ID   ARFD_ARATH              Reviewed;         788 AA.
AC   Q9ZTX9;
DT   13-APR-2004, integrated into UniProtKB/Swiss-Prot.
DT   01-MAY-1999, sequence version 1.
DT   03-AUG-2022, entry version 140.
DE   RecName: Full=Auxin response factor 4;
GN   Name=ARF4; OrderedLocusNames=At5g60450; ORFNames=MUF9.8;
OS   Arabidopsis thaliana (Mouse-ear cress).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC   rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX   NCBI_TaxID=3702;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=10318972; DOI=10.1073/pnas.96.10.5844;
RA   Ulmasov T., Hagen G., Guilfoyle T.J.;
RT   "Activation and repression of transcription by auxin-response factors.";
RL   Proc. Natl. Acad. Sci. U.S.A. 96:5844-5849(1999).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=9679202; DOI=10.1093/dnares/5.2.131;
RA   Kaneko T., Kotani H., Nakamura Y., Sato S., Asamizu E., Miyajima N.,
RA   Tabata S.;
RT   "Structural analysis of Arabidopsis thaliana chromosome 5. V. Sequence
RT   features of the regions of 1,381,565 bp covered by twenty one physically
RT   assigned P1 and TAC clones.";
RL   DNA Res. 5:131-145(1998).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Columbia;
RX   PubMed=27862469; DOI=10.1111/tpj.13415;
RA   Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA   Town C.D.;
RT   "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT   genome.";
RL   Plant J. 89:789-804(2017).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=14593172; DOI=10.1126/science.1088305;
RA   Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA   Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA   Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA   Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA   Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA   Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA   Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA   Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA   Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA   Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA   Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA   Ecker J.R.;
RT   "Empirical analysis of transcriptional activity in the Arabidopsis
RT   genome.";
RL   Science 302:842-846(2003).
RN   [5]
RP   DIMERIZATION, AND TISSUE SPECIFICITY.
RX   PubMed=10476078; DOI=10.1046/j.1365-313x.1999.00538.x;
RA   Ulmasov T., Hagen G., Guilfoyle T.J.;
RT   "Dimerization and DNA binding of auxin response factors.";
RL   Plant J. 19:309-319(1999).
RN   [6]
RP   GENE FAMILY, NOMENCLATURE, AND FUNCTION.
RX   PubMed=12036261; DOI=10.1023/a:1015207114117;
RA   Hagen G., Guilfoyle T.J.;
RT   "Auxin-responsive gene expression: genes, promoters and regulatory
RT   factors.";
RL   Plant Mol. Biol. 49:373-385(2002).
RN   [7]
RP   GENE FAMILY.
RX   PubMed=18986826; DOI=10.1016/j.tplants.2008.09.006;
RA   Swaminathan K., Peterson K., Jack T.;
RT   "The plant B3 superfamily.";
RL   Trends Plant Sci. 13:647-655(2008).
RN   [8]
RP   DISRUPTION PHENOTYPE.
RX   PubMed=27334696; DOI=10.1242/bio.019109;
RA   Matsumura Y., Ohbayashi I., Takahashi H., Kojima S., Ishibashi N., Keta S.,
RA   Nakagawa A., Hayashi R., Saez-Vasquez J., Echeverria M., Sugiyama M.,
RA   Nakamura K., Machida C., Machida Y.;
RT   "A genetic link between epigenetic repressor AS1-AS2 and a putative small
RT   subunit processome in leaf polarity establishment of Arabidopsis.";
RL   Biol. Open 5:942-954(2016).
CC   -!- FUNCTION: Auxin response factors (ARFs) are transcriptional factors
CC       that bind specifically to the DNA sequence 5'-TGTCTC-3' found in the
CC       auxin-responsive promoter elements (AuxREs). Could act as
CC       transcriptional activator or repressor. Formation of heterodimers with
CC       Aux/IAA proteins may alter their ability to modulate early auxin
CC       response genes expression. {ECO:0000269|PubMed:12036261}.
CC   -!- SUBUNIT: Homodimers and heterodimers. {ECO:0000250}.
CC   -!- INTERACTION:
CC       Q9ZTX9; O24409: IAA19; NbExp=2; IntAct=EBI-3946495, EBI-632257;
CC   -!- SUBCELLULAR LOCATION: Nucleus.
CC   -!- TISSUE SPECIFICITY: Expressed in the whole plant.
CC       {ECO:0000269|PubMed:10476078}.
CC   -!- DOMAIN: Interactions between auxin response factors (ARFs) and Aux/IAA
CC       proteins occur through their C-terminal dimerization domains III and
CC       IV.
CC   -!- DISRUPTION PHENOTYPE: Double mutations in this protein and in ARF3
CC       protein significantly suppresses the adaxial development defect of
CC       leaves of the AS2 and RH10 proteins double mutant at high temperatures.
CC       {ECO:0000269|PubMed:27334696}.
CC   -!- SIMILARITY: Belongs to the ARF family. {ECO:0000305}.
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DR   EMBL; AF013466; AAD01512.1; -; mRNA.
DR   EMBL; AB011483; BAB08228.1; -; Genomic_DNA.
DR   EMBL; CP002688; AED97332.1; -; Genomic_DNA.
DR   EMBL; AF344313; AAK06864.1; -; mRNA.
DR   EMBL; AY080832; AAL87308.1; -; mRNA.
