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_00023239-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: 898aa    MW: 99880.8 Da    PI: 6.2884
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
PSME_00023239-RAgenomePRSView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B375.84.7e-24115216199
                       EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SS CS
                B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgr 87 
                       f+k+lt sd++++g +++p++ ae+       +++++  ++l  +d++ ++W++++iyr++++r++lt+GW+ Fv+a++L +gD+vvF   ++
  PSME_00023239-RA 115 FCKTLTASDTSTHGGFSVPRRAAEKVfppldfSMQPPA-QELLARDLHDNVWTFRHIYRGQPKRHLLTTGWSVFVSAKRLVAGDSVVFI--RD 204
                       99*****************************9445444.38************************************************..56 PP

                       SEE..EEEEE-S CS
                B3  88 sefelvvkvfrk 99 
                       ++ +l+++++r+
  PSME_00023239-RA 205 EKLQLLLGIRRA 216
                       99999****997 PP
2Auxin_resp117.61e-38241324183
        Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                       aahaa+++s+F+v+YnPr+s+seFvv+++k++ka++ ++vsvGm f+m+fete+ss rr++Gt++g+s ldpvrWp+S+Wr+L+
  PSME_00023239-RA 241 AAHAAANQSPFTVFYNPRTSPSEFVVPLAKYNKAVYgTQVSVGMHFRMMFETEESSVRRYMGTITGISPLDPVRWPKSQWRNLQ 324
                       79**********************************9*********************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.29E-45105244IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.103.4E-42107229IPR015300DNA-binding pseudobarrel domain
CDDcd100171.07E-21114215No hitNo description
PfamPF023622.1E-22115216IPR003340B3 DNA binding domain
SMARTSM010191.2E-24115217IPR003340B3 DNA binding domain
PROSITE profilePS5086312.266115217IPR003340B3 DNA binding domain
PfamPF065074.8E-34241324IPR010525Auxin response factor
PfamPF023094.6E-7766851IPR033389AUX/IAA domain
PROSITE profilePS5174526.256766850IPR000270PB1 domain
SuperFamilySSF542776.54E-8781844No hitNo description
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
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 898 aa     Download sequence    Send to blast
MKSEQKSINS ELWHACAGPL VSLPSVGSFV YYFPQGHSEQ VAASTQKVAD THIPNYPNLP  60
YQLMCQLHNV TLHADAETDE VYAQMTLQPV NSCNKKEILS SDLGLKQSKQ PTEFFCKTLT  120
ASDTSTHGGF SVPRRAAEKV FPPLDFSMQP PAQELLARDL HDNVWTFRHI YRGQPKRHLL  180
TTGWSVFVSA KRLVAGDSVV FIRDEKLQLL LGIRRANRQQ TSMPLSVLST DSMHIGVLAA  240
AAHAAANQSP FTVFYNPRTS PSEFVVPLAK YNKAVYGTQV SVGMHFRMMF ETEESSVRRY  300
MGTITGISPL DPVRWPKSQW RNLQVRWEES GAGERPIRVS IWEIESVASP FFICPPFFRL  360
KRPVQPGMFG EETDIESTTK RSSPWLREEH DILDFQHPLS VFGLEPWIGL QQRHDVINST  420
VPLEYYRSMA GKTSEEFRSN DACKELSTTT RAINSASAAS TSAPATSSAI APSHKQSVEH  480
PLHDHQQMQP QSSQLHELEG QLLQPSSTRS HASCNLVPTR SQSGLTESDV SFCSTTTPVG  540
SCSWQNVLTR TQPVGVKLEE KSHYSNILRP APVNTQGATY SSNHISEPLV TSWFTSNKEP  600
SQTELRAIPN FHSGEMETSS FGAAISMINA NATAQPGFST LPNTSNSYWY GSTSQDNEIQ  660
TDARNSILFN GANIESPLAD HSNTSSLVGR VFNGVKDVPC QLSAESMMST LSTGKDVQPQ  720
ISSASMLSPH SLAVQDLPDN SDVASTVEDN NFLQKGSLQQ LAPPVRTYTK VYKLGYVGRS  780
IDVTRYRNYG ELRQELARMF GMEGQLEDPM SGWQLVFVDH ENDILLVGDD PWEEFVSCVR  840
SIKILSPQEV LQMSQEGIEI INNTPIQLQT SSYSDDHNAW RDHCYQNSTN PSSISFSH
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A0.0834651389Auxin 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}.
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT1020310.0BT102031.1 Picea glauca clone GQ0163_N22 mRNA sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_024385807.10.0auxin response factor 6-like isoform X2
SwissprotQ8RYC80.0ARFS_ARATH; Auxin response factor 19
TrEMBLA0A2K1LBN00.0A0A2K1LBN0_PHYPA; Auxin response factor
STRINGPP1S163_119V6.10.0(Physcomitrella patens)
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]