PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Rsa1.0_03890.1_g00004.1
Organism
Raphanus sativus
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 SBP
Protein Properties Length: 141aa    MW: 16347.9 Da    PI: 7.0085
Description SBP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_03890.1_g00004.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SBP132.61.3e-4163140178
                              --SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S--- CS
                      SBP   1 lCqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkqa 78 
                              +Cqve+C+ad+s+ak+yh+rhkvCe+h+kap v +sgl qrfCqqCsrfhel efD++krsCrrrLa+hn+rrr++++
  Rsa1.0_03890.1_g00004.1  63 ACQVERCTADMSRAKQYHKRHKVCEFHAKAPLVRISGLYQRFCQQCSRFHELGEFDDTKRSCRRRLAGHNQRRRRNTT 140
                              5*************************************************************************9875 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PIRSFPIRSF0375752.7E-553141IPR017238Squamosa promoter-binding protein
Gene3DG3DSA:4.10.1100.101.4E-3257125IPR004333Transcription factor, SBP-box
PROSITE profilePS5114131.52261138IPR004333Transcription factor, SBP-box
SuperFamilySSF1036124.02E-3763139IPR004333Transcription factor, SBP-box
PfamPF031101.4E-3164137IPR004333Transcription factor, SBP-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009908Biological Processflower development
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 141 aa     Download sequence    Send to blast
MSTRGSKAEG KRILRDMSEE EEENEDTSEE EEDDDEEEEE VALEKKQKGK ATTTTSSSSG  60
TGACQVERCT ADMSRAKQYH KRHKVCEFHA KAPLVRISGL YQRFCQQCSR FHELGEFDDT  120
KRSCRRRLAG HNQRRRRNTT Q
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1ul4_A2e-3855137284squamosa promoter binding protein-like 4
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtTrans-acting factor that binds specifically to the consensus nucleotide sequence 5'-TNCGTACAA-3' of AP1 promoter. Binds specifically to the 5'-GTAC-3' core sequence. Promotes both vegetative phase change and flowering. Regulates phase-specific patterns of leaf epidermal differentiation and flowering time, but does not seem to affect leaf shape. {ECO:0000269|PubMed:16095614, ECO:0000269|PubMed:16914499, ECO:0000269|PubMed:9301089}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_03890.1_g00004.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Negatively regulated by microRNAs miR156. {ECO:0000269|PubMed:12202040, ECO:0000269|PubMed:16914499}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAJ0116337e-73AJ011633.1 Arabidopsis thaliana (ecotype Landsberg erecta) mRNA for squamosa promoter binding protein-like 3.
GenBankAJ2429597e-73AJ242959.1 Arabidopsis thaliana mRNA for Squamosa promoter binding protein-like 3 (SPL3 gene).
GenBankAK1181797e-73AK118179.1 Arabidopsis thaliana At2g33810 mRNA for putative squamosa-promoter binding protein, complete cds, clone: RAFL19-50-A02.
GenBankBT0054437e-73BT005443.1 Arabidopsis thaliana clone U50647 putative squamosa-promoter binding protein (At2g33810) mRNA, complete cds.
GenBankY094277e-73Y09427.1 A.thaliana mRNA for squamosa-promoter binding protein like 3.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009141347.18e-67PREDICTED: squamosa promoter-binding-like protein 3
RefseqXP_013632192.19e-67PREDICTED: squamosa promoter-binding-like protein 3
SwissprotP930152e-56SPL3_ARATH; Squamosa promoter-binding-like protein 3
TrEMBLA0A3P6D2F02e-65A0A3P6D2F0_BRAOL; Squamosa promoter-binding-like protein
TrEMBLM4DZD32e-65M4DZD3_BRARP; Squamosa promoter-binding-like protein
STRINGBra021880.1-P3e-66(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM86828118
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G33810.13e-53squamosa promoter binding protein-like 3
Publications ? help Back to Top
  1. Heidari B,Nemie-Feyissa D,Kangasjärvi S,Lillo C
    Antagonistic regulation of flowering time through distinct regulatory subunits of protein phosphatase 2A.
    PLoS ONE, 2013. 8(7): p. e67987
    [PMID:23976921]
  2. Jorgensen SA,Preston JC
    Differential SPL gene expression patterns reveal candidate genes underlying flowering time and architectural differences in Mimulus and Arabidopsis.
    Mol. Phylogenet. Evol., 2014. 73: p. 129-39
    [PMID:24508602]
  3. Yu N,Niu QW,Ng KH,Chua NH
    The role of miR156/SPLs modules in Arabidopsis lateral root development.
    Plant J., 2015. 83(4): p. 673-85
    [PMID:26096676]
  4. Lei KJ, et al.
    Modulation of the Phosphate-Deficient Responses by MicroRNA156 and its Targeted SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 3 in Arabidopsis.
    Plant Cell Physiol., 2016. 57(1): p. 192-203
    [PMID:26647245]
  5. Xu M, et al.
    Developmental Functions of miR156-Regulated SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) Genes in Arabidopsis thaliana.
    PLoS Genet., 2016. 12(8): p. e1006263
    [PMID:27541584]
  6. Jung JH,Lee HJ,Ryu JY,Park CM
    SPL3/4/5 Integrate Developmental Aging and Photoperiodic Signals into the FT-FD Module in Arabidopsis Flowering.
    Mol Plant, 2016. 9(12): p. 1647-1659
    [PMID:27815142]
  7. Duan HC, et al.
    ALKBH10B Is an RNA N6-Methyladenosine Demethylase Affecting Arabidopsis Floral Transition.
    Plant Cell, 2017. 29(12): p. 2995-3011
    [PMID:29180595]
  8. Negishi K,Endo M,Abe M,Araki T
    SODIUM POTASSIUM ROOT DEFECTIVE1 regulates FLOWERING LOCUS T expression via the microRNA156-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE3 module in response to potassium conditions.
    Plant Cell Physiol., 2018. 59(2): p. 404-413
    [PMID:29253219]