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 AT3G13540.1
Common NameATMYB5, M2, MRP15.2, MYB5
Organism
Arabidopsis thaliana
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family MYB
Protein Properties Length: 249aa    MW: 27793.5 Da    PI: 8.285
Description myb domain protein 5
Gene Model
Gene Model ID Type Source Coding Sequence
AT3G13540.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding52.89.4e-172572148
                     TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
  Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48
                     rg+WT eEde+lv  +k+ G g+W++ +++ g+ R++k+c++rw +yl
      AT3G13540.1 25 RGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYL 72
                     89******************************99************97 PP
2Myb_DNA-binding49.31.1e-1579123248
                      SSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
  Myb_DNA-binding   2 grWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48 
                      g  T +E++l+++++++lG++ W++Ia +++ gRt++++k++w+++l
      AT3G13540.1  79 GGITSDEEDLILRLHRLLGNR-WSLIAGRIP-GRTDNEIKNYWNTHL 123
                      56699****************.*********.************996 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.605.0E-221675IPR009057Homeodomain-like
PROSITE profilePS5129416.5032072IPR017930Myb domain
SuperFamilySSF466892.77E-2921119IPR009057Homeodomain-like
SMARTSM007172.0E-132474IPR001005SANT/Myb domain
PfamPF002497.1E-152572IPR001005SANT/Myb domain
CDDcd001671.11E-112772No hitNo description
PROSITE profilePS5129424.08773127IPR017930Myb domain
Gene3DG3DSA:1.10.10.602.3E-2476127IPR009057Homeodomain-like
SMARTSM007171.1E-1477125IPR001005SANT/Myb domain
PfamPF002493.9E-1480123IPR001005SANT/Myb domain
CDDcd001675.84E-1282123No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006357Biological Processregulation of transcription from RNA polymerase II promoter
GO:0009845Biological Processseed germination
GO:0010090Biological Processtrichome morphogenesis
GO:0010468Biological Processregulation of gene expression
GO:0048354Biological Processmucilage biosynthetic process involved in seed coat development
GO:0005634Cellular Componentnucleus
GO:0000981Molecular FunctionRNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001135Molecular Functiontranscription factor activity, RNA polymerase II transcription factor recruiting
GO:0043565Molecular Functionsequence-specific DNA binding
GO:0044212Molecular Functiontranscription regulatory region DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000084anatomyplant sperm cell
PO:0000282anatomytrichome
PO:0009009anatomyplant embryo
PO:0009089anatomyendosperm
PO:0020021anatomyintegument
PO:0020108anatomysuspensor
PO:0001185developmental stageplant embryo globular stage
Sequence ? help Back to Top
Protein Sequence    Length: 249 aa     Download sequence    Send to blast
MMSCGGKKPV SKKTTPCCTK MGMKRGPWTV EEDEILVSFI KKEGEGRWRS LPKRAGLLRC  60
GKSCRLRWMN YLRPSVKRGG ITSDEEDLIL RLHRLLGNRW SLIAGRIPGR TDNEIKNYWN  120
THLRKKLLRQ GIDPQTHKPL DANNIHKPEE EVSGGQKYPL EPISSSHTDD TTVNGGDGDS  180
KNSINVFGGE HGYEDFGFCY DDKFSSFLNS LINDVGDPFG NIIPISQPLQ MDDCKDGIVG  240
ASSSSLGHD
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1a5j_A5e-27231275108B-MYB
Search in ModeBase
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO425641240.0
Genevisible256985_at0.0
Expression AtlasAT3G13540-
AtGenExpressAT3G13540-
ATTED-IIAT3G13540-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Siliques. {ECO:0000269|PubMed:9839469}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a member of the MYB family of transcriptional regulators. MYB5 act as a negative regulator of trichome branching and play a role in the correct formation of the seed coat and possibly the formation the underlying endosperm layers. Loss of function mutations have defects in seed coat mucilage and columella cells as well as trichome defects (smaller and reduced number of branches).
UniProtTranscription activator, when associated with BHLH002/EGL3/MYC146, BHLH012/MYC1 or BHLH042/TT8. {ECO:0000269|PubMed:15361138}.
Function -- GeneRIF ? help Back to Top
  1. This publication identifies AtMYB5 and TT2, as partially redundant in regulating the outer seed coat developmental process with MYB5 having the major role. MYB5 and TT2 are shown to be expressed in this outer seed coat domain. [MYB5]
    [PMID: 18992236]
  2. MYB5 gene is expressed in trichomes and seeds, and regulates trichome extension and branching.
    [PMID: 19136646]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT3G13540.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT1G71030(A), AT1G79840(A), AT2G23550(A), AT2G23580(A), AT2G37260(A)
Interaction -- BIND ? help Back to Top
Source Intact With Description
BINDAT1G63650EGL3 interacts with AtMYB5.
