PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID ONIVA08G24550.1
Organism
Oryza nivara
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
Family SBP
Protein Properties Length: 451aa    MW: 46189.4 Da    PI: 7.3168
Description SBP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
ONIVA08G24550.1genomeOGEView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SBP112.82e-35117190278
                      -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 rfCqq   fh l+efDe+krsCr+rL++hn+rrrk+q+
  ONIVA08G24550.1 117 CAVDGCKEDLSKCRDYHRRHKVCEAHSKTPLVVVSGREMRFCQQ---FHLLQEFDEAKRSCRKRLDGHNRRRRKPQP 190
                      *******************************************9...***************************987 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:4.10.1100.102.3E-29110175IPR004333Transcription factor, SBP-box
PROSITE profilePS5114128.017114188IPR004333Transcription factor, SBP-box
SuperFamilySSF1036121.7E-33115193IPR004333Transcription factor, SBP-box
PfamPF031101.8E-25117187IPR004333Transcription factor, SBP-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0048653Biological Processanther development
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 451 aa     Download sequence    Send to blast
MEWDLKMPPA ASWELADELE NSGGGGVPAA VSSSSAAVGG GVNAGGGGRQ ECSVDLKLGG  60
LGEFGGGGAQ PRVAVAGELA KGKGPAAAAT GAAAAASSAP AKRPRGAAAG QQQCPSCAVD  120
GCKEDLSKCR DYHRRHKVCE AHSKTPLVVV SGREMRFCQQ FHLLQEFDEA KRSCRKRLDG  180
HNRRRRKPQP DPMNSASYLA SQQGARFSPF ATPRPEASWT GMIKTEESPY YTHHQIPLGI  240
SSRQQHFVGS TSDGGRRFPF LQEGEISFGT GAGAGGVPMD QAAAAAAASV CQPLLKTVAP  300
PPPPHGGGGS GGGKMFSDGG LTQVLDSDCA LSLLSAPANS TAIDVGGGRV VVQPTEHIPI  360
AQPLISGLQF GGGGGSSAWF AARPHHQAAT GATATAVVVS TAGFSCPVVE SEQLNTVLSS  420
NDNEMNYNGM FHVGGEGSSD GTSSSLPFSW Q
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1ul4_A2e-231171871184squamosa promoter binding protein-like 4
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1170187KRSCRKRLDGHNRRRRKP
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
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
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
TrEMBLA0A0E0IF010.0A0A0E0IF01_ORYNI; Uncharacterized protein
STRINGONIVA08G24550.10.0(Oryza nivara)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP17553795
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G50670.14e-38SBP 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. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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]