ARFI_ARATH
ID ARFI_ARATH Reviewed; 638 AA.
AC Q9XED8; O22991; Q0WRN8; Q2V3F5; Q56X14;
DT 26-APR-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 25-MAY-2022, entry version 142.
DE RecName: Full=Auxin response factor 9;
GN Name=ARF9; OrderedLocusNames=At4g23980; ORFNames=T19F6.20, T32A16.150;
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] (ISOFORM 1).
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=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
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] (ISOFORM 1).
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 326-638 (ISOFORM 1).
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [6]
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 [7]
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 [8]
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).
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 Q9XED8; Q8L7G0: ARF1; NbExp=3; IntAct=EBI-3946762, EBI-2324259;
CC Q9XED8; Q9C5W9: ARF18; NbExp=4; IntAct=EBI-3946762, EBI-3946783;
CC Q9XED8; Q9ZTX8: ARF6; NbExp=3; IntAct=EBI-3946762, EBI-3946770;
CC Q9XED8; Q38828: IAA10; NbExp=3; IntAct=EBI-3946762, EBI-3946434;
CC Q9XED8; P93830: IAA17; NbExp=5; IntAct=EBI-3946762, EBI-632243;
CC Q9XED8; O24409: IAA19; NbExp=2; IntAct=EBI-3946762, EBI-632257;
CC Q9XED8; Q9XFM0: IAA28; NbExp=3; IntAct=EBI-3946762, EBI-3133404;
CC Q9XED8; Q9C5X0: IAA34; NbExp=4; IntAct=EBI-3946762, EBI-3946459;
CC -!- SUBCELLULAR LOCATION: Nucleus.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9XED8-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9XED8-2; Sequence=VSP_037314;
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 -!- MISCELLANEOUS: [Isoform 2]: May be due to a competing acceptor splice
CC site. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the ARF family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAB63625.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AF082176; AAD24427.1; -; mRNA.
DR EMBL; AC002343; AAB63625.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL078468; CAB43898.1; -; Genomic_DNA.
DR EMBL; AL161560; CAB81316.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE84835.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE84836.1; -; Genomic_DNA.
DR EMBL; AF344312; AAK06863.1; -; mRNA.
DR EMBL; AK221865; BAD94156.1; -; mRNA.
DR EMBL; AK228263; BAF00211.1; -; mRNA.
DR PIR; T08917; T08917.
DR RefSeq; NP_001031706.1; NM_001036629.2. [Q9XED8-2]
DR RefSeq; NP_194129.1; NM_118530.5. [Q9XED8-1]
DR AlphaFoldDB; Q9XED8; -.
DR SMR; Q9XED8; -.
DR BioGRID; 13787; 41.
DR IntAct; Q9XED8; 39.
DR STRING; 3702.AT4G23980.1; -.
DR iPTMnet; Q9XED8; -.
DR PaxDb; Q9XED8; -.
DR PRIDE; Q9XED8; -.
DR ProteomicsDB; 245184; -. [Q9XED8-1]
DR EnsemblPlants; AT4G23980.1; AT4G23980.1; AT4G23980. [Q9XED8-1]
DR EnsemblPlants; AT4G23980.2; AT4G23980.2; AT4G23980. [Q9XED8-2]
DR GeneID; 828498; -.
DR Gramene; AT4G23980.1; AT4G23980.1; AT4G23980. [Q9XED8-1]
DR Gramene; AT4G23980.2; AT4G23980.2; AT4G23980. [Q9XED8-2]
DR KEGG; ath:AT4G23980; -.
DR Araport; AT4G23980; -.
DR TAIR; locus:2138096; AT4G23980.
DR eggNOG; ENOG502QTME; Eukaryota.
DR InParanoid; Q9XED8; -.
DR OMA; ITNEGCI; -.
DR PhylomeDB; Q9XED8; -.
DR PRO; PR:Q9XED8; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q9XED8; baseline and differential.
DR Genevisible; Q9XED8; 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:0009734; P:auxin-activated signaling pathway; IEA:UniProtKB-KW.
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; IPR033389; AUX/IAA_dom.
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; PF02309; AUX_IAA; 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 Alternative splicing; Auxin signaling pathway; DNA-binding; Nucleus;
KW Reference proteome; Transcription; Transcription regulation.
FT CHAIN 1..638
FT /note="Auxin response factor 9"
FT /id="PRO_0000111513"
FT DOMAIN 523..623
FT /note="PB1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01081"
FT DNA_BIND 116..218
FT /note="TF-B3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00326"
FT REGION 467..530
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 487..510
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 511..529
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 371..372
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_037314"
SQ SEQUENCE 638 AA; 72278 MW; 6EBA72A9F8909C82 CRC64;
MANRGGEYLY DELWKLCAGP LVDVPQAQER VYYFPQGHME QLEASTQQVD LNTMKPLFVL
PPKILCNVMN VSLQAEKDTD EVYAQITLIP VGTEVDEPMS PDPSPPELQR PKVHSFSKVL
TASDTSTHGG FSVLRKHATE CLPPLDMTQQ TPTQELVAED VHGYQWKFKH IFRGQPRRHL
LTTGWSTFVT SKRLVAGDTF VFLRGENGEL RVGVRRANLQ QSSMPSSVIS SHSMHLGVLA
TARHATQTKT MFIVYYKPRT SQFIISLNKY LEAMSNKFSV GMRFKMRFEG EDSPERRYSG
TVIGVKDCSP HWKDSKWRCL EVHWDEPASI SRPNKVSPWE IEPFVNSENV PKSVMLKNKR
PRQVSEVSAL DVGITASNLW SSVLTQPHEF AQSCITSQWS SPQQCHRDAN EDAKKSDWLN
NSYSVSNVAK DSTLNDQMVS PVEQKKPETT ANYRLFGIDL MSSSLAVPEE KTAPMRPINI
SKPTMDSHSD PKSEISKVSE EKKQEPAEGS PKEVQSKQSS STRSRTKVQM QGVPVGRAVD
LNALKGYNEL IDDIEKLFDI KGELRSRNQW EIVFTDDEGD MMLVGDDPWP EFCNMVKRIF
IWSKEEVKKM TPGNQLRMLL REVETTLTTT SKTDNHSN