DR   EMBL; AY113977; AAM45025.1; -; mRNA.
DR   RefSeq; NP_200853.1; NM_125438.4.
DR   AlphaFoldDB; Q9ZTX9; -.
DR   SMR; Q9ZTX9; -.
DR   BioGRID; 21410; 35.
DR   IntAct; Q9ZTX9; 17.
DR   STRING; 3702.AT5G60450.1; -.
DR   PaxDb; Q9ZTX9; -.
DR   PRIDE; Q9ZTX9; -.
DR   ProteomicsDB; 241056; -.
DR   EnsemblPlants; AT5G60450.1; AT5G60450.1; AT5G60450.
DR   GeneID; 836166; -.
DR   Gramene; AT5G60450.1; AT5G60450.1; AT5G60450.
DR   KEGG; ath:AT5G60450; -.
DR   Araport; AT5G60450; -.
DR   TAIR; locus:2175098; AT5G60450.
DR   eggNOG; ENOG502QTCY; Eukaryota.
DR   HOGENOM; CLU_002626_2_2_1; -.
DR   InParanoid; Q9ZTX9; -.
DR   OrthoDB; 214403at2759; -.
DR   PhylomeDB; Q9ZTX9; -.
DR   PRO; PR:Q9ZTX9; -.
DR   Proteomes; UP000006548; Chromosome 5.
DR   ExpressionAtlas; Q9ZTX9; baseline and differential.
DR   Genevisible; Q9ZTX9; AT.
DR   GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR   GO; GO:0003700; F:DNA-binding transcription factor activity; ISS:TAIR.
DR   GO; GO:0000976; F:transcription cis-regulatory region binding; IPI:TAIR.
DR   GO; GO:0010158; P:abaxial cell fate specification; IGI:TAIR.
DR   GO; GO:0009734; P:auxin-activated signaling pathway; IEA:UniProtKB-KW.
DR   GO; GO:0010050; P:vegetative phase change; IGI:TAIR.
DR   CDD; cd10017; B3_DNA; 1.
DR   Gene3D; 2.40.330.10; -; 1.
DR   InterPro; IPR010525; ARF_dom.
DR   InterPro; IPR044835; ARF_plant.
DR   InterPro; IPR003340; B3_DNA-bd.
DR   InterPro; IPR015300; DNA-bd_pseudobarrel_sf.
DR   InterPro; IPR000270; PB1_dom.
DR   PANTHER; PTHR31384; PTHR31384; 1.
DR   Pfam; PF06507; Auxin_resp; 1.
DR   Pfam; PF02362; B3; 1.
DR   SMART; SM01019; B3; 1.
DR   SUPFAM; SSF101936; SSF101936; 1.
DR   PROSITE; PS50863; B3; 1.
DR   PROSITE; PS51745; PB1; 1.
PE   1: Evidence at protein level;
KW   Auxin signaling pathway; DNA-binding; Nucleus; Reference proteome;
KW   Transcription; Transcription regulation.
FT   CHAIN           1..788
FT                   /note="Auxin response factor 4"
FT                   /id="PRO_0000111508"
FT   DOMAIN          665..747
FT                   /note="PB1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01081"
FT   DNA_BIND        177..279
FT                   /note="TF-B3"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00326"
FT   REGION          1..53
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          413..433
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1..20
FT                   /note="Acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        35..53
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ   SEQUENCE   788 AA;  87284 MW;  BF9D5056D1DD7A6F CRC64;
     MEFDLNTEIA EVEEEENDDV GVGVGGGTRI DKGRLGISPS SSSSCSSGSS SSSSSTGSAS
     SIYSELWHAC AGPLTCLPKK GNVVVYFPQG HLEQDAMVSY SSPLEIPKFD LNPQIVCRVV
     NVQLLANKDT DEVYTQVTLL PLQEFSMLNG EGKEVKELGG EEERNGSSSV KRTPHMFCKT
     LTASDTSTHG GFSVPRRAAE DCFAPLDYKQ QRPSQELIAK DLHGVEWKFR HIYRGQPRRH
     LLTTGWSIFV SQKNLVSGDA VLFLRDEGGE LRLGIRRAAR PRNGLPDSII EKNSCSNILS
     LVANAVSTKS MFHVFYSPRA THAEFVIPYE KYITSIRSPV CIGTRFRMRF EMDDSPERRC
     AGVVTGVCDL DPYRWPNSKW RCLLVRWDES FVSDHQERVS PWEIDPSVSL PHLSIQSSPR
     PKRPWAGLLD TTPPGNPITK RGGFLDFEES VRPSKVLQGQ ENIGSASPSQ GFDVMNRRIL
     DFAMQSHANP VLVSSRVKDR FGEFVDATGV NPACSGVMDL DRFPRVLQGQ EICSLKSFPQ
     FAGFSPAAAP NPFAYQANKS SYYPLALHGI RSTHVPYQNP YNAGNQSSGP PSRAINFGEE
     TRKFDAQNEG GLPNNVTADL PFKIDMMGKQ KGSELNMNAS SGCKLFGFSL PVETPASKPQ
     SSSKRICTKV HKQGSQVGRA IDLSRLNGYD DLLMELERLF NMEGLLRDPE KGWRILYTDS
     ENDMMVVGDD PWHDFCNVVW KIHLYTKEEV ENANDDNKSC LEQAALMMEA SKSSSVSQPD
     SSPTITRV