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 XP_009132954.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family SBP
Protein Properties Length: 137aa    MW: 15994.5 Da    PI: 6.3599
Description SBP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009132954.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SBP1339.9e-4259136178
                     --SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S--- CS
             SBP   1 lCqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkqa 78 
                     +Cqve+C+ad+s+ak+yh+rhkvCe+h+kapvv +sg  qrfCqqCsrfhel+efDe+krsCrrrLa+hnerrrk+++
  XP_009132954.1  59 CCQVERCTADMSRAKQYHKRHKVCEFHAKAPVVRISGGYQRFCQQCSRFHELREFDEAKRSCRRRLAGHNERRRKSTN 136
                     6**************************************************************************976 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PIRSFPIRSF0375751.2E-551137IPR017238Squamosa promoter-binding protein
Gene3DG3DSA:4.10.1100.102.2E-3253121IPR004333Transcription factor, SBP-box
PROSITE profilePS5114131.82957134IPR004333Transcription factor, SBP-box
SuperFamilySSF1036124.84E-3758135IPR004333Transcription factor, SBP-box
PfamPF031104.8E-3260133IPR004333Transcription factor, SBP-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009911Biological Processpositive regulation of flower development
GO:0010228Biological Processvegetative to reproductive phase transition of meristem
GO:0010229Biological Processinflorescence development
GO:0010321Biological Processregulation of vegetative phase change
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 137 aa     Download sequence    Send to blast
MSARRSNAEG KRSLIEMSEE EEQEEDDDDT FVEEDGEEEE EEASEKKQKG KATSSSGVCC  60
QVERCTADMS RAKQYHKRHK VCEFHAKAPV VRISGGYQRF CQQCSRFHEL REFDEAKRSC  120
RRRLAGHNER RRKSTNE
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1ul4_A4e-3850133184squamosa promoter binding protein-like 4
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Increases during floral transition and stay high thereafter. {ECO:0000269|PubMed:10524240, ECO:0000269|PubMed:14573523, ECO:0000269|PubMed:16914499, ECO:0000269|PubMed:9301089}.
UniprotTISSUE SPECIFICITY: Expressed in vegetative and inflorescence apical meristems, floral meristems, leaf and flower organ primordia, inflorescence stem tissue and to lower extent in roots. {ECO:0000269|PubMed:10524240, ECO:0000269|PubMed:9301089}.
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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00290DAPTransfer from AT2G33810Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009132954.1
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
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2411461e-178AC241146.1 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrH072P15, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009132954.12e-94PREDICTED: squamosa promoter-binding-like protein 3
SwissprotP930152e-58SPL3_ARATH; Squamosa promoter-binding-like protein 3
TrEMBLA0A397ZVP35e-93A0A397ZVP3_BRACM; Squamosa promoter-binding-like protein
STRINGBo3g027460.11e-65(Brassica oleracea)
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
AT2G33810.11e-56squamosa 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]