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_Os02g47280.2
Common NameGRF4, LOC4330436, OJ1111_E07.19, Os02g0701300, OsJ_08054
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 GRF
Protein Properties Length: 395aa    MW: 41835.6 Da    PI: 8.5535
Description GRF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os02g47280.2genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1WRC789.4e-25125169145
               WRC   1 daepgrCrRtDGKkWRCsrrvlegkklCErHlhrgrsrsrkskee 45 
                       d+epgrCrRtDGKkWRCs+++ +++k+CErH+hrgr+rsrk++e+
  LOC_Os02g47280.2 125 DPEPGRCRRTDGKKWRCSKEAAPDSKYCERHMHRGRNRSRKPVET 169
                       79****************************************997 PP
2QLQ60.93.5e-216499237
               QLQ  2 aFTaaQlqlLksQilAyKyLaanqPvPpeLlqaiqk 37
                      +FTaaQ ++L++Q+l+yKyL+a++PvPp+L+++i++
  LOC_Os02g47280.2 64 PFTAAQYEELEQQALIYKYLVAGVPVPPDLVLPIRR 99
                      9*********************************86 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM009511.7E-116399IPR014978Glutamine-Leucine-Glutamine, QLQ
PfamPF088806.7E-156498IPR014978Glutamine-Leucine-Glutamine, QLQ
PROSITE profilePS5166622.8796499IPR014978Glutamine-Leucine-Glutamine, QLQ
PROSITE profilePS5166725.486125169IPR014977WRC domain
PfamPF088794.0E-21126168IPR014977WRC domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0005524Molecular FunctionATP 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: 395 aa     Download sequence    Send to blast
MAMPYASLSP AVADHRSSPA AATASLLPFC RSTPLSAGGG GVAMGEDAPM TARWPPAAAA  60
RLPPFTAAQY EELEQQALIY KYLVAGVPVP PDLVLPIRRG LDSLAARFYN HPALGYGPYF  120
GKKLDPEPGR CRRTDGKKWR CSKEAAPDSK YCERHMHRGR NRSRKPVETQ LVAQSQPPSS  180
VVGSAAAPLA AASNGSSFQN HSLYPAIAGS NGGGGGRNMP SSFGSALGSQ LHMDNAAPYA  240
AVGGGTGKDL RYTAYGTRSL ADEQSQLITE AINTSIENPW RLLPSQNSPF PLSSYSQLGA  300
LSDLGQNTPS SLSKVQRQPL SFFGNDYAAV DSVKQENQTL RPFFDEWPKG RDSWSDLADE  360
NANLSSFSGT QLSISIPMAS SDFSAASSRS TNGD*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.497480.0callus| panicle| seed
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329740010.0
Expression AtlasQ6ZIK5-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in stems (PubMed:27107174). Expressed in panicles (PubMed:26187814, PubMed:27250747, PubMed:27250749, PubMed:27107174). {ECO:0000269|PubMed:26187814, ECO:0000269|PubMed:27107174, ECO:0000269|PubMed:27250747, ECO:0000269|PubMed:27250749}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription activator that plays a role in the regulation of meristematic function in leaves, stems and inflorescences (PubMed:24532604). Transcription activator that plays a regulatory role in grain development (PubMed:26187814, PubMed:27250747, PubMed:27250749, PubMed:26936408, PubMed:27107174). Positively regulates grain size by promoting cell division and expansion, leading to increased grain length and width (PubMed:26187814, PubMed:27250747, PubMed:27250749, PubMed:26936408, PubMed:27107174). Positively regulates the expression of genes promoting cell proliferation (PubMed:26187814, PubMed:26936408). Activates the expression of expansin genes to promote cell expansion and grain size (PubMed:27250747). May promote grain size by activating brassinosteroid responses (PubMed:27250747). Component of a network formed by the microRNA396 (miRNA396), the GRFs and their interacting factors (GIFs) acting in the regulation of meristem function, at least partially through the control of cell proliferation (Probable). Component of the miRNA396c-GRF4-GIF1 regulatory module that plays an important role in grain size determination (Probable) (PubMed:27250747, PubMed:27250749, PubMed:27107174). {ECO:0000269|PubMed:24532604, ECO:0000269|PubMed:26187814, ECO:0000269|PubMed:26936408, ECO:0000269|PubMed:27107174, ECO:0000269|PubMed:27250747, ECO:0000269|PubMed:27250749, ECO:0000305|PubMed:26187814, ECO:0000305|PubMed:27107174, ECO:0000305|PubMed:27250747, ECO:0000305|PubMed:27250749}.
