ID   ARFY_ORYSJ              Reviewed;         899 AA.
AC   Q2QM84; A0A0P0YD34; Q8S980;
DT   11-SEP-2007, integrated into UniProtKB/Swiss-Prot.
DT   24-JAN-2006, sequence version 1.
DT   03-AUG-2022, entry version 102.
DE   RecName: Full=Auxin response factor 25;
DE   AltName: Full=OsARF6b;
GN   Name=ARF25; Synonyms=ARF6B; OrderedLocusNames=Os12g0613700, LOC_Os12g41950;
GN   ORFNames=OsJ_035418;
OS   Oryza sativa subsp. japonica (Rice).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC   Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX   NCBI_TaxID=39947;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=16188032; DOI=10.1186/1741-7007-3-20;
RG   The rice chromosomes 11 and 12 sequencing consortia;
RT   "The sequence of rice chromosomes 11 and 12, rich in disease resistance
RT   genes and recent gene duplications.";
RL   BMC Biol. 3:20-20(2005).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=16100779; DOI=10.1038/nature03895;
RG   International rice genome sequencing project (IRGSP);
RT   "The map-based sequence of the rice genome.";
RL   Nature 436:793-800(2005).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=18089549; DOI=10.1093/nar/gkm978;
RG   The rice annotation project (RAP);
RT   "The rice annotation project database (RAP-DB): 2008 update.";
RL   Nucleic Acids Res. 36:D1028-D1033(2008).
RN   [4]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA   Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA   Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA   Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA   Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT   "Improvement of the Oryza sativa Nipponbare reference genome using next
RT   generation sequence and optical map data.";
RL   Rice 6:4-4(2013).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA   Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA   Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA   Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA   Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA   Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA   Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA   Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA   Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA   Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA   Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA   Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA   Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA   Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA   McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT   "The genomes of Oryza sativa: a history of duplications.";
RL   PLoS Biol. 3:266-281(2005).
RN   [6]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=12869764; DOI=10.1126/science.1081288;
RG   The rice full-length cDNA consortium;
RT   "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT   japonica rice.";
RL   Science 301:376-379(2003).
RN   [7]
RP   NUCLEOTIDE SEQUENCE [MRNA] OF 20-899.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=11922106; DOI=10.1266/ggs.76.373;
RA   Sato Y., Nishimura A., Ito M., Ashikari M., Hirano H.-Y., Matsuoka M.;
RT   "Auxin response factor family in rice.";
RL   Genes Genet. Syst. 76:373-380(2001).
RN   [8]
RP   GENE FAMILY, TISSUE SPECIFICITY, AND NOMENCLATURE.
RX   PubMed=17408882; DOI=10.1016/j.gene.2007.01.006;
RA   Wang D., Pei K., Fu Y., Sun Z., Li S., Liu H., Tang K., Han B., Tao Y.;
RT   "Genome-wide analysis of the auxin response factors (ARF) gene family in
RT   rice (Oryza sativa).";
RL   Gene 394:13-24(2007).
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).
CC   -!- SUBUNIT: Homodimers and heterodimers. {ECO:0000250}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00326}.
CC   -!- TISSUE SPECIFICITY: Expressed in roots, culms, leaves and young
CC       panicles. {ECO:0000269|PubMed:17408882}.
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   -!- SIMILARITY: Belongs to the ARF family. {ECO:0000305}.
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DR   EMBL; DP000011; ABA99400.1; -; Genomic_DNA.
DR   EMBL; AP008218; BAF30285.1; -; Genomic_DNA.
DR   EMBL; AP014968; BAT18068.1; -; Genomic_DNA.
DR   EMBL; CM000149; EAZ21209.1; -; Genomic_DNA.
DR   EMBL; AK121703; -; NOT_ANNOTATED_CDS; mRNA.
DR   EMBL; AB071295; BAB85915.1; -; mRNA.
DR   RefSeq; XP_015619766.1; XM_015764280.1.
DR   AlphaFoldDB; Q2QM84; -.
DR   SMR; Q2QM84; -.
DR   STRING; 4530.OS12T0613700-01; -.
DR   PaxDb; Q2QM84; -.
