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 RrC226_p4
Organism
Raphanus raphanistrum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family GRF
Protein Properties Length: 382aa    MW: 42276.8 Da    PI: 8.7195
Description GRF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC226_p4genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1WRC82.82.9e-26142186145
        WRC   1 daepgrCrRtDGKkWRCsrrvlegkklCErHlhrgrsrsrkskee 45 
                d+epgrCrRtDGKkWRCsr+v +g+k+CErH+hrgr+rsrk++e+
  RrC226_p4 142 DPEPGRCRRTDGKKWRCSRDVFPGHKYCERHMHRGRNRSRKPVET 186
                79****************************************996 PP
2QLQ552.5e-1973109137
        QLQ   1 saFTaaQlqlLksQilAyKyLaanqPvPpeLlqaiqk 37 
                s F++aQ+q+L+ Q+l+y+y++a++ +P+eLl++i+k
  RrC226_p4  73 SFFSWAQWQELELQALIYRYMMAGAAIPQELLLPIKK 109
                67*********************************86 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM009511.2E-1173109IPR014978Glutamine-Leucine-Glutamine, QLQ
PROSITE profilePS5166620.91474109IPR014978Glutamine-Leucine-Glutamine, QLQ
PfamPF088805.3E-1375107IPR014978Glutamine-Leucine-Glutamine, QLQ
PROSITE profilePS5166726.714142186IPR014977WRC domain
PfamPF088794.7E-22143185IPR014977WRC domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0006995Biological Processcellular response to nitrogen starvation
GO:0008285Biological Processnegative regulation of cell proliferation
GO:0009624Biological Processresponse to nematode
GO:0009631Biological Processcold acclimation
GO:0016036Biological Processcellular response to phosphate starvation
GO:0048364Biological Processroot development
GO:0048366Biological Processleaf development
GO:0050826Biological Processresponse to freezing
GO:0051365Biological Processcellular response to potassium ion starvation
GO:0061062Biological Processregulation of nematode larval development
GO:0005634Cellular Componentnucleus
GO:0005737Cellular Componentcytoplasm
GO:0005524Molecular FunctionATP binding
GO:0044212Molecular Functiontranscription regulatory region DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 382 aa     Download sequence    Send to blast
MDLQLKQWRS QQQQQTESED QPSAAKIPKH VFDQIQSRTA TSTALPLFSS EPTSSKLSSL  60
SHDSSSRFPK MGSFFSWAQW QELELQALIY RYMMAGAAIP QELLLPIKKS LLHLPPSYFL  120
HHPLHHLPHY QPAWYMGKGA MDPEPGRCRR TDGKKWRCSR DVFPGHKYCE RHMHRGRNRS  180
RKPVETPTVN ATTTTTSIAP ASAPAAKASL FAFGGGGEEV GQGESSCFFF SGSSSSSSSQ  240
LLNLSQSSEL KQGSNNNKRP YESHNGFGNN SSDGGHTLRH FFDDWPRSEA DNSSSPMTST  300
TCLSISMPVN SSSDVSLKLF TGNEEEEARS NNNGRDQQNM SWWSGGGSLP NHHNMGGPLA  360
EALRSSSSSS PTSVLHQLWR TV
Functional Description ? help Back to Top
Source Description
UniProtTranscription activator that plays a role in the regulation of cell expansion in leaf and cotyledons tissues. Component of a network formed by miR396, the GRFs and their interacting factors (GIFs) acting in the regulation of meristem function, at least partially through the control of cell proliferation. microRNA396-GRF1/GRF3 regulatory module acts as a developmental regulator in the reprogramming of root cells during cyst nematode infection, leading to the formation of the syncytium. {ECO:0000269|PubMed:12974814, ECO:0000269|PubMed:22419826}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: microRNA 396 (miR396a or miR396b) negatively regulates growth-regulating factors (GRF1-4 and GRF7-9). Up-regulated in response to cyst nematode infection. {ECO:0000269|PubMed:15200956, ECO:0000269|PubMed:19453503, ECO:0000269|PubMed:20023165, ECO:0000269|PubMed:22419826}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY1026360.0AY102636.1 Arabidopsis thaliana transcription activator (GRF3) mRNA, complete cds.
GenBankBT0264720.0BT026472.1 Arabidopsis thaliana At2g36400 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009143588.10.0PREDICTED: growth-regulating factor 3-like
RefseqXP_013748432.10.0growth-regulating factor 3
SwissprotQ9SJR51e-178GRF3_ARATH; Growth-regulating factor 3
TrEMBLA0A397Z8C60.0A0A397Z8C6_BRACM; Uncharacterized protein
STRINGBra005268.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM19262667
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G36400.16e-70growth-regulating factor 3
Publications ? help Back to Top
  1. Casadevall R,Rodriguez RE,Debernardi JM,Palatnik JF,Casati P
    Repression of growth regulating factors by the microRNA396 inhibits cell proliferation by UV-B radiation in Arabidopsis leaves.
    Plant Cell, 2013. 25(9): p. 3570-83
    [PMID:24076976]
  2. Vercruyssen L, et al.
    ANGUSTIFOLIA3 binds to SWI/SNF chromatin remodeling complexes to regulate transcription during Arabidopsis leaf development.
    Plant Cell, 2014. 26(1): p. 210-29
    [PMID:24443518]
  3. Liu J,Rice JH,Chen N,Baum TJ,Hewezi T
    Synchronization of developmental processes and defense signaling by growth regulating transcription factors.
    PLoS ONE, 2014. 9(5): p. e98477
    [PMID:24875638]
  4. Cao Y,Han Y,Jin Q,Lin Y,Cai Y
    Comparative Genomic Analysis of the GRF Genes in Chinese Pear (Pyrus bretschneideri Rehd), Poplar (Populous), Grape (Vitis vinifera), Arabidopsis and Rice (Oryza sativa).
    Front Plant Sci, 2016. 7: p. 1750
    [PMID:27933074]