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 Cagra.0996s0001.1.p
Organism
Capsella grandiflora
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: 666aa    MW: 73849.9 Da    PI: 5.9545
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cagra.0996s0001.1.pgenomeJGIView 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-EEEEE CS
                   B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFk 83 
                          f+k+lt sd++++g +++ +++a+++       +++    ++l+ +d+++++W +++i+r++++r++lt+GW+ Fv++++L +gD ++F 
  Cagra.0996s0001.1.p 124 FCKTLTASDTSTHGGFSVLRRHADDClppldmsQQP--PWQELVATDLHNNEWHFRHIFRGQPRRHLLTTGWSVFVSSKKLVAGDAFIFL 211
                          99****************************964333..4459************************************************ PP

                          E-SSSEE..EEEEE-S CS
                   B3  84 ldgrsefelvvkvfrk 99 
                            + +++el+v+v+r+
  Cagra.0996s0001.1.p 212 --RGENEELRVGVRRH 225
                          ..3488889****996 PP
2Auxin_resp112.34.7e-37250332183
           Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                          aaha++t+++F+v+Y+Pr+s+seF+v+v+++++a ++k+svGmRfkm+fe+e+++e+r+sGt+vgv++ +++ W++S+WrsLk
  Cagra.0996s0001.1.p 250 AAHAITTGTIFSVFYKPRTSRSEFIVSVNRYLEAKTQKLSVGMRFKMRFEGEEAPEKRFSGTIVGVQENKSSVWHDSEWRSLK 332
                          79*******************************************************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019363.53E-44113253IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.104.1E-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
PfamPF065073.5E-34250332IPR010525Auxin response factor
PfamPF023092.1E-11537632IPR033389AUX/IAA domain
PROSITE profilePS5174530.586542635IPR000270PB1 domain
SuperFamilySSF542771.31E-11543619No hitNo description
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: 666 aa     Download sequence    Send to blast
MAATNPSSEK PGGVLSDALC RELWHACAGP LVTLPHEGER VYYFPEGHME QLEASMHQGL  60
EQQMPSFNLP SKILCKVINI QRRAEPETDE VYAQITLLPE LDQSEPISPD APVQEPEKCT  120
VHSFCKTLTA SDTSTHGGFS VLRRHADDCL PPLDMSQQPP WQELVATDLH NNEWHFRHIF  180
RGQPRRHLLT TGWSVFVSSK KLVAGDAFIF LRGENEELRV GVRRHMRQQT NVPSSVISSH  240
SMHIGVLATA AHAITTGTIF SVFYKPRTSR SEFIVSVNRY LEAKTQKLSV GMRFKMRFEG  300
EEAPEKRFSG TIVGVQENKS SVWHDSEWRS LKVQWDEPSS VFRPERVSPW ELEPLVANST  360
PSSQPQPPQR NKRPRPPGLP APTTGPSAAV TPDSVWKSPA DTPSSVPLFS PPAKAAMFGP  420
GGNKSFGVSI GSAFWPTHAD SAAESFASAF NNESTEKKQT NGNVCRLFGF ELVENVNVDE  480
CFSAASVSGA VAVDQPVPSN EFDSGQQSEP LNINQSDIPS GSGDPEKSSL RSPQESQSRQ  540
IRTCTKVHMQ GSAVGRAVDL TRSECYEDLF KKLEEMFDIK GELIESTKKW QVVYTDDEDD  600
MMMVGDDPWN EFCGMVRKIF IYTPEEVKKL SPKNKLTVNA RMQPKNDVEE NGNTEGRSSS  660
MAGSR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A0.013591359Auxin response factor 1
4ldw_A0.013591359Auxin response factor 1
4ldw_B0.013591359Auxin response factor 1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1371375KRPRP
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
PlantRegMapCagra.0996s0001.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK3172140.0AK317214.1 Arabidopsis thaliana AT1G59750 mRNA, complete cds, clone: RAFL22-03-B07.
GenBankATU832450.0U83245.1 Arabidopsis thaliana auxin response factor 1 (ARF1) mRNA, complete cds.
GenBankBT0027480.0BT002748.1 Arabidopsis thaliana clone C105458 auxin response factor 1 (At1g59750) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006300434.10.0auxin response factor 1 isoform X1
RefseqXP_023644040.10.0auxin response factor 1 isoform X1
RefseqXP_023644041.10.0auxin response factor 1 isoform X1
SwissprotQ8L7G00.0ARFA_ARATH; Auxin response factor 1
TrEMBLR0GC660.0R0GC66_9BRAS; Auxin response factor
STRINGCagra.0996s0001.1.p0.0(Capsella grandiflora)
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]