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 PGSC0003DMP400004998
Organism
Solanum tuberosum
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
Family B3
Protein Properties Length: 238aa    MW: 26992.4 Da    PI: 4.6195
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
PGSC0003DMP400004998genomePGSCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B354.52.1e-17139220489
                           E-..-HHHHTT-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSE CS
                    B3   4 vltpsdvlksgrlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrse 89 
                            + ps+v++ + l++p kfa+ + +g+   s  l+l+ +   sW vk+i+ +k+ +   t GWk Fv +n+Lk gD++v++++++++
  PGSC0003DMP400004998 139 FMHPSYVSRPHALYIPLKFARMYfMGN---SGNLVLRVPGKGSWPVKCIMLRKDAK--VTCGWKAFVLDNKLKYGDVCVLEVINDTK 220
                           5789*******************7544...346***************99888766..79*********************987644 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.108.3E-23128222IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019362.55E-22129221IPR015300DNA-binding pseudobarrel domain
CDDcd100174.57E-19134230No hitNo description
SMARTSM010195.4E-13135232IPR003340B3 DNA binding domain
PROSITE profilePS5086311.632136232IPR003340B3 DNA binding domain
PfamPF023629.7E-16138221IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 238 aa     Download sequence    Send to blast
MFGYNARSHF NVTIFDFSAA EIEYPPAEIE SDDSIDILDV VEHSSEYLSY DPVVQERKRI  60
RQEGEEEDDI PVEHQTNVID EEEFQGNVVS LVISEDCEEH EQQSNIVTSK RKAERDEGIA  120
DNYQRAKAFK SKNPFIVSFM HPSYVSRPHA LYIPLKFARM YFMGNSGNLV LRVPGKGSWP  180
VKCIMLRKDA KVTCGWKAFV LDNKLKYGDV CVLEVINDTK LSLIDVTIFP GISDGTN*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A5e-1712622939140B3 domain-containing transcription factor VRN1
4i1k_B5e-1712622939140B3 domain-containing transcription factor VRN1
Search in ModeBase
Cis-element ? help Back to Top
SourceLink
PlantRegMapPGSC0003DMP400004998
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2154041e-127AC215404.2 Solanum lycopersicum cultivar Heinz 1706 chromosome 2 clone C02HBa0163K16, complete sequence.
GenBankHG9755141e-127HG975514.1 Solanum lycopersicum chromosome ch02, complete genome.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006344812.11e-175PREDICTED: B3 domain-containing transcription factor VRN1-like
TrEMBLM0ZSM91e-176M0ZSM9_SOLTU; Uncharacterized protein
STRINGPGSC0003DMT4000071991e-174(Solanum tuberosum)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G49480.18e-20related to vernalization1 1
Publications ? help Back to Top
  1. Xu X, et al.
    Genome sequence and analysis of the tuber crop potato.
    Nature, 2011. 475(7355): p. 189-95
    [PMID:21743474]