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_Os04g56170.1
Common NameLG1, LOC4337258, Os04g0656500, OSJNBa0071I13.12, SPL8
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: 417aa    MW: 45029.5 Da    PI: 7.6456
Description SBP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os04g56170.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SBP128.62.4e-40184262178
                       --SSTT-----TT--HHHHHTT--HHHHT-S-EE.ETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S--- CS
               SBP   1 lCqvegCeadlseakeyhrrhkvCevhskapvvl.vsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkqa 78 
                       +Cq+egC+adls+ak+yhrrhkvCe+hskapvv+ + gl+qrfCqqCsrfh l+efD++k+sCr+rLa+hn+rrrk+++
  LOC_Os04g56170.1 184 RCQAEGCKADLSSAKRYHRRHKVCEHHSKAPVVVtAGGLHQRFCQQCSRFHLLDEFDDAKKSCRKRLADHNRRRRKSKP 262
                       6******************************98725689*************************************975 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:4.10.1100.101.0E-33179247IPR004333Transcription factor, SBP-box
PROSITE profilePS5114130.291182260IPR004333Transcription factor, SBP-box
SuperFamilySSF1036126.8E-37183263IPR004333Transcription factor, SBP-box
PfamPF031108.6E-31185259IPR004333Transcription factor, SBP-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0046872Molecular Functionmetal ion binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009049anatomyinflorescence
PO:0001083developmental stageinflorescence development stage
PO:0007006developmental stageIL.00 inflorescence just visible stage
Sequence ? help Back to Top
Protein Sequence    Length: 417 aa     Download sequence    Send to blast
MMNVPSAAAA SSCDDFGYNA TPPPPPSLLP IMDQDGGGGS IQRDHHQHHN HQQLGYNLEP  60
SSLALLPPSN AAAAAAHHAT IAHASPHDLL QFYPTSHYLA AAGGAGGGGN PYSHFTAAAA  120
AGSTFQSYYQ QPPQDAPEYY FPTLVSSAEE NMASFAATQL GLNLGYRTYF PPRGGYTYGH  180
HPPRCQAEGC KADLSSAKRY HRRHKVCEHH SKAPVVVTAG GLHQRFCQQC SRFHLLDEFD  240
DAKKSCRKRL ADHNRRRRKS KPSDGEHSGE KRRAQANKSA ATKDKAGSSS KNAGIGDGFE  300
TQLLGGAHMS KDQDQAMDLG EVVKEAVDPK GKASMQQQQQ QAHHGIHQQS HQQHGFPFPS  360
SSGSCLFPQS QGAVSSTDTS NIAQVQEPSL AFHQQHHQHS NILQLGQAMF DLDFDH*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1ul4_A6e-271852591184squamosa promoter binding protein-like 4
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1254272RRRRKSKPSDGEHSGEKRR
2255260RRRKSK
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.525760.0leaf| panicle| stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329781220.0
Expression AtlasQ7XPY1-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in developing laminar joint and meristematic regions.
UniprotTISSUE SPECIFICITY: Expressed in stems, leaf sheaths, and young panicles. Weakly expressed in ligules, auricles, and leaf sheaths at the basal region. {ECO:0000269|PubMed:16861571, ECO:0000269|PubMed:17594063}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor that plays an important role in building the laminar joint between leaf blade and leaf sheath boundary, thereby controlling ligule and auricle development. {ECO:0000269|PubMed:17594063}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os04g56170.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: Plants show upright attitudes and the absence of laminar joints, ligules and auricules in all the leaves including the flag leaves. {ECO:0000269|PubMed:17594063}.
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs04g56170
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB7769910.0AB776991.1 Oryza sativa Japonica Group LG1 mRNA for squamosa promoter-binding-like protein 8, complete cds, cultivar: Nipponbare.
GenBankAK0681040.0AK068104.1 Oryza sativa Japonica Group cDNA clone:J013129G14, full insert sequence.
GenBankJX4627830.0JX462783.1 Oryza sativa Indica Group cultivar Teqing PAC1 mRNA, complete cds.
GenBankJX4627840.0JX462784.1 Oryza rufipogon strain C4 PAC1 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015634037.10.0squamosa promoter-binding-like protein 8
SwissprotQ7XPY10.0SPL8_ORYSJ; Squamosa promoter-binding-like protein 8
TrEMBLL8B8S30.0L8B8S3_ORYSJ; Squamosa promoter-binding-like protein 8
TrEMBLS4UXR10.0S4UXR1_ORYSI; PAC1
TrEMBLS4UY490.0S4UY49_ORYRU; PAC1
STRINGOS04T0656500-010.0(Oryza sativa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP69903452
Representative plantOGRP9717230
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G02065.11e-42squamosa promoter binding protein-like 8
Publications ? help Back to Top
  1. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]
  2. 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]
  3. Lee J,Park JJ,Kim SL,Yim J,An G
    Mutations in the rice liguleless gene result in a complete loss of the auricle, ligule, and laminar joint.
    Plant Mol. Biol., 2007. 65(4): p. 487-99
    [PMID:17594063]
  4. 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]
  5. Ishii T, et al.
    OsLG1 regulates a closed panicle trait in domesticated rice.
    Nat. Genet., 2013. 45(4): p. 462-5, 465e1-2
    [PMID:23435087]