PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Cagra.0096s0050.1.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: 594aa    MW: 64703.1 Da    PI: 6.2469
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cagra.0096s0050.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B375.17.9e-24123224199
                          EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEE CS
                   B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFk 83 
                          f k+ltpsd+++ g +++p+ +a++          ++ +  +l ++d +g +W++++iyr++++r++lt+GW++Fv++++L +gD+vvF+
  Cagra.0096s0050.1.p 123 FAKILTPSDANNGGGFSVPRYCADSVfppldflADPPVQ--KLFITDIHGSVWDFRHIYRGTPRRHLLTTGWSKFVNSKKLIAGDSVVFM 210
                          89*********************999*****98666666..7************************************************ PP

                          E-SSSEE..EEEEE-S CS
                   B3  84 ldgrsefelvvkvfrk 99 
                            ++s  e++++v+r+
  Cagra.0096s0050.1.p 211 --RKSADEMFIGVRRT 224
                          ..44788899***997 PP
2Auxin_resp89.75.2e-30280362183
           Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrl.sGtvvgvsdldpvrWpnSkWrsLk 83 
                          a+++as++ +FevvY+P a++s+Fvv++e+ve+++++ +++G+R+kma+etedss++++ +G+v+++ + ++  W++S+W++L+
  Cagra.0096s0050.1.p 280 AMNRASQGLPFEVVYYPTAGWSDFVVRAEDVESSMSMFWTPGTRVKMAMETEDSSRITWfQGIVSSTYQ-ETGPWRGSPWKQLQ 362
                          6899*******************************************************9999999999.888*********97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.103.5E-33116225IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019362.49E-27116224IPR015300DNA-binding pseudobarrel domain
SMARTSM010192.3E-20123225IPR003340B3 DNA binding domain
CDDcd100171.83E-20123219No hitNo description
PROSITE profilePS5086312.985123225IPR003340B3 DNA binding domain
PfamPF023623.6E-21123224IPR003340B3 DNA binding domain
PfamPF065071.2E-24280362IPR010525Auxin response factor
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:0010208Biological Processpollen wall assembly
GO:0048830Biological Processadventitious root development
GO:0052543Biological Processcallose deposition in cell wall
GO:0005634Cellular Componentnucleus
GO:0000987Molecular Functioncore promoter proximal region sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 594 aa     Download sequence    Send to blast
MSPPSESAAG DILHRGVDPT IWRACAGASV QIPQLYSRVY YFPQGHVEHC CASSPLSSSP  60
PPSTSPVPCR ISSIQLLADP ITDEVFAHLL LQPMSQDQFA PTNFSRFPAY EGDVDDNNKV  120
TTFAKILTPS DANNGGGFSV PRYCADSVFP PLDFLADPPV QKLFITDIHG SVWDFRHIYR  180
GTPRRHLLTT GWSKFVNSKK LIAGDSVVFM RKSADEMFIG VRRTPTSNHG GGTSYYGGDE  240
YNGYYSQING ALAKEDDGSA KKMFRRTGKG KLTPEAVSEA MNRASQGLPF EVVYYPTAGW  300
SDFVVRAEDV ESSMSMFWTP GTRVKMAMET EDSSRITWFQ GIVSSTYQET GPWRGSPWKQ  360
LQITWDEPEV LQNVKRVNPW QVEIVANATQ LHPTFPPAKR LKYPQTGGFL SGDDGEILYP  420
PQRGLSSAAA PDSSPFLNSY TTFPAGMQGA RHYEFGSHNP TGFIGENPPQ LSTNNFFSPL  480
PGLGKVSTEK NFGSPPSDNL SPNSNSTNLS SGNDLVGNRV PNTAKANSIK LFGKTITVQE  540
PSESGLAESG LCEEDGSKES SDNTTQLSLT HGPRTREDSR CTPTATQSIS AKV*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A2e-651039012360Auxin response factor 1
4ldw_A2e-651039012360Auxin response factor 1
4ldw_B2e-651039012360Auxin response factor 1
4ldx_A2e-651039012360Auxin response factor 1
4ldx_B2e-651039012360Auxin 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
PlantRegMapCagra.0096s0050.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006302016.20.0auxin response factor 17
SwissprotQ84WU60.0ARFQ_ARATH; Auxin response factor 17
TrEMBLR0HYF10.0R0HYF1_9BRAS; Auxin response factor (Fragment)
STRINGCagra.0096s0050.1.p0.0(Capsella grandiflora)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM58027130
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G77850.10.0auxin response factor 17
Publications ? help Back to Top
  1. Shi ZH, et al.
    Overexpression of AtTTP affects ARF17 expression and leads to male sterility in Arabidopsis.
    PLoS ONE, 2015. 10(3): p. e0117317
    [PMID:25822980]
  2. de Lucas M, et al.
    Transcriptional Regulation of Arabidopsis Polycomb Repressive Complex 2 Coordinates Cell-Type Proliferation and Differentiation.
    Plant Cell, 2016. 28(10): p. 2616-2631
    [PMID:27650334]
  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. Wang B, et al.
    Fine regulation of ARF17 for anther development and pollen formation.
    BMC Plant Biol., 2017. 17(1): p. 243
    [PMID:29258431]
  5. Wójcik AM,Nodine MD,Gaj MD
    miR160 and miR166/165 Contribute to the LEC2-Mediated Auxin Response Involved in the Somatic Embryogenesis Induction in Arabidopsis.
    Front Plant Sci, 2017. 8: p. 2024
    [PMID:29321785]
  6. Lin JS, et al.
    MicroRNA160 Modulates Plant Development and Heat Shock Protein Gene Expression to Mediate Heat Tolerance in Arabidopsis.
    Front Plant Sci, 2018. 9: p. 68
    [PMID:29449855]