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 Carubv10010422m
Common NameCARUB_v10010422mg
Organism
Capsella rubella
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella
Family SBP
Protein Properties Length: 181aa    MW: 20737.2 Da    PI: 9.7755
Description SBP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Carubv10010422mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SBP134.92.5e-4260135277
                      -SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S-- CS
              SBP   2 CqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkq 77 
                      Cqv++C+adl+eak+yhrrhkvCevh+ka++v++sg++qrfCqqCsrfhe++efDe+krsCrrrLa+hnerrrk++
  Carubv10010422m  60 CQVDRCTADLKEAKQYHRRHKVCEVHAKASSVFLSGVSQRFCQQCSRFHEIQEFDEAKRSCRRRLAGHNERRRKSS 135
                      **************************************************************************87 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PIRSFPIRSF0375752.3E-611146IPR017238Squamosa promoter-binding protein
Gene3DG3DSA:4.10.1100.101.2E-3353121IPR004333Transcription factor, SBP-box
PROSITE profilePS5114132.18857134IPR004333Transcription factor, SBP-box
SuperFamilySSF1036122.49E-3859138IPR004333Transcription factor, SBP-box
PfamPF031103.2E-3260133IPR004333Transcription 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: 181 aa     Download sequence    Send to blast
MEGRRTQGQG YLKSKSYLVE EEMEDDMDGE EEAVRNEEKK KGLMDRVIRG YSSGSSSRLC  60
QVDRCTADLK EAKQYHRRHK VCEVHAKASS VFLSGVSQRF CQQCSRFHEI QEFDEAKRSC  120
RRRLAGHNER RRKSSGESFG EGSGRRGGIT GQVLIQNQER SRVEMTLPMP NSSFKRPQIR  180
*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1ul4_A1e-4752133284squamosa 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
PlantRegMapCarubv10010422m
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
GenBankAJ0116321e-135AJ011632.1 Arabidopsis thaliana (ecotype Landsberg erecta) mRNA for squamosa promoter binding protein-like 4, partial.
GenBankAY0849021e-135AY084902.1 Arabidopsis thaliana clone 12071 mRNA, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006303186.21e-114squamosa promoter-binding-like protein 4
SwissprotQ9S7A96e-86SPL4_ARATH; Squamosa promoter-binding-like protein 4
TrEMBLR0I1J91e-128R0I1J9_9BRAS; Squamosa promoter-binding-like protein
STRINGXP_006303186.11e-128(Capsella rubella)
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
AT1G53160.21e-75squamosa 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]