PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Araha.4425s0003.1.p
Organism
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: 678aa    MW: 75838.7 Da    PI: 8.0438
Description SBP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Araha.4425s0003.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SBP115.82.3e-36783177
                         --SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S-- CS
                  SBP  1 lCqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkq 77
                         +Cqv++Cead+se+k yh+rh+vC  +++a++v+++g+++r+CqqC++fh l +fDe+krsCrr+L++hn+rr++k 
  Araha.4425s0003.1.p  7 RCQVPDCEADISELKGYHKRHRVCLRCANASSVVLDGENKRYCQQCGKFHVLPDFDEGKRSCRRKLERHNNRRKRKP 83
                         6************************************************************************9975 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:4.10.1100.101.5E-28369IPR004333Transcription factor, SBP-box
PROSITE profilePS5114129.188582IPR004333Transcription factor, SBP-box
SuperFamilySSF1036129.42E-34686IPR004333Transcription factor, SBP-box
PfamPF031107.0E-27881IPR004333Transcription 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: 678 aa     Download sequence    Send to blast
GGSGVARCQV PDCEADISEL KGYHKRHRVC LRCANASSVV LDGENKRYCQ QCGKFHVLPD  60
FDEGKRSCRR KLERHNNRRK RKPVDKGGVA AKQQQVLSQN DNSVIDVEDG KDNTCSSDQR  120
AEQEPSLIFE DRHIPTQGSV PFTQSINADN FVSVTGSGEA QPDEGMNDTK FERSPSNGDN  180
KSAYSTVCPT GRISFKLYDW NPAEFPRRLR HQIFQWLANM PVELEGYIRP GCTILTVFIA  240
MPEIMWAKLS KDPVAYLDEF ILKPGKMLFG RGSMTVYLNN MIFRLIKGGT TLKRVDVKLE  300
SPKLQFVYPT CFEAGKPIEL VVCGQNLLQP KCRFLVSFSG KYLPHNYSVV PAPDQDGKRS  360
CINKFYKINI VNSDPNLFGP AFVEVENESG LSNFIPLIIG DEAICSEMKL IEQKFNATLF  420
PEGQGVTACS SLTCCCRNFG ERQSTFSGLL LDIAWSVKVP SAERTEQPVN RCQINRYNRV  480
LNYLIQNNSA SILGSVLHNL ETLVKKMEPD SLIHCTCDCD VRLLHENMDL ASDLHKRHQS  540
HKESKVNPGN VLPSSGCCCV SSFQKDIPSR ILNFNQDPEA GLDCKERIQS DCSPDSGGKE  600
TDPLINKEVV MNVNDIGDWP RKKSCITTHS ALTFRSRQTV FLIATFAVCF AVCAVLYHPN  660
KVTQLAVAIR MRLVHKI*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1ul5_A1e-51590388squamosa 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
PlantRegMapAraha.4425s0003.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMap-Retrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF3673550.0AF367355.1 Arabidopsis thaliana AT5g18830/F17K4_80 mRNA, complete cds.
GenBankAJ0116120.0AJ011612.1 Arabidopsis thaliana (ecotype Columbia) mRNA for squamosa promoter binding protein-like 7.
GenBankAY0780500.0AY078050.1 Arabidopsis thaliana AT5g18830/F17K4_80 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002871844.10.0squamosa promoter-binding-like protein 7 isoform X2
SwissprotQ8S9G80.0SPL7_ARATH; Squamosa promoter-binding-like protein 7
TrEMBLD7LYI00.0D7LYI0_ARALL; Uncharacterized protein
STRINGscaffold_601959.10.0(Arabidopsis lyrata)
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-GarcĂ­a 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]