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.1961s0078.1.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: 1018aa    MW: 112919 Da    PI: 6.4772
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cagra.1961s0078.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B373.33e-2370171199
                          EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEE CS
                   B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFk 83 
                          f+k+lt sd++++g +++p++ ae++       + +++  ++++ +d++  +W++++iyr++++r++lt+GW+ Fv+ ++L +gD+v+F 
  Cagra.1961s0078.1.p  70 FCKTLTASDTSTHGGFSVPRRAAEKIfppldfsM-QPPA-QEIVAKDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDSVLFV 157
                          99*****************************954.4444.48************************************************ PP

                          E-SSSEE..EEEEE-S CS
                   B3  84 ldgrsefelvvkvfrk 99 
                            ++++ +l+++++r+
  Cagra.1961s0078.1.p 158 --RDEKSQLMLGIRRA 171
                          ..4567778****997 PP
2Auxin_resp118.64.9e-39196278183
           Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                          aaha +++s+F++++nPras+seFvv+++k++kal+ +vs+GmRf+m+feted+  rr++Gtv+g+sdldpvrW++S+Wr+L+
  Cagra.1961s0078.1.p 196 AAHANANSSPFTIFFNPRASPSEFVVPLAKYNKALYAQVSLGMRFRMMFETEDCGVRRYMGTVTGISDLDPVRWKGSQWRNLQ 278
                          799******************************************************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019363.14E-4460199IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.107.4E-4264185IPR015300DNA-binding pseudobarrel domain
CDDcd100176.11E-2169170No hitNo description
PROSITE profilePS5086312.53470172IPR003340B3 DNA binding domain
PfamPF023621.4E-2170171IPR003340B3 DNA binding domain
SMARTSM010191.0E-2470172IPR003340B3 DNA binding domain
PfamPF065076.9E-34196278IPR010525Auxin response factor
PfamPF023091.2E-9887975IPR033389AUX/IAA domain
PROSITE profilePS5174524.801889982IPR000270PB1 domain
SuperFamilySSF542771.5E-8903967No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009723Biological Processresponse to ethylene
GO:0009733Biological Processresponse to auxin
GO:0010311Biological Processlateral root formation
GO:0048366Biological Processleaf development
GO:0005634Cellular Componentnucleus
GO:0043565Molecular Functionsequence-specific DNA binding
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 1018 aa     Download sequence    Send to blast
MQKQTDFIPN YPNLPSKLIC LLHSVTLHAD TETDEVYAQM TLQPVNKYDR EALLASDMGL  60
KLNRQPTEFF CKTLTASDTS THGGFSVPRR AAEKIFPPLD FSMQPPAQEI VAKDLHDTTW  120
TFRHIYRGQP KRHLLTTGWS VFVSTKRLFA GDSVLFVRDE KSQLMLGIRR ANRQTPTLSS  180
SVISSDSMHI GILAAAAHAN ANSSPFTIFF NPRASPSEFV VPLAKYNKAL YAQVSLGMRF  240
RMMFETEDCG VRRYMGTVTG ISDLDPVRWK GSQWRNLQVG WDESTAGDRP SRVSIWEIEP  300
VITPFYICPP PFFRPKYPRQ PGMPDDELDM ENAFKRAMPW MGEEFGMKDA QSSMFPGLSL  360
VQWMSMQQNN PLSGSATPQL PSALSSYNLP NNFASNDPSK LLNFQSPNLS SANSQFNKLN  420
TVNHISQQMQ AQPAMVKSQQ QQQQQQLQMS HQQLQQQGIY NTGSINNDVS AVANQVSCQN  480
PHQSTTQSQL QQQSMLPNGV KMTHQNIHSG NKGSSQMTSF AQELQFQQQL ELHNSSQSLR  540
NQQEQSSLHS LQQSLSQNPQ QLQMQQQSPK PSPSQQLQLQ LLQKLQQQQQ QQSIPPVTSS  600
LQPQFSALQQ PQSHQLQQLL SSQNQQPLAH GNNSFSASTF MQPPQIQVNH QQQGQINNKP  660
LVAAGRSHSG HTDGEAPSCS TSPSANNTGH DNVSPTNFLS RNQQQGQAVS VSASESVFER  720
ASNPVQELYA KTDNRINQGM VNLKSAGEQF KFKGAVTDQI DVSTAGTTYC PDVVGSAQQQ  780
QTFPLPSFGF DGDCQSHQPR NNLAFASNLE AVTSDALYSQ KDFENLVPNY GNAPRDIETE  840
LSSAAISSQS FGIPSIPFKS GCSNEVGGIN DSGIMNGGGL WPNQTQRMRT YTKVQKRGSV  900
GRSIDVTRYS GYDELRHDLA RMFGIEGQLE DPLTSDWKLV YTDHENDILL VGDDPWEEFV  960
NCVQNIKILS SAEVQQMSLD GDLAAIPATN QACSETDSGN AWKVHYEDTS AAASFNR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A1e-148829996388Auxin response factor 5
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. Involved in ethylene responses. Regulates lateral root formation through direct regulation of LBD16 and/or LBD29. Functionally redundant with ARF7. {ECO:0000269|PubMed:12036261, ECO:0000269|PubMed:16461383, ECO:0000269|PubMed:17259263}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapCagra.1961s0078.1.p
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By auxin and ethylene. {ECO:0000269|PubMed:16461383}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB4934670.0AB493467.1 Arabidopsis thaliana At1g19220 mRNA for hypothetical protein, partial cds, clone: RAAt1g19220.
