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 RrC7190_p3
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 MYB
Protein Properties Length: 238aa    MW: 27426.8 Da    PI: 6.8513
Description MYB family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC7190_p3genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding38.43e-121771148
                     TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHT.......TTS-HHHHHHHHHHHT CS
  Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmg.......kgRtlkqcksrwqkyl 48
                     rg+W+ eE  +l   + + G ++W++ ++  g       + R++k+c++rw +yl
       RrC7190_p3 17 RGPWSDEESRRLEAFILKNGHHNWRSLPKLAGkflavygLMRCGKSCRLRWINYL 71
                     89***************************************************97 PP
2Myb_DNA-binding50.83.8e-1677122148
                      TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
  Myb_DNA-binding   1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48 
                      rg +T+eE e ++++++ lG++ W++Ia++++ gRt++++k+ w+++l
       RrC7190_p3  77 RGDFTKEEVETIIHLHQVLGNK-WSKIASHLP-GRTDNEIKNVWNTHL 122
                      899*******************.*********.************986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5129411.4221271IPR017930Myb domain
SuperFamilySSF466892.64E-2614118IPR009057Homeodomain-like
SMARTSM007179.1E-81673IPR001005SANT/Myb domain
PfamPF002498.8E-111771IPR001005SANT/Myb domain
Gene3DG3DSA:1.10.10.606.5E-181878IPR009057Homeodomain-like
CDDcd001672.18E-61971No hitNo description
PROSITE profilePS5129424.98572126IPR017930Myb domain
SMARTSM007171.6E-1476124IPR001005SANT/Myb domain
PfamPF002498.5E-1577122IPR001005SANT/Myb domain
Gene3DG3DSA:1.10.10.606.2E-2779127IPR009057Homeodomain-like
CDDcd001671.86E-1080122No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 238 aa     Download sequence    Send to blast
MGKRRAPCCD NSQELKRGPW SDEESRRLEA FILKNGHHNW RSLPKLAGKF LAVYGLMRCG  60
KSCRLRWINY LRPGLKRGDF TKEEVETIIH LHQVLGNKWS KIASHLPGRT DNEIKNVWNT  120
HLKKRLVKSN SSASDVTNQA SSSSSSSVSN DVINSENHSQ EEELEEILVE HMPYGFEVNA  180
PQSLEYLFED RQIPPLPISK PDSLEIHRQS HDELCSQMVE PGLDVYNEWL NYFDNQTL
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1a5j_A7e-23141264108B-MYB
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtInvolved in metal ions homeostasis, including iron ions (Fe) acquisition, via the regulation of NAS4 and NAS2 genes expression. Necessary for plant survival in alkaline soil where iron availability is greatly restricted. Triggers tolerance to nickel (Ni) and zinc (Zn) ions. {ECO:0000269|PubMed:24278034}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00352DAPTransfer from AT3G12820Download
Motif logo
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Accumulates strongly in the root stele and in the outer layers of the lateral roots when exposed to iron (Fe)-deficient conditions (PubMed:24278034). Slightly induced by ethylene and by darkness conditions (PubMed:9839469). Accumulates upon potassium (K) depletion (PubMed:15489280). Induced by zinc (Zn) and cadmium (Cd) ions (PubMed:18088336). {ECO:0000269|PubMed:15489280, ECO:0000269|PubMed:18088336, ECO:0000269|PubMed:24278034, ECO:0000269|PubMed:9839469}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY5195865e-72AY519586.1 Arabidopsis thaliana MYB transcription factor (At3g12820) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_013651974.11e-143transcription factor MYB63-like
SwissprotQ9LTV41e-108MYB10_ARATH; Transcription factor MYB10
TrEMBLM4CB921e-141M4CB92_BRARP; Uncharacterized protein
STRINGBra001472.1-P1e-141(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM140961624
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G12820.11e-94myb domain protein 10
Publications ? help Back to Top
  1. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
    [PMID:16280546]