ARFD_ORYSJ
ID ARFD_ORYSJ Reviewed; 808 AA.
AC Q5JK20; A0A0P0VCI4; Q8S982;
DT 11-SEP-2007, integrated into UniProtKB/Swiss-Prot.
DT 15-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 101.
DE RecName: Full=Auxin response factor 4;
DE AltName: Full=OsARF2;
GN Name=ARF4; Synonyms=ARF2; OrderedLocusNames=Os01g0927600, LOC_Os01g70270;
GN ORFNames=OSJNBa0093F16.35;
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=12447438; DOI=10.1038/nature01184;
RA Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Katayose Y.,
RA Wu J., Niimura Y., Cheng Z., Nagamura Y., Antonio B.A., Kanamori H.,
RA Hosokawa S., Masukawa M., Arikawa K., Chiden Y., Hayashi M., Okamoto M.,
RA Ando T., Aoki H., Arita K., Hamada M., Harada C., Hijishita S., Honda M.,
RA Ichikawa Y., Idonuma A., Iijima M., Ikeda M., Ikeno M., Ito S., Ito T.,
RA Ito Y., Ito Y., Iwabuchi A., Kamiya K., Karasawa W., Katagiri S.,
RA Kikuta A., Kobayashi N., Kono I., Machita K., Maehara T., Mizuno H.,
RA Mizubayashi T., Mukai Y., Nagasaki H., Nakashima M., Nakama Y.,
RA Nakamichi Y., Nakamura M., Namiki N., Negishi M., Ohta I., Ono N., Saji S.,
RA Sakai K., Shibata M., Shimokawa T., Shomura A., Song J., Takazaki Y.,
RA Terasawa K., Tsuji K., Waki K., Yamagata H., Yamane H., Yoshiki S.,
RA Yoshihara R., Yukawa K., Zhong H., Iwama H., Endo T., Ito H., Hahn J.H.,
RA Kim H.-I., Eun M.-Y., Yano M., Jiang J., Gojobori T.;
RT "The genome sequence and structure of rice chromosome 1.";
RL Nature 420:312-316(2002).
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 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 [6]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 18-808.
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 [7]
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AK072309; Type=Erroneous termination; Note=Truncated C-terminus.; Evidence={ECO:0000305};
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DR EMBL; AP004332; BAD88200.1; -; Genomic_DNA.
DR EMBL; AP008207; BAF07184.1; -; Genomic_DNA.
DR EMBL; AP014957; BAS76004.1; -; Genomic_DNA.
DR EMBL; AK072309; -; NOT_ANNOTATED_CDS; mRNA.
DR EMBL; AB071293; BAB85913.1; -; mRNA.
DR RefSeq; XP_015650953.1; XM_015795467.1.
DR AlphaFoldDB; Q5JK20; -.
DR SMR; Q5JK20; -.
DR STRING; 4530.OS01T0927600-01; -.
DR PaxDb; Q5JK20; -.
DR PRIDE; Q5JK20; -.
DR EnsemblPlants; Os01t0927600-01; Os01t0927600-01; Os01g0927600.
DR GeneID; 4326957; -.
DR Gramene; Os01t0927600-01; Os01t0927600-01; Os01g0927600.
DR KEGG; osa:4326957; -.
DR eggNOG; ENOG502QRXI; Eukaryota.
DR HOGENOM; CLU_002626_2_2_1; -.
DR InParanoid; Q5JK20; -.
DR OMA; LHFWNGQ; -.
DR OrthoDB; 214403at2759; -.
DR PlantReactome; R-OSA-5608118; Auxin signalling.
DR Proteomes; UP000000763; Chromosome 1.
DR Proteomes; UP000059680; Chromosome 1.
DR Genevisible; Q5JK20; 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; 2.
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..808
FT /note="Auxin response factor 4"
FT /id="PRO_0000299257"
FT DOMAIN 692..785
FT /note="PB1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01081"
FT DNA_BIND 129..231
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 342..433
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 661..691
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 778..808
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..16
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 359..384
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 400..433
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 781..808
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 808 AA; 90855 MW; 8891BD0691F05BBB CRC64;
MPPAAMAPPP PPQGSSTGDP LYDELWHACA GPLVTVPRVG DLVFYFPQGH IEQVEASMNQ
VADSQMRLYD LPSKLLCRVL NVELKAEQDT DEVYAQVMLM PEPEQNEMAV EKTTPTSGPV
QARPPVRSFC KTLTASDTST HGGFSVLRRH ADECLPPLDM TQSPPTQELV AKDLHSMDWR
FRHIFRGQPR RHLLQSGWSV FVSSKRLVAG DAFIFLRGEN GELRVGVRRA MRQLSNVPSS
VISSQSMHLG VLATAWHAIN TKSMFTVYYK PRTSPSEFII PYDQYMESVK NNYSVGMRFR
MRFEGEEAPE QRFTGTIIGS ENLDPVWPES SWRSLKVRWD EPSTIPRPDR VSPWKIEPAS
SPPVNPLPLS RVKRPRPNAP PASPESPILT KEAATKVDTD PAQAQRSQNS TVLQGQEQMT
LRSNLTESND SDVTAHKPMM WSPSPNAAKA HPLTFQQRPP MDNWMQLGRR ETDFKDVRSG
SQSFGDSPGF FMQNFDEAPN RLTSFKNQFQ DQGSARHFSD PYYYVSPQPS LTVESSTQMH
TDSKELHFWN GQSTVYGNSR DRPQNFRFEQ NSSSWLNQSF ARPEQPRVIR PHASIAPVEL
EKTEGSGFKI FGFKVDTTNA PNNHLSSPMA ATHEPMLQTP SSLNQLQPVQ TDCIPEVSVS
TAGTATENEK SGQQAQQSSK DVQSKTQVAS TRSCTKVHKQ GVALGRSVDL SKFSNYDELK
AELDKMFEFD GELVSSNKNW QIVYTDNEGD MMLVGDDPWE EFCSIVRKIY IYTKEEVQKM
NSKSNAPRKD DSSENEKGHL PMPNKSDN
