SPL4_ORYSJ
ID SPL4_ORYSJ Reviewed; 251 AA.
AC Q6H509; Q6H507; Q6H508;
DT 23-OCT-2007, integrated into UniProtKB/Swiss-Prot.
DT 19-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 97.
DE RecName: Full=Squamosa promoter-binding-like protein 4;
GN Name=SPL4; OrderedLocusNames=Os02g0174100, LOC_Os02g07780;
GN ORFNames=OSJNBa0073A21.21-1, OSJNBa0073A21.21-2, OSJNBa0073A21.21-3;
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=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 [2]
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 [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
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 [5]
RP TISSUE SPECIFICITY, INDUCTION, GENE FAMILY, AND NOMENCLATURE.
RX PubMed=16861571; DOI=10.1104/pp.106.084475;
RA Xie K., Wu C., Xiong L.;
RT "Genomic organization, differential expression, and interaction of SQUAMOSA
RT promoter-binding-like transcription factors and microRNA156 in rice.";
RL Plant Physiol. 142:280-293(2006).
RN [6]
RP GENE FAMILY.
RX PubMed=17629421; DOI=10.1016/j.gene.2007.02.034;
RA Yang Z., Wang X., Gu S., Hu Z., Xu H., Xu C.;
RT "Comparative study of SBP-box gene family in Arabidopsis and rice.";
RL Gene 407:1-11(2008).
CC -!- FUNCTION: Trans-acting factor that binds specifically to the consensus
CC nucleotide sequence 5'-TNCGTACAA-3' (By similarity). May be involved in
CC panicle development. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q6H509-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q6H509-2; Sequence=VSP_028927, VSP_028928;
CC -!- TISSUE SPECIFICITY: Expressed in stems, leaf sheaths, and young
CC panicles. {ECO:0000269|PubMed:16861571}.
CC -!- INDUCTION: Negatively regulated by microRNAs miR156b and miR156h.
CC {ECO:0000305|PubMed:16861571}.
CC -!- DOMAIN: The SBP-type zinc finger is required for the binding to DNA.
CC {ECO:0000250}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAD26192.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AP005772; BAD26190.1; -; Genomic_DNA.
DR EMBL; AP005772; BAD26191.1; -; Genomic_DNA.
DR EMBL; AP005772; BAD26192.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP008208; BAF07960.1; -; Genomic_DNA.
DR EMBL; AP014958; BAS77228.1; -; Genomic_DNA.
DR EMBL; AP014958; BAS77229.1; -; Genomic_DNA.
DR EMBL; AK061484; -; NOT_ANNOTATED_CDS; mRNA.
DR EMBL; AK066057; -; NOT_ANNOTATED_CDS; mRNA.
DR RefSeq; XP_015623077.1; XM_015767591.1. [Q6H509-1]
DR AlphaFoldDB; Q6H509; -.
DR SMR; Q6H509; -.
DR STRING; 4530.OS02T0174100-02; -.
DR PaxDb; Q6H509; -.
DR PRIDE; Q6H509; -.
DR EnsemblPlants; Os02t0174100-01; Os02t0174100-01; Os02g0174100. [Q6H509-2]
DR EnsemblPlants; Os02t0174100-02; Os02t0174100-02; Os02g0174100. [Q6H509-1]
DR GeneID; 4328461; -.
DR Gramene; Os02t0174100-01; Os02t0174100-01; Os02g0174100. [Q6H509-2]
DR Gramene; Os02t0174100-02; Os02t0174100-02; Os02g0174100. [Q6H509-1]
DR KEGG; osa:4328461; -.
DR eggNOG; ENOG502SKF7; Eukaryota.
DR InParanoid; Q6H509; -.
DR OMA; RRLYDHN; -.
DR OrthoDB; 607491at2759; -.
DR Proteomes; UP000000763; Chromosome 2.
DR Proteomes; UP000059680; Chromosome 2.
DR ExpressionAtlas; Q6H509; baseline and differential.
DR Genevisible; Q6H509; OS.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR Gene3D; 4.10.1100.10; -; 1.
DR InterPro; IPR004333; SBP_dom.
DR InterPro; IPR036893; SBP_sf.
DR InterPro; IPR044817; SPL.
DR PANTHER; PTHR31251; PTHR31251; 1.
DR Pfam; PF03110; SBP; 1.
DR SUPFAM; SSF103612; SSF103612; 1.
DR PROSITE; PS51141; ZF_SBP; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; DNA-binding; Metal-binding; Nucleus;
KW Reference proteome; Transcription; Transcription regulation; Zinc;
KW Zinc-finger.
FT CHAIN 1..251
FT /note="Squamosa promoter-binding-like protein 4"
FT /id="PRO_0000308227"
FT ZN_FING 65..142
FT /note="SBP-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00470"
FT REGION 1..64
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 125..141
FT /note="Bipartite nuclear localization signal"
FT /evidence="ECO:0000255"
FT BINDING 68
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00470"
FT BINDING 73
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00470"
FT BINDING 90
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00470"
FT BINDING 93
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00470"
FT BINDING 109
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00470"
FT BINDING 112
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00470"
FT BINDING 116
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00470"
FT BINDING 128
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00470"
FT VAR_SEQ 225..234
FT /note="DFSAATIWMF -> GMIFQRCKFS (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:12869764"
FT /id="VSP_028927"
FT VAR_SEQ 235..251
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:12869764"
FT /id="VSP_028928"
SQ SEQUENCE 251 AA; 28158 MW; C0EDEBEE8CBDB42F CRC64;
MDWMPPPKPT SPRSPPLLWD WADAAVPGSS SGEVSAAAAA AAAHPGRRRK EKRGRAEEGG
GGGGEVRCQV EGCGVELVGV KDYHRKHRVC EAHSKFPRVV VAGQERRFCQ QCSRFHALSE
FDQKKRSCRR RLYDHNARRR KPQTDVFSYA SARPPSSLLF DDNRQISFVW NKAPLSHVRP
FAISPWESSS EVGTTDGHIY LDKSHISKSL PAFNTDIDEL LPMKDFSAAT IWMFFGVLFI
RTAQESCMSF H