BINDAT4G00480MYC1 (AtBHLH012) interacts with AtMYB5.
BINDAT4G09820TT8 interacts with AtMYB5.
Interaction ? help Back to Top
Source Intact With
BioGRIDAT4G09820, AT4G00480, AT1G63650
IntActSearch Q38850
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT3G13540
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY5195870.0AY519587.1 Arabidopsis thaliana MYB transcription factor (At3g13540) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_187963.10.0myb domain protein 5
SwissprotQ388500.0MYB5_ARATH; Transcription repressor MYB5
TrEMBLA0A178VAR40.0A0A178VAR4_ARATH; MYB5
STRINGAT3G13540.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM4282646
Representative plantOGRP5171784
Publications ? help Back to Top
  1. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  2. Stracke R,Werber M,Weisshaar B
    The R2R3-MYB gene family in Arabidopsis thaliana.
    Curr. Opin. Plant Biol., 2001. 4(5): p. 447-56
    [PMID:11597504]
  3. Zimmermann IM,Heim MA,Weisshaar B,Uhrig JF
    Comprehensive identification of Arabidopsis thaliana MYB transcription factors interacting with R/B-like BHLH proteins.
    Plant J., 2004. 40(1): p. 22-34
    [PMID:15361138]
  4. Yanhui C, et al.
    The MYB transcription factor superfamily of Arabidopsis: expression analysis and phylogenetic comparison with the rice MYB family.
    Plant Mol. Biol., 2006. 60(1): p. 107-24
    [PMID:16463103]
  5. Ishida T, et al.
    Arabidopsis TRANSPARENT TESTA GLABRA2 is directly regulated by R2R3 MYB transcription factors and is involved in regulation of GLABRA2 transcription in epidermal differentiation.
    Plant Cell, 2007. 19(8): p. 2531-43
    [PMID:17766401]
  6. Jakoby MJ, et al.
    Transcriptional profiling of mature Arabidopsis trichomes reveals that NOECK encodes the MIXTA-like transcriptional regulator MYB106.
    Plant Physiol., 2008. 148(3): p. 1583-602
    [PMID:18805951]
  7. Gonzalez A,Mendenhall J,Huo Y,Lloyd A
    TTG1 complex MYBs, MYB5 and TT2, control outer seed coat differentiation.
    Dev. Biol., 2009. 325(2): p. 412-21
    [PMID:18992236]
  8. Li SF, et al.
    The Arabidopsis MYB5 transcription factor regulates mucilage synthesis, seed coat development, and trichome morphogenesis.
    Plant Cell, 2009. 21(1): p. 72-89
    [PMID:19136646]
  9. Arsovski AA,Villota MM,Rowland O,Subramaniam R,Western TL
    MUM ENHANCERS are important for seed coat mucilage production and mucilage secretory cell differentiation in Arabidopsis thaliana.
    J. Exp. Bot., 2009. 60(9): p. 2601-12
    [PMID:19401413]
  10. Van Minnebruggen A, et al.
    The ang3 mutation identified the ribosomal protein gene RPL5B with a role in cell expansion during organ growth.
    Physiol Plant, 2010. 138(1): p. 91-101
    [PMID:19878482]
  11. Ranocha P,Francoz E,Burlat V,Dunand C
    Expression of PRX36, PMEI6 and SBT1.7 is controlled by complex transcription factor regulatory networks for proper seed coat mucilage extrusion.
    Plant Signal Behav, 2014. 9(11): p. e977734
    [PMID:25531128]
  12. Jin J, et al.
    An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.
    Mol. Biol. Evol., 2015. 32(7): p. 1767-73
    [PMID:25750178]
  13. Li SF,Santini JM,Nicolaou O,Parish RW
    A novel myb-related gene from Arabidopsis thaliana.
    FEBS Lett., 1996. 379(2): p. 117-21
    [PMID:8635574]
  14. Quaedvlieg N, et al.
    Identification of a light-regulated MYB gene from an Arabidopsis transcription factor gene collection.
    Plant Mol. Biol., 1996. 32(5): p. 987-93
    [PMID:8980549]
  15. Kranz HD, et al.
    Towards functional characterisation of the members of the R2R3-MYB gene family from Arabidopsis thaliana.
    Plant J., 1998. 16(2): p. 263-76
    [PMID:9839469]