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 Carubv10019991m
Common NameCARUB_v10019991mg
Organism
Capsella rubella
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: 617aa    MW: 67256.2 Da    PI: 6.2461
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Carubv10019991mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B3758.4e-24146247199
                      EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SS CS
               B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgr 87 
                      f k+ltpsd+++ g +++p+ +a++          ++ +  +l ++d +g +W++++iyr++++r++lt+GW++Fv++++L +gD+vvF+  ++
  Carubv10019991m 146 FAKILTPSDANNGGGFSVPRYCADSVfppldflADPPVQ--KLFITDIHGSVWDFRHIYRGTPRRHLLTTGWSKFVNSKKLIAGDSVVFM--RK 235
                      89*********************999*****98666666..7************************************************..44 PP

                      SEE..EEEEE-S CS
               B3  88 sefelvvkvfrk 99 
                      s  e++++v+r+
  Carubv10019991m 236 SADEMFIGVRRT 247
                      788899***997 PP
2Auxin_resp87.72.3e-29303385183
       Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrl.sGtvvgvsdldpvrWpnSkWrsLk 83 
                      a+++a+++  FevvY+P a++s+Fvv++e+ve+++++ +++G+R+kma+etedss++++ +G+v+++ + ++  W++S+W++L+
  Carubv10019991m 303 AMNRAAQGLSFEVVYYPTAGWSDFVVRAEDVESSMSMFWTPGTRVKMAMETEDSSRITWfQGIVSSTYQ-ETGPWRGSPWKQLQ 385
                      67899******************************************************9999999999.888*********97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.103.7E-33139248IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019362.62E-27139247IPR015300DNA-binding pseudobarrel domain
PROSITE profilePS5086312.985146248IPR003340B3 DNA binding domain
PfamPF023623.8E-21146247IPR003340B3 DNA binding domain
SMARTSM010192.3E-20146248IPR003340B3 DNA binding domain
CDDcd100172.02E-20146242No hitNo description
PfamPF065073.4E-24303385IPR010525Auxin response factor
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009734Biological Processauxin-activated signaling pathway
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: 617 aa     Download sequence    Send to blast
YLPLLLLLLL LLSLTSLQCN QTPMSPPSES AAGDILHRGV DPTIWRACAG ASVQIPQLYS  60
RVYYFPQGHV EHCCASSPLS SSPPPSTSPV PCRISSIQLL ADPITDEVFA HLLLQPMSQD  120
QFAPTNFSRF PAYEGDVDDN NKVTTFAKIL TPSDANNGGG FSVPRYCADS VFPPLDFLAD  180
PPVQKLFITD IHGSVWDFRH IYRGTPRRHL LTTGWSKFVN SKKLIAGDSV VFMRKSADEM  240
FIGVRRTPTS NHGGGTSYYG GDEYNGYYSQ INGALAKEDD GSAKKMFRRT GKGKLTPEAV  300
SEAMNRAAQG LSFEVVYYPT AGWSDFVVRA EDVESSMSMF WTPGTRVKMA METEDSSRIT  360
WFQGIVSSTY QETGPWRGSP WKQLQITWDE PEILQNVKRV NPWQVEIVAN ATQLHPTFPP  420
AKRLKYPQTG GFLSGDDGEI LYPPQRGLSS AAAPDSSPFL NSYTTFPAGM QGARHYEFGS  480
HNPTGFIGEN PPQLSTNNFF SPLPGLGKVS TEKNFGSPPS DNLSPNSNST NLSSGNDLVG  540
NRVPNTAKAN SIKLFGKTIT VQEPSESGLA ESGLCEEDGS KESSDNTTQL SLTHGPRTRE  600
DSRCTPTATQ SISAKV*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A4e-653341312360Auxin response factor 1
4ldw_A4e-653341312360Auxin response factor 1
4ldw_B4e-653341312360Auxin response factor 1
4ldx_A5e-653341312360Auxin response factor 1
4ldx_B5e-653341312360Auxin 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
PlantRegMapCarubv10019991m
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)
STRINGXP_006302016.10.0(Capsella rubella)
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]