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_009142046.1
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: 363aa    MW: 39785.7 Da    PI: 8.0344
Description SBP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009142046.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SBP1352.4e-4270147178
                     --SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S--- CS
             SBP   1 lCqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkqa 78 
                     +CqvegC +dl++ak y+ rh+vC +hsk+p v+v+g+eqrfCqqCsrfh+l+efD ekrsCrrrLa+hnerrrk+q+
  XP_009142046.1  70 RCQVEGCGVDLTNAKGYYLRHRVCGMHSKTPRVIVAGIEQRFCQQCSRFHQLQEFDLEKRSCRRRLAGHNERRRKPQP 147
                     6**************************************************************************986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:4.10.1100.102.7E-3463132IPR004333Transcription factor, SBP-box
PROSITE profilePS5114131.87268145IPR004333Transcription factor, SBP-box
SuperFamilySSF1036122.49E-4069149IPR004333Transcription factor, SBP-box
PfamPF031105.2E-3271144IPR004333Transcription factor, SBP-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0010228Biological Processvegetative to reproductive phase transition of meristem
GO:0048653Biological Processanther development
GO:2000025Biological Processregulation of leaf formation
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 363 aa     Download sequence    Send to blast
MNMGSNSGQG LGPGQAESGG SSNESSSFSG GLMFGQRIYF EDGGGGSSSS GGSNRRVRGG  60
GSGQSSQIPR CQVEGCGVDL TNAKGYYLRH RVCGMHSKTP RVIVAGIEQR FCQQCSRFHQ  120
LQEFDLEKRS CRRRLAGHNE RRRKPQPASL SVLSSRYGRI APSLYGNAET TMNGSFLGSQ  180
DMSWTSSRTL DTRVMRRPVA TPSWQINPMD VFSQGSVSGG GGISFSSPEI MDTKPESYKG  240
IGGDSNCALS LLSNPHQPAD NNNTWRTSSG FGPMTVTMAQ PPPAPSQHQY LNPPWVFKDD  300
DNNCPNDMSP VLNLARFTET DTTMGEFELS DHHHPQHQNR RQYMEDENTR AYDSSSHHNN  360
WSL
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1ul4_A7e-3061144184squamosa promoter binding protein-like 4
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed constitutively during plant development, with a strong increase during flower development. {ECO:0000269|PubMed:10524240, ECO:0000269|PubMed:14573523}.
Functional Description ? help Back to Top
Source Description
UniProtTrans-acting factor that binds specifically to the consensus nucleotide sequence 5'-TNCGTACAA-3'. {ECO:0000250}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00307DAPTransfer from AT2G42200Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009142046.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Negatively regulated by microRNAs miR156 and miR157. {ECO:0000305|PubMed:12202040}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK3535380.0AK353538.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-50-J24.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009142046.10.0PREDICTED: squamosa promoter-binding-like protein 9
SwissprotQ700W20.0SPL9_ARATH; Squamosa promoter-binding-like protein 9
TrEMBLM4DK630.0M4DK63_BRARP; Uncharacterized protein
STRINGBra016891.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM21442775
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G42200.10.0squamosa promoter binding protein-like 9
Publications ? help Back to Top
  1. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
    [PMID:16280546]
  2. Stief A, et al.
    Arabidopsis miR156 Regulates Tolerance to Recurring Environmental Stress through SPL Transcription Factors.
    Plant Cell, 2014. 26(4): p. 1792-1807
    [PMID:24769482]
  3. Yu ZX, et al.
    Progressive Regulation of Sesquiterpene Biosynthesis in Arabidopsis and Patchouli (Pogostemon cablin) by the miR156-Targeted SPL Transcription Factors.
    Mol Plant, 2015.
    [PMID:25355059]
  4. 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]
  5. Morea EG, et al.
    Functional and evolutionary analyses of the miR156 and miR529 families in land plants.
    BMC Plant Biol., 2016. 16: p. 40
    [PMID:26841873]
  6. Hyun Y, et al.
    Multi-layered Regulation of SPL15 and Cooperation with SOC1 Integrate Endogenous Flowering Pathways at the Arabidopsis Shoot Meristem.
    Dev. Cell, 2016. 37(3): p. 254-66
    [PMID:27134142]
  7. 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]
  8. Mahmood K,Xu Z,El-Kereamy A,Casaretto JA,Rothstein SJ
    The Arabidopsis Transcription Factor ANAC032 Represses Anthocyanin Biosynthesis in Response to High Sucrose and Oxidative and Abiotic Stresses.
    Front Plant Sci, 2016. 7: p. 1548
    [PMID:27790239]
  9. Mao YB, et al.
    Jasmonate response decay and defense metabolite accumulation contributes to age-regulated dynamics of plant insect resistance.
    Nat Commun, 2017. 8: p. 13925
    [PMID:28067238]
  10. Nguyen ST,Greaves T,McCurdy DW
    Heteroblastic Development of Transfer Cells Is Controlled by the microRNA miR156/SPL Module.
    Plant Physiol., 2017. 173(3): p. 1676-1691
    [PMID:28082719]
  11. 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]
  12. Dotto M,Gómez MS,Soto MS,Casati P
    UV-B radiation delays flowering time through changes in the PRC2 complex activity and miR156 levels in Arabidopsis thaliana.
    Plant Cell Environ., 2018. 41(6): p. 1394-1406
    [PMID:29447428]
  13. He J, et al.
    Threshold-dependent repression of SPL gene expression by miR156/miR157 controls vegetative phase change in Arabidopsis thaliana.
    PLoS Genet., 2018. 14(4): p. e1007337
    [PMID:29672610]