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_009147623.1
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: 180aa    MW: 20581.1 Da    PI: 10.012
Description SBP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009147623.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SBP134.92.6e-4260135277
                     -SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S-- CS
             SBP   2 CqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkq 77 
                     Cqv++C+adl+eak+yhrrhkvCevh+ka++v+++g++qrfCqqCsrfhel efDe+krsCr+rLa+hnerrrk++
  XP_009147623.1  60 CQVDRCTADLKEAKQYHRRHKVCEVHAKASSVYLTGVKQRFCQQCSRFHELLEFDEAKRSCRKRLAGHNERRRKSS 135
                     **************************************************************************87 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PIRSFPIRSF0375757.3E-581147IPR017238Squamosa promoter-binding protein
Gene3DG3DSA:4.10.1100.104.2E-3354121IPR004333Transcription factor, SBP-box
PROSITE profilePS5114131.96657134IPR004333Transcription factor, SBP-box
SuperFamilySSF1036121.57E-3859138IPR004333Transcription factor, SBP-box
PfamPF031102.9E-3260133IPR004333Transcription 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: 180 aa     Download sequence    Send to blast
MDGKKTQGQG YLKKKASVSY LVEEELENDT DGEEEEKRKC VTDRFKGSSG SNDRGSSRLC  60
QVDRCTADLK EAKQYHRRHK VCEVHAKASS VYLTGVKQRF CQQCSRFHEL LEFDEAKRSC  120
RKRLAGHNER RRKSSGESIG EGSGGRRGIT AQMIQNQERS RVEMTLPMSN TSSFKRPQIR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1ul4_A2e-4547133184squamosa 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}.
UniprotDEVELOPMENTAL STAGE: Increases during floral transition and stay high thereafter. {ECO:0000269|PubMed:10524240, ECO:0000269|PubMed:14573523}.
UniprotTISSUE SPECIFICITY: Expressed in the inflorescence apical meristem and young flowers. {ECO:0000269|PubMed:10524240}.
UniprotTISSUE SPECIFICITY: Expressed in the rib meristem and inter-primordial tissue of the inflorescence apex. {ECO:0000269|PubMed:10524240}.
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. Promotes both vegetative phase change and flowering. {ECO:0000269|PubMed:10524240, ECO:0000269|PubMed:16914499}.
UniProtTrans-acting factor that binds specifically to the consensus nucleotide sequence 5'-TNCGTACAA-3' of AP1 promoter. Promotes both vegetative phase change and flowering. {ECO:0000269|PubMed:10524240, ECO:0000269|PubMed:16914499}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009147623.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Negatively regulated by microRNAs miR156 and miR157. {ECO:0000305|PubMed:12202040, ECO:0000305|PubMed:16914499}.
UniProtINDUCTION: Negatively regulated by microRNAs miR156. {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
GenBankAK3534391e-118AK353439.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-30-M04.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009147624.11e-130PREDICTED: squamosa promoter-binding-like protein 4 isoform X2
SwissprotQ9S7582e-79SPL5_ARATH; Squamosa promoter-binding-like protein 5
SwissprotQ9S7A92e-79SPL4_ARATH; Squamosa promoter-binding-like protein 4
TrEMBLM4FEY41e-129M4FEY4_BRARP; Squamosa promoter-binding-like protein
STRINGBra039656.1-P1e-129(Brassica rapa)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G53160.21e-63squamosa promoter binding protein-like 4
Publications ? help Back to Top
  1. 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]
  2. Hyun Y, et al.
    Site-directed mutagenesis in Arabidopsis thaliana using dividing tissue-targeted RGEN of the CRISPR/Cas system to generate heritable null alleles.
    Planta, 2015. 241(1): p. 271-84
    [PMID:25269397]
  3. 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]
  4. Ioannidi E, et al.
    Trichome patterning control involves TTG1 interaction with SPL transcription factors.
    Plant Mol. Biol., 2016. 92(6): p. 675-687
    [PMID:27631431]
  5. 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]