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 474435
Common NameARALYDRAFT_474435
Organism
Arabidopsis lyrata
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family SBP
Protein Properties Length: 174aa    MW: 19938.3 Da    PI: 10.1381
Description SBP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
474435genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SBP1344.8e-4254129277
             -SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S-- CS
     SBP   2 CqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkq 77 
             Cqv++C++d++eak yhrrhkvCevh+ka++v++sgl+qrfCqqCsrfhel+efDe+krsCrrrLa+hnerrrk++
  474435  54 CQVDRCTSDMKEAKLYHRRHKVCEVHAKASSVFLSGLNQRFCQQCSRFHELQEFDEAKRSCRRRLAGHNERRRKSS 129
             **************************************************************************87 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PIRSFPIRSF0375752.5E-621141IPR017238Squamosa promoter-binding protein
Gene3DG3DSA:4.10.1100.101.0E-3248115IPR004333Transcription factor, SBP-box
PROSITE profilePS5114131.93251128IPR004333Transcription factor, SBP-box
SuperFamilySSF1036121.03E-3753131IPR004333Transcription factor, SBP-box
PfamPF031109.6E-3254127IPR004333Transcription factor, SBP-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009908Biological Processflower development
GO:0010321Biological Processregulation of vegetative phase change
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 174 aa     Download sequence    Send to blast
MEGKRTQGQG YLKKKSYRVE EEMEYDTDGE EEVGRDRVRG SSGSIDRGGS SRLCQVDRCT  60
SDMKEAKLYH RRHKVCEVHA KASSVFLSGL NQRFCQQCSR FHELQEFDEA KRSCRRRLAG  120
HNERRRKSSG ESSFGEGSGR RGITGQVIQN QERSRVEMTL PMPNSSFKRP QIR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1ul4_A5e-5040127184squamosa 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. Promotes both vegetative phase change and flowering. {ECO:0000269|PubMed:10524240, ECO:0000269|PubMed:16914499}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00634PBMTransfer from PK22320.1Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMap474435
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Negatively regulated by microRNAs miR156 and miR157. {ECO:0000305|PubMed:12202040, ECO:0000305|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
GenBankAY0849020.0AY084902.1 Arabidopsis thaliana clone 12071 mRNA, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_020867200.11e-114squamosa promoter-binding-like protein 4 isoform X1
RefseqXP_020867201.11e-114squamosa promoter-binding-like protein 4 isoform X1
SwissprotQ9S7A91e-103SPL4_ARATH; Squamosa promoter-binding-like protein 4
TrEMBLD7KKE31e-122D7KKE3_ARALL; Squamosa promoter-binding-like protein
STRINGfgenesh2_kg.1__4389__AT1G53160.21e-123(Arabidopsis lyrata)
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
AT1G53160.22e-74squamosa 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]