DR   PRIDE; Q2QM84; -.
DR   EnsemblPlants; Os12t0613700-01; Os12t0613700-01; Os12g0613700.
DR   GeneID; 4352783; -.
DR   Gramene; Os12t0613700-01; Os12t0613700-01; Os12g0613700.
DR   KEGG; osa:4352783; -.
DR   eggNOG; ENOG502QSCZ; Eukaryota.
DR   HOGENOM; CLU_002626_1_1_1; -.
DR   InParanoid; Q2QM84; -.
DR   OMA; KRWYISS; -.
DR   OrthoDB; 162380at2759; -.
DR   Proteomes; UP000000763; Chromosome 12.
DR   Proteomes; UP000007752; Chromosome 12.
DR   Proteomes; UP000059680; Chromosome 12.
DR   ExpressionAtlas; Q2QM84; baseline and differential.
DR   Genevisible; Q2QM84; OS.
DR   GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0009734; P:auxin-activated signaling pathway; IEA:UniProtKB-KW.
DR   GO; GO:0006355; P:regulation of transcription, DNA-templated; IEA:InterPro.
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   2: Evidence at transcript level;
KW   Auxin signaling pathway; DNA-binding; Nucleus; Reference proteome;
KW   Transcription; Transcription regulation.
FT   CHAIN           1..899
FT                   /note="Auxin response factor 25"
FT                   /id="PRO_0000299285"
FT   DOMAIN          766..850
FT                   /note="PB1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01081"
FT   DNA_BIND        132..234
FT                   /note="TF-B3"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00326"
FT   REGION          1..20
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          546..586
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        546..567
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   CONFLICT        168
FT                   /note="P -> S (in Ref. 6; AK121703)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        774
FT                   /note="S -> L (in Ref. 6; AK121703)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   899 AA;  99862 MW;  18B0C9281D9D9EB3 CRC64;
     MKLSPPASAD MPQALPENDG EQRCLNSELW HACAGPLVSL PVVRSRVVYF PQGHSEQVAA
     STNKEVDAQI PNYPNLPPQL ICQLHNVTMH ADAETDEVYA QMTLQPLSPE EQKEPFLPME
     LGAASKQPTN YFCKTLTASD TSTHGGFSVP RRAAEKVFPP LDFSQQPPAQ ELIARDLHDN
     EWKFRHIFRG QPKRHLLTTG WSVFVSAKRL VAGDSVIFIW NDNNQLLLGI RRANRQQTVM
     PSSVLSSDSM HIGLLAAAAH AAATNSRFTI FYNPRASPSE FVIPLAKYVK AVYHTRVSVG
     MRFRMLFETE ESSVRRYMGT ITSISDLDSV RWPNSHWRSV KVGWDESTTG DKQPRVSLWE
     IEPLTTFPMY PSAFPLRLKR PWASGLPMHG MFNGGGNDDF ARYSSLMWLR DGNRGTQSLN
     FQGHGVSPWL QPRIDSPLLG LKPDTYQQMA AAALEEIRYG DPSKQHPATL QYQQTHNLNS
     GLNSLFASHV LGQVQFQPQQ SPLQVVQQGH CQNTGDSGFL QGQLPRLQLH NTQQLLKEQE
     LQQQQRQHVL QEQSSQEMQQ QLPSSDHHVA DVASESGSAP QAQSSLLSGS SFYNQNLLEG
     NSDPPLHLHN NFHNFSNQEA SNLLILPRSS QLMASDGWPS KRLTLESAVH PEAPSMHPKI
     EKVNHQGISH FPGAFPPQSA RGCSIVQDCR ADAENRLLSS SFELQDGMTS IITDANRETD
     TMAIPLLRYS GADLTTENTL ATSNCLGESG TFNPLNNISV NPSQGATFVK VYKSGSLGRS
     LDISRFSSYC ELRSELERLF GLEGQLEDPV RSGWQLVFVD RENDILLVGD DPWQEFANSV
     WCIKILSPQE VQQLVRGGDG LLSSPGARMQ QSNACDDYSA SHNMQNIAGN IASVAPLDY