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 RrC12373_p1
Organism
Raphanus raphanistrum
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: 189aa    MW: 21427.8 Da    PI: 9.3865
Description SBP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC12373_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SBP131.13.8e-4161136277
                  -SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S-- CS
          SBP   2 CqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkq 77 
                  Cqv++C+++l++ak+y+rrhkvCevh+ka++++v+g ++rfCqqCsrfhel efDe+krsCrrrLa+hnerrrk +
  RrC12373_p1  61 CQVDRCTSNLTDAKQYYRRHKVCEVHAKASAATVAGAKRRFCQQCSRFHELPEFDEAKRSCRRRLAGHNERRRKIS 136
                  *************************************************************************976 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:4.10.1100.101.4E-3156122IPR004333Transcription factor, SBP-box
PROSITE profilePS5114131.13758135IPR004333Transcription factor, SBP-box
SuperFamilySSF1036128.5E-3760137IPR004333Transcription factor, SBP-box
PfamPF031107.7E-3161134IPR004333Transcription factor, SBP-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 189 aa     Download sequence    Send to blast
MERSQGWSYV KDKAIVSNHA EQEWENGMDE EEEDGGDEDK RKGVMERARG TNTDRGPSRL  60
CQVDRCTSNL TDAKQYYRRH KVCEVHAKAS AATVAGAKRR FCQQCSRFHE LPEFDEAKRS  120
CRRRLAGHNE RRRKISGDGC GEGAGRRGLS GQLIQTQERN RVDMKLPMTN SSFKRPQIRS  180
IGGQSGDPP
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1ul4_A4e-3859134984squamosa 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
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Negatively regulated by microRNAs miR156. {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
GenBankAJ0116101e-173AJ011610.1 Arabidopsis thaliana (ecotype Landsberg erecta) mRNA for squamosa promoter binding protein-like 5.
GenBankAJ2429601e-173AJ242960.1 Arabidopsis thaliana mRNA for Squamosa promoter binding protein-like 5, (SPL5 gene).
GenBankAK1186111e-173AK118611.1 Arabidopsis thaliana At3g15270 mRNA for squamosa promoter binding protein-like 5, putative, complete cds, clone: RAFL19-86-N19.
GenBankBT0037141e-173BT003714.1 Arabidopsis thaliana At3g15270 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018438013.11e-130PREDICTED: squamosa promoter-binding-like protein 5 isoform X1
SwissprotQ9S7581e-96SPL5_ARATH; Squamosa promoter-binding-like protein 5
TrEMBLA0A398AYA71e-107A0A398AYA7_BRACM; Uncharacterized protein
STRINGBo9g137270.11e-107(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
AT3G15270.12e-73squamosa promoter binding protein-like 5
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. 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]
  3. 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]
  4. 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]