Function -- GeneRIF ? help Back to Top
  1. GRF4 role in the grain size and yield, and also brassinosteroid metabolism
    [PMID: 27250747]
  2. GRF4 regulation by Mir396 controls the grain size and yield.
    [PMID: 27250749]
  3. Transcriptome profiling of 7-cm-long young panicles of NIL-Osgrf4 and NIL-OsGRF4 using RNAs sequence analyses identified 80 differentially expressed genes. The pleiotropic target gene OsGRF4 was up-regulated in NIL-OsGRF4 plants. It may also be involve in abiotic stress resistance.
    [PMID: 29924832]
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os02g47280.2
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: The microRNA396c negatively regulates GRF4 at the transcriptional level. {ECO:0000269|PubMed:26187814, ECO:0000269|PubMed:26936408, ECO:0000269|PubMed:27107174, ECO:0000269|PubMed:27250747}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs02g47280
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK0639830.0AK063983.1 Oryza sativa Japonica Group cDNA clone:001-124-D07, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015624297.10.0growth-regulating factor 4
SwissprotQ6ZIK50.0GRF4_ORYSJ; Growth-regulating factor 4
TrEMBLA0A0E0NJQ40.0A0A0E0NJQ4_ORYRU; Uncharacterized protein
TrEMBLA0A2Z5U5F20.0A0A2Z5U5F2_ORYSJ; Growth-regulating factor 4 protein (Fragment)
STRINGORUFI02G30740.10.0(Oryza rufipogon)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G13960.12e-46growth-regulating factor 5
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. Ye R,Yao QH,Xu ZH,Xue HW
    Development of an efficient method for the isolation of factors involved in gene transcription during rice embryo development.
    Plant J., 2004. 38(2): p. 348-57
    [PMID:15078336]
  3. Choi D,Kim JH,Kende H
    Whole genome analysis of the OsGRF gene family encoding plant-specific putative transcription activators in rice (Oryza sativa L.).
    Plant Cell Physiol., 2004. 45(7): p. 897-904
    [PMID:15295073]
  4. Kuijt SJ, et al.
    Interaction between the GROWTH-REGULATING FACTOR and KNOTTED1-LIKE HOMEOBOX families of transcription factors.
    Plant Physiol., 2014. 164(4): p. 1952-66
    [PMID:24532604]
  5. Hu J, et al.
    A Rare Allele of GS2 Enhances Grain Size and Grain Yield in Rice.
    Mol Plant, 2015. 8(10): p. 1455-65
    [PMID:26187814]
  6. Sun P, et al.
    OsGRF4 controls grain shape, panicle length and seed shattering in rice.
    J Integr Plant Biol, 2016. 58(10): p. 836-847
    [PMID:26936408]
  7. Li S, et al.
    The OsmiR396c-OsGRF4-OsGIF1 regulatory module determines grain size and yield in rice.
    Plant Biotechnol. J., 2016. 14(11): p. 2134-2146
    [PMID:27107174]
  8. Che R, et al.
    Control of grain size and rice yield by GL2-mediated brassinosteroid responses.
    Nat Plants, 2015. 2: p. 15195
    [PMID:27250747]
  9. Duan P, et al.
    Regulation of OsGRF4 by OsmiR396 controls grain size and yield in rice.
    Nat Plants, 2015. 2: p. 15203
    [PMID:27250749]
  10. Zhang W,Sun P,He Q,Shu F,Deng H
    Transcriptome analysis of near-isogenic line provides novel insights into genes associated with panicle traits regulation in rice.
    PLoS ONE, 2018. 13(6): p. e0199077
    [PMID:29924832]