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_Os08g41940.1
Common NameLOC4346133, Os08g0531600, P0702E04.9, SPL16
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: 456aa    MW: 46578.9 Da    PI: 7.502
Description SBP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os08g41940.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SBP129.89.6e-41118194278
                       -SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S--- CS
               SBP   2 CqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkqa 78 
                       C v+gC++dls++++yhrrhkvCe+hsk+p v+vsg+e rfCqqCsrfh l+efDe+krsCr+rL++hn+rrrk+q+
  LOC_Os08g41940.1 118 CAVDGCKEDLSKCRDYHRRHKVCEAHSKTPLVVVSGREMRFCQQCSRFHLLQEFDEAKRSCRKRLDGHNRRRRKPQP 194
                       **************************************************************************987 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:4.10.1100.102.0E-34111179IPR004333Transcription factor, SBP-box
PROSITE profilePS5114132.154115192IPR004333Transcription factor, SBP-box
SuperFamilySSF1036122.22E-38116197IPR004333Transcription factor, SBP-box
PfamPF031101.9E-30118191IPR004333Transcription factor, SBP-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0048653Biological Processanther development
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:0009037anatomylemma
PO:0001047developmental stagelemma development stage
PO:0007130developmental stagesporophyte reproductive stage
Sequence ? help Back to Top
Protein Sequence    Length: 456 aa     Download sequence    Send to blast
MEWDLKMPPA ASWELADELE NSGGGGVPAA VSSSSAAVGG GVNAGGGGRQ ECSVDLKLGG  60
LGEFGGGGAQ PRVAVAGEPA KGKGPAAAAT GAAAAASSAP AKRPRGAAAA GQQQCPSCAV  120
DGCKEDLSKC RDYHRRHKVC EAHSKTPLVV VSGREMRFCQ QCSRFHLLQE FDEAKRSCRK  180
RLDGHNRRRR KPQPDPMNSA SYLASQQGAR FSPFATPRPE ASWTGMIKTE ESPYYTHHQI  240
PLGISSRQQH FVGSTSDGGR RFPFLQEGEI SFGTGAGAGG VPMDQAAAAA AASVCQPLLK  300
TVAPPPPPHG GGGSGGGKMF SDGGLTQVLD SDCALSLLSA PANSTAIDVG GGRVVVQPTE  360
HIPMAQPLIS GLQFGGGGGS SAWFAARPHH QAATGAAATA VVVSTAGFSC PVVESEQLNT  420
VLSSNDNEMN YNGMFHVGGE GSSDGTSSSL PFSWQ*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1ul4_A1e-271181911184squamosa promoter binding protein-like 4
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1174191KRSCRKRLDGHNRRRRKP
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.561570.0panicle
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329946780.0
Expression AtlasQ6YZE8-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in young panicles. {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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00555DAPTransfer from AT5G50570Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os08g41940.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Negatively regulated by microRNAs miR156b and miR156h. {ECO:0000305|PubMed:16861571}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs08g41940
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1094690.0AK109469.1 Oryza sativa Japonica Group cDNA clone:001-128-D02, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015649377.10.0squamosa promoter-binding-like protein 16
SwissprotQ6YZE80.0SPL16_ORYSJ; Squamosa promoter-binding-like protein 16
TrEMBLL0AP480.0L0AP48_ORYSI; Squamosa promoter binding protein-like 16
STRINGOS08T0531600-010.0(Oryza sativa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP17553795
Representative plantOGRP9717230
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G50670.12e-42SBP family protein
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. 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]
  4. Wang SS,Wang CS,Tseng TH,Hou YL,Chen KY
    High-resolution genetic mapping and candidate gene identification of the SLP1 locus that controls glume development in rice.
    Theor. Appl. Genet., 2011. 122(8): p. 1489-96
    [PMID:21327937]
  5. Wang S, et al.
    Control of grain size, shape and quality by OsSPL16 in rice.
    Nat. Genet., 2012. 44(8): p. 950-4
    [PMID:22729225]
  6. Wang S, et al.
    The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and grain quality.
    Nat. Genet., 2015. 47(8): p. 949-54
    [PMID:26147620]
  7. Wang Y, et al.
    A comprehensive meta-analysis of plant morphology, yield, stay-green, and virus disease resistance QTL in maize (Zea mays L.).
    Planta, 2016. 243(2): p. 459-71
    [PMID:26474992]
  8. Lee CM, et al.
    Influence of Multi-Gene Allele Combinations on Grain Size of Rice and Development of a Regression Equation Model to Predict Grain Parameters.
    Rice (N Y), 2015. 8(1): p. 33
    [PMID:26519289]
  9. Bessho-Uehara K, et al.
    Loss of function at RAE2, a previously unidentified EPFL, is required for awnlessness in cultivated Asian rice.
    Proc. Natl. Acad. Sci. U.S.A., 2016. 113(32): p. 8969-74
    [PMID:27466405]