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 PSME_00020341-RA
Organism
Pseudotsuga menziesii
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Acrogymnospermae; Pinidae; Pinales; Pinaceae; Pseudotsuga
Family ARF
Protein Properties Length: 820aa    MW: 91019.3 Da    PI: 6.473
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
PSME_00020341-RAgenomePRSView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B373.42.7e-23193294199
                       EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-S CS
                B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldg 86 
                       f+k+lt sd++++g +++p++ ae++       ++++++  +l+ +d++   W++++iyr++++r++lt+GW+ Fv+a++L +gD+v+F   +
  PSME_00020341-RA 193 FCKTLTASDTSTHGGFSVPRRAAEKIfpsldytMQPPAQ--ELMARDLHDHAWTFRHIYRGQPKRHLLTTGWSVFVSAKRLFAGDSVLFI--R 281
                       99*****************************96555544..8************************************************..4 PP

                       SSEE..EEEEE-S CS
                B3  87 rsefelvvkvfrk 99 
                       +++ +l+++++r+
  PSME_00020341-RA 282 DEKSQLLLGIRRA 294
                       5677789999997 PP
2Auxin_resp117.51.1e-38319402183
        Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                       aahaas++s+F+v+YnPras+seFv++++k+++a++ ++vs+GmRf+m+fete+s  rr++Gt++g+sdldp++WpnS+Wr+++
  PSME_00020341-RA 319 AAHAASNHSPFTVFYNPRASPSEFVIPLSKYNNAIYgTQVSLGMRFRMMFETEESGVRRYMGTITGISDLDPLKWPNSQWRNIQ 402
                       79**********************************9********************************************986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.7E-45180322IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.104.0E-42185308IPR015300DNA-binding pseudobarrel domain
CDDcd100172.35E-19192293No hitNo description
PfamPF023625.2E-21193294IPR003340B3 DNA binding domain
PROSITE profilePS5086312.224193295IPR003340B3 DNA binding domain
SMARTSM010192.3E-22193295IPR003340B3 DNA binding domain
PfamPF065073.6E-33319402IPR010525Auxin response factor
PROSITE profilePS5174526.838688772IPR000270PB1 domain
PfamPF023096.1E-8690774IPR033389AUX/IAA domain
SuperFamilySSF542778.34E-9705767No 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: 820 aa     Download sequence    Send to blast
MNTTQQSFSY GSFANLRFVR ETTEFSPYFR QSGGKGPGSV NVSRFISEGF LSCMGIEVDT  60
WLGSRKMKAP SNGYFPQPQD GERRSINSEL WHACAGPLVS LPQVGSLVVY FPQGHSEQVA  120
ASMQKETDGH IPNYPNLPSK LICQLHNVTL HADAETDEVY AQMTLQPVNA HDKEASSHSD  180
LGLKQSKQPT EFFCKTLTAS DTSTHGGFSV PRRAAEKIFP SLDYTMQPPA QELMARDLHD  240
HAWTFRHIYR GQPKRHLLTT GWSVFVSAKR LFAGDSVLFI RDEKSQLLLG IRRANRQQTA  300
MSSSVLSSDS MHIGVLAAAA HAASNHSPFT VFYNPRASPS EFVIPLSKYN NAIYGTQVSL  360
GMRFRMMFET EESGVRRYMG TITGISDLDP LKWPNSQWRN IQVGWDESSA GERQNRVSIW  420
EIEPVATPFF ICPPPFFRPK RPRQPGMLGE ESEIESALKR SLPWFGEDTG IGNSQNPTMP  480
GVGLLQWMNM HQRPDIINSA IHYPLQNILT RANQSAIMND EKPHCANMLR PSASSTQAAL  540
PASNFLGDPQ IASLLPSIKE PNQAALQTYL SAQLGQMEAS SSSGTSYSLT PDVAISQSLP  600
LLPLQSSPFM FRDVSHDNDI QTDPRRNMLP TFSTGKDNQA QVSATINSQT FSVPDLPLNS  660
GVTSDLGISD SSILQRGGSW QQQPPPVRTY TKVYKLGSVG RSIDVTRCKN YDELRRELAR  720
MFGLEGQLED PQRSGWQLVF VDNENDVLLV GDDPWEEFVS CVRCIRILSP TEVLQMSQDG  780
MLLNTLPLQQ QAGSSSDGGI VWRDHCDQNS TNPSVGSFEH
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A1e-1797942343388Auxin 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}.
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
GenBankBT1180250.0BT118025.1 Picea glauca clone GQ04001_F16 mRNA sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_027170288.10.0auxin response factor 6-like isoform X2
SwissprotQ8RYC80.0ARFS_ARATH; Auxin response factor 19
TrEMBLA0A1R3IUW20.0A0A1R3IUW2_9ROSI; Auxin response factor
STRINGPavir.Db01975.1.p0.0(Panicum virgatum)
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]