GenBankATU536720.0U53672.2 Arabidopsis thaliana early auxin-induced IAA22 mRNA, complete cds.
GenBankAY6697940.0AY669794.1 Arabidopsis thaliana clone C105352 ARF19 (At1g19220) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006306645.10.0auxin response factor 19
SwissprotQ8RYC80.0ARFS_ARATH; Auxin response factor 19
TrEMBLR0GUD50.0R0GUD5_9BRAS; Auxin response factor
STRINGCagra.1961s0078.1.p0.0(Capsella grandiflora)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM26292665
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G19220.10.0auxin response factor 19
Publications ? help Back to Top
  1. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
    [PMID:16280546]
  2. Perilli S, et al.
    RETINOBLASTOMA-RELATED protein stimulates cell differentiation in the Arabidopsis root meristem by interacting with cytokinin signaling.
    Plant Cell, 2013. 25(11): p. 4469-78
    [PMID:24285791]
  3. Sun Y, et al.
    Manipulation of Auxin Response Factor 19 affects seed size in the woody perennial Jatropha curcas.
    Sci Rep, 2017. 7: p. 40844
    [PMID:28102350]
  4. 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]
  5. Olmo R, et al.
    Molecular Transducers from Roots Are Triggered in Arabidopsis Leaves by Root-Knot Nematodes for Successful Feeding Site Formation: A Conserved Post-Embryogenic De novo Organogenesis Program?
    Front Plant Sci, 2017. 8: p. 875
    [PMID:28603536]
  6. Lee K,Seo PJ
    High-temperature promotion of callus formation requires the BIN2-ARF-LBD axis in Arabidopsis.
    Planta, 2017. 246(4): p. 797-802
    [PMID:28766014]
  7. Ayala-Rodríguez JÁ,Barrera-Ortiz S,Ruiz-Herrera LF,López-Bucio J
    Folic acid orchestrates root development linking cell elongation with auxin response and acts independently of the TARGET OF RAPAMYCIN signaling in Arabidopsis thaliana.
    Plant Sci., 2017. 264: p. 168-178
    [PMID:28969797]
  8. Nakamura M, et al.
    Auxin and ROP GTPase Signaling of Polar Nuclear Migration in Root Epidermal Hair Cells.
    Plant Physiol., 2018. 176(1): p. 378-391
    [PMID:29084900]
  9. Hong L, et al.
    Alternative polyadenylation is involved in auxin-based plant growth and development.
    Plant J., 2018. 93(2): p. 246-258
    [PMID:29155478]
  10. Lee K,Park OS,Seo PJ
    Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD genes to facilitate cellular dedifferentiation.
    Sci Signal, 2018.
    [PMID:29184030]
  11. Kimura T, et al.
    Asymmetric Auxin Distribution is Not Required to Establish Root Phototropism in Arabidopsis.
    Plant Cell Physiol., 2018. 59(4): p. 823-835
    [PMID:29401292]
  12. Schoenaers S, et al.
    The Auxin-Regulated CrRLK1L Kinase ERULUS Controls Cell Wall Composition during Root Hair Tip Growth.
    Curr. Biol., 2018. 28(5): p. 722-732.e6
    [PMID:29478854]
  13. Huang KL, et al.
    The ARF7 and ARF19 Transcription Factors Positively Regulate PHOSPHATE STARVATION RESPONSE1 in Arabidopsis Roots.
    Plant Physiol., 2018. 178(1): p. 413-427
    [PMID:30026290]