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 Rsa1.0_01789.1_g00010.1
Organism
Raphanus sativus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family ARF
Protein Properties Length: 889aa    MW: 98228.7 Da    PI: 7.6789
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_01789.1_g00010.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B373.62.4e-23127228199
                              EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-E CS
                       B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDf 79 
                              f+k+lt sd++++g +++p++ ae++       + +++  ++++ +d++  +W++++iyr++++r++lt+GW+ Fv+ ++L +gD+
  Rsa1.0_01789.1_g00010.1 127 FCKTLTASDTSTHGGFSVPRRAAEKIfppldfsM-QPPA-QEIVAKDLHDTTWTFRHIYRGQPKRHLLTSGWSVFVSTKRLFAGDS 210
                              99*****************************954.4444.48******************************************** PP

                              EEEEE-SSSEE..EEEEE-S CS
                       B3  80 vvFkldgrsefelvvkvfrk 99 
                              v+F   ++++ +l+++++r+
  Rsa1.0_01789.1_g00010.1 211 VLFV--RDEKSHLMLGIRRA 228
                              ****..5578888****997 PP
2Auxin_resp115.44.9e-38253335183
               Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                              aaha +++s+F++++nPras+seFvv+++k++kal  +vs+GmRf+m feted+  rr++Gtv+g+sdldpvrW++S+Wr+L+
  Rsa1.0_01789.1_g00010.1 253 AAHANANSSPFTIFFNPRASPSEFVVPLAKYNKALFAQVSLGMRFRMVFETEDCGVRRYMGTVTGISDLDPVRWKGSQWRNLQ 335
                              799******************************************************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019368.11E-43117256IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.106.5E-42121242IPR015300DNA-binding pseudobarrel domain
CDDcd100171.57E-21126227No hitNo description
SMARTSM010191.8E-24127229IPR003340B3 DNA binding domain
PROSITE profilePS5086312.478127229IPR003340B3 DNA binding domain
PfamPF023621.3E-21127228IPR003340B3 DNA binding domain
PfamPF065076.4E-33253335IPR010525Auxin 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:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 889 aa     Download sequence    Send to blast
MKAPSNGFYP NSIEGEEKKP INSQLWHACA GPLVSLPPVG SLVVYFPQGH SEQVAASMQK  60
QTEFIPNYPN LPSKLICLLH SVTLHADTET DEVYAQMTLQ PVNKYDRETL LASDMGLKLN  120
RQPTEFFCKT LTASDTSTHG GFSVPRRAAE KIFPPLDFSM QPPAQEIVAK DLHDTTWTFR  180
HIYRGQPKRH LLTSGWSVFV STKRLFAGDS VLFVRDEKSH LMLGIRRANR QTPTLSSSVI  240
SSDSMHIGIL AAAAHANANS SPFTIFFNPR ASPSEFVVPL AKYNKALFAQ VSLGMRFRMV  300
FETEDCGVRR YMGTVTGISD LDPVRWKGSQ WRNLQVGWDE STAGDRPSRV SIWEIEPVIT  360
PFYICPPPFF RPKYPRQPGM QDDELDRAMP WMGEEFGMKD AQSSMFPGLS LVQWMSMQQN  420
NNNTLSATAT QLPSALSSYN LPNSFSPNDP SKLLNFQSPN LSSENSQFNK PNMVSHISQQ  480
MQAQPAVVKS QQQEQQMQQQ VQMSHQQLQK GVYNACSVNN GVSVVSNQVS SQIQSTGFSQ  540
SQQSMLSNGA KMNHQNVVGN KVSSQMASFA QELQFQQQME LHNSSQLSRN QQEQSSMQSL  600
QQNLSQNPQQ LQLQLLQTLQ QQQQSIPPVS SSLQPQLSAL QQTTQSHQLQ QLLSSQNQQP  660
FSTSPVMQPP QVQVSHQQQG HMNNKTLVTA GRSHSGHTDG EAPSCSTSPS TNNTGHNNVS  720
PTNFLSRNRQ QGQAGSAPAS DTVFNRASNQ VQELYTKTES LVNLKSSAEY KFKGAVTDQI  780
IVSTTGTTYC PDAAGPVQQQ QTFPLPSFGF DGDCQPQHPR NNLAGNLESV TSEALYSQKD  840
FQNLAPNYGN APRDIETELS SAAISSQSFG IPSIPFKSGG STNANVYKG
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A1e-1731535645388Auxin 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
PlantRegMapRsa1.0_01789.1_g00010.1
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
GenBankJN9794830.0JN979483.1 Brassica rapa subsp. pekinensis auxin response factor 19-1 (ARF19-1) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018450274.10.0PREDICTED: auxin response factor 19-like
RefseqXP_018451575.10.0PREDICTED: auxin response factor 19-like
SwissprotQ8RYC80.0ARFS_ARATH; Auxin response factor 19
TrEMBLV4KB060.0V4KB06_EUTSA; Auxin response factor
STRINGXP_006416527.10.0(Eutrema salsugineum)
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]