PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Solyc08g005430.2.1
Common NameLOC101245679
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon
Family GRF
Protein Properties Length: 357aa    MW: 39116.2 Da    PI: 8.5474
Description GRF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc08g005430.2.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1WRC76.82.1e-2492136145
                 WRC   1 daepgrCrRtDGKkWRCsrrvlegkklCErHlhrgrsrsrkskee 45 
                         d+epgrCrRtDGKkWRCs+++ +++k+CErH+hrgr+rsrk++e+
  Solyc08g005430.2.1  92 DPEPGRCRRTDGKKWRCSKDAHPDSKYCERHMHRGRNRSRKPVES 136
                         79****************************************986 PP

2QLQ65.51.3e-223166237
                 QLQ  2 aFTaaQlqlLksQilAyKyLaanqPvPpeLlqaiqk 37
                        +FTa Q+q+L++Q+++yKyL+a++PvPp+L+++i++
  Solyc08g005430.2.1 31 PFTAVQWQELEHQAMIYKYLVAGLPVPPDLVVPIRR 66
                        9*********************************86 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM009517.9E-133066IPR014978Glutamine-Leucine-Glutamine, QLQ
PfamPF088804.4E-173165IPR014978Glutamine-Leucine-Glutamine, QLQ
PROSITE profilePS5166624.3433166IPR014978Glutamine-Leucine-Glutamine, QLQ
PROSITE profilePS5166725.83192136IPR014977WRC domain
PfamPF088796.6E-2193135IPR014977WRC 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
Sequence ? help Back to Top
Protein Sequence    Length: 357 aa     Download sequence    Send to blast
MSGTSTTSVV GVGLVGGGGE VGYNDYGFRP PFTAVQWQEL EHQAMIYKYL VAGLPVPPDL  60
VVPIRRSFDA ISARFFSHPS LGYCSYYGKK FDPEPGRCRR TDGKKWRCSK DAHPDSKYCE  120
RHMHRGRNRS RKPVESQTTS QSLSTSKSHT ATGSSNRSGS FQSNSSGSFQ NMPLYSVANS  180
DGISYGSTTT KLQMEPASYG ITNKEYRYGM APDVDDHNFM PVASTSVRGL GGTGSNTDNM  240
WRLMPSQDHS KANLKNDSQL LGSLPNPFEP VIESKQQPQH CFFSSDIDSP STVKQEPQHP  300
MRSFFDEWPT SKESWSNLDE GSGKNNFSTT QLSISIPNIS SGFSSRSASS PKCADA*
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapSolyc08g005430.2.1
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-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAP0095940.0Solanum lycopersicum DNA, chromosome 8, clone: C08HBa0022E13, complete sequence
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_010324483.10.0growth-regulating factor 4-like isoform X1
RefseqXP_019070921.10.0growth-regulating factor 4-like isoform X1
RefseqXP_019070922.10.0growth-regulating factor 4-like isoform X1
SwissprotQ6ZIK52e-85GRF4_ORYSJ; Growth-regulating factor 4
TrEMBLA0A3Q7IDJ00.0A0A3Q7IDJ0_SOLLC; Uncharacterized protein
STRINGSolyc08g005430.2.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA7432384
Representative plantOGRP4601684
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G13960.13e-49growth-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. Wang Y,van der Hoeven RS,Nielsen R,Mueller LA,Tanksley SD
    Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments.
    Theor. Appl. Genet., 2005. 112(1): p. 72-84
    [PMID:16208505]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. Che R, et al.
    Control of grain size and rice yield by GL2-mediated brassinosteroid responses.
    Nat Plants, 2015. 2: p. 15195
    [PMID:27250747]
  8. Duan P, et al.
    Regulation of OsGRF4 by OsmiR396 controls grain size and yield in rice.
    Nat Plants, 2015. 2: p. 15203
    [PMID:27250749]