PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Tp6g25540
Organism
Thellungiella parvula
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassicaceae incertae sedis; Schrenkiella
Family SBP
Protein Properties Length: 798aa    MW: 89712.6 Da    PI: 7.2108
Description SBP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Tp6g25540genomethellungiellaView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SBP115.23.5e-36144220177
                --SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S-- CS
        SBP   1 lCqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkq 77 
                +Cqv+gC+ad+se+k yhrrh+vC  +++++ v+++g+ +r+CqqC++fh ls+fDe+krsCrr+L++hn+rr++k 
  Tp6g25540 144 RCQVPGCKADISELKGYHRRHRVCLRCANSSFVVLDGEDKRYCQQCGKFHVLSDFDEGKRSCRRKLERHNNRRKRKP 220
                6************************************************************************9975 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:4.10.1100.101.3E-28138206IPR004333Transcription factor, SBP-box
PROSITE profilePS5114129.53142219IPR004333Transcription factor, SBP-box
SuperFamilySSF1036126.67E-34143223IPR004333Transcription factor, SBP-box
PfamPF031106.1E-27145218IPR004333Transcription factor, SBP-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0055070Biological Processcopper ion homeostasis
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 798 aa     Download sequence    Send to blast
MSSMSQSPSA PEIEIQPPAL LDDDPSTYSS AMWDWGDLLD FAADERLLVS FDSHQTPFSP  60
VLLPPPPPPP TLIATQPPAQ SESYPSPDES GSGSDRVRKR DPRLLCSNFL EGMLPCSCPE  120
LDQKLEEAEL PKKKRVRGGS GVARCQVPGC KADISELKGY HRRHRVCLRC ANSSFVVLDG  180
EDKRYCQQCG KFHVLSDFDE GKRSCRRKLE RHNNRRKRKP VDKGGVASEK QVLSQNENSV  240
IDVDDGKDNA CSSDQRVEQE ASLIFEDRHI PTQGSVPFTH SINADNFVSV TGSGEPHPDE  300
RMNDTKFELS PSCGDNKSAY STVCPTGRIS FKLYDWNPAE FPRRLRHQIF QWLATMPVEL  360
EGYIRPGCTI LTVFIAMPEI MWVKLSKDPV AYLDEFILKP GKMLFGKGSM TVYLNNMIFR  420
LIKGGTTLKR VDVKLESPKL QFVYPTCFEA GKPIELVVCG LNLLQPKCRF LVSFSGKYLP  480
HNYSVVPAPS QDGKRSCNNK LYRINIVNSD PNLFGPAFVE VENESGLSNF IPLIIGDKAI  540
CSEMKLIEQK FNATLFPEEQ DVTACCSLTC CCRDFEERQS TFTGLLLDIA WSVKVPSSEC  600
TDQTVNRCQI KRYNRVLNYL IQSNSASILG NVLHNLDNLV KKMEPDSLVH CTCDCDVRLL  660
HENMNLARKQ QRHEDSKVNP VTSACCCESS FKDIPSRILN FNQDPEAVLD CKERTPDTGG  720
KETDPLLNKE VVMNVNDIGE WPRKSCIPRH SAQTFRFRQS VFLITTFVIC FAVCAVLYHP  780
NKVTQLAVAI RTRLAHKL
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1ul5_A5e-48142227388squamosa promoter binding protein-like 7
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that participates in reprogramming global gene expression during copper deficiency in order to improve the metal uptake and prioritize its distribution to copper proteins of major importance (Probable). Binds directly to 5'-GTAC-3' motifs in the microRNA (miRNA) promoter of the stress-responsive miRNAs miR398b and miR398c to activate their transcription. During copper deficiency, activates the copper transporters COPT1 and COPT2, and the copper chaperone CCH, directly or indirectly via miRNAs. Required for the expression of the miRNAs miR397, miR408 and miR857 (PubMed:19122104). Acts coordinately with HY5 to regulate miR408 and its target genes in response to changes in light and copper conditions (PubMed:25516599). Activates miR857 and its target genes in response to low copper conditions (PubMed:26511915). Involved in cadmium stress response by regulating miR397a, miR398b, miR398c and miR857 (PubMed:27352843). Required for iron homeostasis during copper deficiency (PubMed:22374396). {ECO:0000269|PubMed:19122104, ECO:0000269|PubMed:22374396, ECO:0000269|PubMed:25516599, ECO:0000269|PubMed:26511915, ECO:0000269|PubMed:27352843}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00604PBMTransfer from AT5G18830Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapTp6g25540
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK3535520.0AK353552.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-52-E05.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006400438.10.0squamosa promoter-binding-like protein 7
SwissprotQ8S9G80.0SPL7_ARATH; Squamosa promoter-binding-like protein 7
TrEMBLE4MYF50.0E4MYF5_EUTHA; mRNA, clone: RTFL01-52-E05
TrEMBLV4N8650.0V4N865_EUTSA; Uncharacterized protein
STRINGXP_006400438.10.0(Eutrema salsugineum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM63582644
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G18830.10.0squamosa promoter binding protein-like 7
Publications ? help Back to Top
  1. Zhang H, et al.
    MicroRNA408 is critical for the HY5-SPL7 gene network that mediates the coordinated response to light and copper.
    Plant Cell, 2014. 26(12): p. 4933-53
    [PMID:25516599]
  2. Zhao Y, et al.
    MicroRNA857 Is Involved in the Regulation of Secondary Growth of Vascular Tissues in Arabidopsis.
    Plant Physiol., 2015. 169(4): p. 2539-52
    [PMID:26511915]
  3. Perea-García A, et al.
    Modulation of copper deficiency responses by diurnal and circadian rhythms in Arabidopsis thaliana.
    J. Exp. Bot., 2016. 67(1): p. 391-403
    [PMID:26516126]
  4. Gielen H,Remans T,Vangronsveld J,Cuypers A
    Toxicity responses of Cu and Cd: the involvement of miRNAs and the transcription factor SPL7.
    BMC Plant Biol., 2016. 16(1): p. 145
    [PMID:27352843]
  5. Yan J, et al.
    Arabidopsis Pollen Fertility Requires the Transcription Factors CITF1 and SPL7 That Regulate Copper Delivery to Anthers and Jasmonic Acid Synthesis.
    Plant Cell, 2017. 29(12): p. 3012-3029
    [PMID:29114014]
  6. Araki R, et al.
    SPL7 locally regulates copper-homeostasis-related genes in Arabidopsis.
    J. Plant Physiol., 2018.
    [PMID:29635212]