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_Os03g56950.3
Common NameOs03g0782500, OSNPB_030782500
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 bHLH
Protein Properties Length: 411aa    MW: 43854.9 Da    PI: 6.6986
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os03g56950.3genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH55.69.5e-18224270455
                       HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
               HLH   4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                        hn  ErrRRdriN+++  L+el+P++      K +Ka+iL +A+eY+ksLq
  LOC_Os03g56950.3 224 VHNLSERRRRDRINEKMRALQELIPHC-----NKTDKASILDEAIEYLKSLQ 270
                       6*************************8.....6******************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd000831.71E-18215274No hitNo description
SuperFamilySSF474592.09E-21218285IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profilePS5088818.635220269IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000105.8E-15224270IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:4.10.280.104.1E-22224279IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003536.2E-18226275IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0006783Biological Processheme biosynthetic process
GO:0009740Biological Processgibberellic acid mediated signaling pathway
GO:0009959Biological Processnegative gravitropism
GO:0010100Biological Processnegative regulation of photomorphogenesis
GO:0010161Biological Processred light signaling pathway
GO:0010187Biological Processnegative regulation of seed germination
GO:0015995Biological Processchlorophyll biosynthetic process
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0010313Molecular Functionphytochrome binding
GO:0042802Molecular Functionidentical protein binding
GO:0046983Molecular Functionprotein dimerization activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0020039anatomyleaf lamina
Sequence ? help Back to Top
Protein Sequence    Length: 411 aa     Download sequence    Send to blast
MAICSTDNEL VELLWHNGGV VAQPQAAQAR VVSSSGRGQS ASVLTGDDTE TAAWFPDTLD  60
DALEKDLYTQ LWRSVTGDAF PAAAAAGPSS HHAPPPDLPP PAARPPMRSG IGSSWTGDIC  120
SAFCGSNHIP ETAAQRCRDA GAALPPERPR RSSTHDGAGT SSSGGSGSNF GASGLPSESA  180
SAHKRKGRED SDSRSEDAEC EATEETKSSS RRYGSKRRTR AAEVHNLSER RRRDRINEKM  240
RALQELIPHC NKTDKASILD EAIEYLKSLQ MQVQIMWMTT GMAPMMFPGA HQFMPPMAVG  300
MNSACMPAAQ GLSHMSRLPY MNHSMPNHIP LNSSPAMNPM NVANQMQNIQ LREASNPFLH  360
PDGWQTVPPQ VSGPYASGPQ VAQQNQIPKA SASTVLPNSG AEQPPTSDGI *
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1215232KRRTRAAEVHNLSERRRR
2228233ERRRRD
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.51780.0flower| leaf| panicle| seed| stem
Expression -- Microarray ? help Back to Top
Source ID
Expression AtlasQ10CH5
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Highly expressed in the node portions of the stem. Expressed in the leaves and the basal part of shoots. {ECO:0000269|PubMed:22984180}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that may act as negative regulator of phyB-dependent light signal transduction (PubMed:17485859). Transcription activator that acts as positive regulator of internode elongation. May function via regulation of cell wall-related genes. May play a role in a drought-associated growth-restriction mechanism in response to drought stress (PubMed:22984180). {ECO:0000269|PubMed:17485859, ECO:0000269|PubMed:22984180}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00074ChIP-chipTransfer from AT2G20180Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os03g56950.3
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Induced by light in dark-grown etiolated seedlings (PubMed:17485859). Circadian oscillation under 12 h light/12 h dark cycle conditions, with peaks in the middle of the light period (PubMed:17485859, PubMed:22984180). Down-regulated by cold and drought stresses (PubMed:22984180). {ECO:0000269|PubMed:17485859, ECO:0000269|PubMed:22984180}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs03g56950
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1056370.0AK105637.1 Oryza sativa Japonica Group cDNA clone:001-200-E02, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015633324.10.0transcription factor PHYTOCHROME INTERACTING FACTOR-LIKE 13-like isoform X4
SwissprotQ10CH50.0PIL13_ORYSJ; Transcription factor PHYTOCHROME INTERACTING FACTOR-LIKE 13
TrEMBLA0A0E0P2470.0A0A0E0P247_ORYRU; Uncharacterized protein
STRINGOS03T0782500-010.0(Oryza sativa)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G09530.24e-32phytochrome interacting factor 3
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. Nakamura Y,Kato T,Yamashino T,Murakami M,Mizuno T
    Characterization of a set of phytochrome-interacting factor-like bHLH proteins in Oryza sativa.
    Biosci. Biotechnol. Biochem., 2007. 71(5): p. 1183-91
    [PMID:17485859]
  3. Zhao XL,Shi ZY,Peng LT,Shen GZ,Zhang JL
    An atypical HLH protein OsLF in rice regulates flowering time and interacts with OsPIL13 and OsPIL15.
    N Biotechnol, 2011. 28(6): p. 788-97
    [PMID:21549224]
  4. Todaka D, et al.
    Rice phytochrome-interacting factor-like protein OsPIL1 functions as a key regulator of internode elongation and induces a morphological response to drought stress.
    Proc. Natl. Acad. Sci. U.S.A., 2012. 109(39): p. 15947-52
    [PMID:22984180]