + +
  XP_009103121.1 124 FCKTLTASDTSTHGGFSVLRRHADDClppldmsQQP--PWQELVATDLHNNEWHFRHIFRGQPRRHLLTTGWSVFVSSKKLVAGDAFIFL--RGE 214
                     99****************************964333..4459************************************************..348 PP

                     EE..EEEEE-S CS
              B3  89 efelvvkvfrk 99 
                     ++el+v+v+r+
  XP_009103121.1 215 NEELRVGVRRH 225
                     8889****996 PP
2Auxin_resp112.44.4e-37250332183
      Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                     aaha++t+++F+v+Y+Pr+s+seF+v+v+++++a ++k++vGmRfkm+fe+e+++e+r+sGt+vgv++ +++ W++S+WrsLk
  XP_009103121.1 250 AAHAITTGTIFSVFYKPRTSRSEFIVSVNRYLEAKNQKLAVGMRFKMRFEGEEAPEKRFSGTIVGVQENKSSVWHDSEWRSLK 332
                     79*******************************************************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.86E-44113253IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.103.9E-40121239IPR015300DNA-binding pseudobarrel domain
CDDcd100171.88E-19122224No hitNo description
PfamPF023621.1E-19124225IPR003340B3 DNA binding domain
SMARTSM010194.9E-21124226IPR003340B3 DNA binding domain
PROSITE profilePS5086310.588124226IPR003340B3 DNA binding domain
PfamPF065073.0E-34250332IPR010525Auxin response factor
PfamPF023097.4E-6533578IPR033389AUX/IAA domain
PROSITE profilePS5174530.558542635IPR000270PB1 domain
SuperFamilySSF542771.44E-11543619No hitNo description
PfamPF023093.4E-6582632IPR033389AUX/IAA domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009733Biological Processresponse to auxin
GO:0010150Biological Processleaf senescence
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0042802Molecular Functionidentical protein binding
Sequence ? help Back to Top
Protein Sequence    Length: 665 aa     Download sequence    Send to blast
MAASNHPCGK PGGALSDALC RELWHACAGP LVTLPREGER VYYFPEGHME QLEASMHQGL  60
EQQMPSFNLP SKILCKVINI QRRAEPETDE VYAQITLLPE ADQSEPMSPD APVQEPEKCT  120
VHSFCKTLTA SDTSTHGGFS VLRRHADDCL PPLDMSQQPP WQELVATDLH NNEWHFRHIF  180
RGQPRRHLLT TGWSVFVSSK KLVAGDAFIF LRGENEELRV GVRRHMRQQT NIPSSVISSH  240
SMHIGVLATA AHAITTGTIF SVFYKPRTSR SEFIVSVNRY LEAKNQKLAV GMRFKMRFEG  300
EEAPEKRFSG TIVGVQENKS SVWHDSEWRS LKVQWDEPSS VFRPERVSPW ELEPLVANNT  360
PSAHLPPQRN KRPRPPGLLS PTTAPSTPVT ADGVWKSPAD NPSSVPLFSP PAKTAAFGLG  420
GNKSFGVSIG SAFWPTHADG AAESFASALN NESPTEKKQT NGNVCRLFGF ELVENMNVDE  480
CFSAASVSGA VAVDQPVPSN EFDSGQQSES LNINQANLPS GSGDHEKSSL RSPQKSQSRQ  540
IRSCTKVHMQ GSAVGRAVDL TRSECYEDLF KKLEEMFDIK GELLESTKKW QVVYTDDEDD  600
MMMVGDDPWN EFCGMVRKIF IYTPEEVKKL SPKNKLTVNV RMQPKTDADE NGNTEGRSSS  660
MAGSR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A0.013551355Auxin response factor 1
4ldw_A0.013551355Auxin response factor 1
4ldw_B0.013551355Auxin response factor 1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1370374KRPRP
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. {ECO:0000269|PubMed:16176952}.
UniprotTISSUE SPECIFICITY: Expressed in the whole plant. {ECO:0000269|PubMed:10476078}.
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). Seems to act as transcriptional 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. Acts as repressor of IAA2, IAA3 and IAA7. {ECO:0000269|PubMed:12036261, ECO:0000269|PubMed:16176952}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00097PBMTransfer from AT1G59750Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009103121.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankJN9794580.0JN979458.1 Brassica rapa subsp. pekinensis auxin response factor 1 (ARF1) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009103121.10.0PREDICTED: auxin response factor 1 isoform X1
RefseqXP_009103129.10.0PREDICTED: auxin response factor 1 isoform X1
RefseqXP_009103136.10.0PREDICTED: auxin response factor 1 isoform X1
SwissprotQ8L7G00.0ARFA_ARATH; Auxin response factor 1
TrEMBLH9B4B90.0H9B4B9_BRARP; Auxin response factor
STRINGBra035427.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM88252227
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G59750.30.0auxin response factor 1
Publications ? help Back to Top
  1. Montesinos JC,Pastor-Cantizano N,Robinson DG,Marcote MJ,Aniento F
    Arabidopsis p24δ5 and p24δ9 facilitate Coat Protein I-dependent transport of the K/HDEL receptor ERD2 from the Golgi to the endoplasmic reticulum.
    Plant J., 2014. 80(6): p. 1014-30
    [PMID:25312353]
  2. Marais C, et al.
    The Qb-SNARE Memb11 interacts specifically with Arf1 in the Golgi apparatus of Arabidopsis thaliana.
    J. Exp. Bot., 2015. 66(21): p. 6665-78
    [PMID:26208648]
  3. 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]
  4. 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]