PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID LOC_Os02g04680.1
Common NameLOC9270639, OJ1679_B08.6, Os02g0139400, OsJ_005170, OSJNBa0026E05.40, SPL3
Organism
Oryza sativa subsp. japonica
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
Family SBP
Protein Properties Length: 470aa    MW: 50264.9 Da    PI: 8.0635
Description SBP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os02g04680.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SBP127.26.4e-40182258278
                       -SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S--- CS
               SBP   2 CqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkqa 78 
                       CqvegC++dls+ak yhr+h+vCe hsk+ +v+v+gle+rfCqqCsrfh l efD++krsCrrrL++hn+rrrk+q+
  LOC_Os02g04680.1 182 CQVEGCNVDLSSAKPYHRKHRVCEPHSKTLKVIVAGLERRFCQQCSRFHGLAEFDQKKRSCRRRLHDHNARRRKPQP 258
                       **************************************************************************997 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:4.10.1100.105.0E-33174243IPR004333Transcription factor, SBP-box
PROSITE profilePS5114131.718179256IPR004333Transcription factor, SBP-box
SuperFamilySSF1036121.05E-38180261IPR004333Transcription factor, SBP-box
PfamPF031104.3E-31182255IPR004333Transcription factor, SBP-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0048510Biological Processregulation of timing of transition from vegetative to reproductive phase
GO:0048653Biological Processanther development
GO:0005634Cellular Componentnucleus
GO:0044212Molecular Functiontranscription regulatory region DNA binding
GO:0046872Molecular Functionmetal ion binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0025281anatomypollen
PO:0001015developmental stageK second mitotic division stage
PO:0007130developmental stagesporophyte reproductive stage
Sequence ? help Back to Top
Protein Sequence    Length: 470 aa     Download sequence    Send to blast
MGSFGMDWNQ KSSVLWDWEN MPPIGNSANE NPKNVMLAES KLAGVGVDIG HESGHSSGGT  60
FSSSSEIGYG SSKSSISASI DSPSKVGNTI ELNFASAEEH DKNMDKGKSK VDDTGTSRSP  120
VVAANRVEPL IGLKLGKRTY FEDVCGGQNV KSSPSGVSVA TPSPGLAKKV KVAQQNTQNP  180
HCQVEGCNVD LSSAKPYHRK HRVCEPHSKT LKVIVAGLER RFCQQCSRFH GLAEFDQKKR  240
SCRRRLHDHN ARRRKPQPEA ISLSSSRLST LLYGDARQQA SFLFGQAPYG QMGSCASSWD  300
NPVPGGFKFT ATKAPWSRPT IAAGVDGTHV SNQQASGNVL PHGAHHSFDG LMAFKETNAK  360
VLNQGMEASA VASGSARGPD FEHALSLLSI DSVGAANLQP GSQIHPGVTA IAGTSNPVMM  420
PSPAIWQGGL SLDQQAQFQA FDRLGNDDDE DHLQLPKPSY DNSHYDQMN*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1ul4_A7e-271822551184squamosa promoter binding protein-like 4
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1237254KKRSCRRRLHDHNARRRK
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.480860.0callus| flower| leaf| panicle| root| stem
Expression -- Microarray ? help Back to Top
Source ID
Expression AtlasA3A2Z8
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Ubiquitous. {ECO:0000269|PubMed:16861571}.
UniprotTISSUE SPECIFICITY: Ubiquitous. {ECO:0000269|PubMed:16861571}.
Functional Description ? help Back to Top
Source Description
UniProtTrans-acting factor that binds specifically to the consensus nucleotide sequence 5'-TNCGTACAA-3' (By similarity). May be involved in panicle development. {ECO:0000250}.
UniProtTrans-acting factor that binds specifically to the consensus nucleotide sequence 5'-TNCGTACAA-3' (By similarity). May be involved in panicle development. {ECO:0000250}.
Function -- GeneRIF ? help Back to Top
  1. In OsmiR156 transgenic rice cell lines, the transcript levels of OsLEA3, OsRab16A, OsDREB2A, OsKNOLLE2, OsCTP1, OsCycB1.1, OsCycB2.1, and OsCDC20.1 were increased by OsWRKY71 knockdown and inversely regulated by OsWRKY71 overexpression, indicating that OsmiR156 enhances cold stress tolerance by regulating the expression of transcription factor genes in plant cells.
    [PMID: 30478522]
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os02g04680.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs02g04680
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2429840.0AK242984.1 Oryza sativa Japonica Group cDNA, clone: J090094N03, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015626878.10.0squamosa promoter-binding-like protein 3 isoform X2
SwissprotA2X0Q60.0SPL3_ORYSI; Squamosa promoter-binding-like protein 3
SwissprotA3A2Z80.0SPL3_ORYSJ; Squamosa promoter-binding-like protein 3
TrEMBLA0A0E0N9L20.0A0A0E0N9L2_ORYRU; Uncharacterized protein
STRINGORUFI02G03180.30.0(Oryza rufipogon)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP36973776
Representative plantOGRP9717230
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G43270.33e-43squamosa promoter binding protein-like 2
Publications ? help Back to Top
  1. Xie K,Wu C,Xiong L
    Genomic organization, differential expression, and interaction of SQUAMOSA promoter-binding-like transcription factors and microRNA156 in rice.
    Plant Physiol., 2006. 142(1): p. 280-93
    [PMID:16861571]
  2. Yang Z, et al.
    Comparative study of SBP-box gene family in Arabidopsis and rice.
    Gene, 2008. 407(1-2): p. 1-11
    [PMID:17629421]
  3. Zhou M,Tang W
    MicroRNA156 amplifies transcription factor-associated cold stress tolerance in plant cells.
    Mol. Genet. Genomics, 2019. 294(2): p. 379-393
    [PMID:30478522]