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 AT5G18830.2
Common NameATSPL7, F17K4.80, SPL7
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: 775aa    MW: 86841.2 Da    PI: 6.5943
Description squamosa promoter binding protein-like 7
Gene Model
Gene Model ID Type Source Coding Sequence
AT5G18830.2genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SBP114.18e-36137213177
                  --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 
  AT5G18830.2 137 RCQVPDCEADISELKGYHKRHRVCLRCATASFVVLDGENKRYCQQCGKFHLLPDFDEGKRSCRRKLERHNNRRKRKP 213
                  6************************************************************************9975 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:4.10.1100.105.6E-28131199IPR004333Transcription factor, SBP-box
PROSITE profilePS5114129.137135212IPR004333Transcription factor, SBP-box
SuperFamilySSF1036126.41E-34136216IPR004333Transcription factor, SBP-box
PfamPF031101.6E-26138211IPR004333Transcription 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:0016021Cellular Componentintegral component of membrane
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0046872Molecular Functionmetal ion binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000084anatomyplant sperm cell
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009005anatomyroot
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009025anatomyvascular leaf
PO:0009029anatomystamen
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0009052anatomyflower pedicel
PO:0020030anatomycotyledon
PO:0020038anatomypetiole
PO:0020100anatomyhypocotyl
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
PO:0025195anatomypollen tube cell
PO:0025281anatomypollen
PO:0001016developmental stageL mature pollen stage
PO:0001017developmental stageM germinated pollen stage
PO:0001054developmental stagevascular leaf senescent stage
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007064developmental stageLP.12 twelve leaves visible stage
PO:0007095developmental stageLP.08 eight leaves visible stage
PO:0007098developmental stageLP.02 two leaves visible stage
PO:0007103developmental stageLP.10 ten leaves visible stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 775 aa     Download sequence    Send to blast
MSSLSQSPPP PEMDIQPPAL VNDDPSTYSS ALWDWGDLLD FAADERLLVD QIHFPPVLSP  60
PLPPLIPTQT PAESELDPSP EESGSGSDRV RKRDPRLICS NFIEGMLPCS CPELDQKLED  120
AELPKKKRVR GGSGVARCQV PDCEADISEL KGYHKRHRVC LRCATASFVV LDGENKRYCQ  180
QCGKFHLLPD FDEGKRSCRR KLERHNNRRK RKPVDKGGVA AEQQQVLSQN DNSVIDVEDG  240
KDITCSSDQR AEEEPSLIFE DRHITTQGSV PFTRSINADN FVSVTGSGEA QPDEGMNDTK  300
FERSPSNGDN KSAYSTVCPT GRISFKLYDW NPAEFPRRLR HQIFQWLANM PVELEGYIRP  360
GCTILTVFIA MPEIMWAKLS KDPVAYLDEF ILKPGKMLFG RGSMTVYLNN MIFRLIKGGT  420
TLKRVDVKLE SPKLQFVYPT CFEAGKPIEL VVCGQNLLQP KCRFLVSFSG KYLPHNYSVV  480
PAPDQDGKRS CNNKFYKINI VNSDPSLFGP AFVEVENESG LSNFIPLIIG DAAVCSEMKL  540
IEQKFNATLF PEGQEVTACS SLTCCCRDFG ERQSTFSGLL LDIAWSVKVP SAERTEQPVN  600
RCQIKRYNRV LNYLIQNNSA SILGNVLHNL ETLVKKMEPD SLVHCTCDCD VRLLHENMDL  660
ASDIHRKHQS PIESKDPEAG LDCKERIQAD CSPDSGGKET DPLLNKEVVM NVNDIGDWPR  720
KSCIKTHSAL AFRSRQTMFL IATFAVCFAV CAVLYHPNKV TQLAVAIRMR LVHKI
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1ul5_A5e-54135220388squamosa promoter binding protein-like 7
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.4950.0flower| silique
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO306870270.0
Genevisible249960_at1e-156
Expression AtlasAT5G18830-
AtGenExpressAT5G18830-
ATTED-IIAT5G18830-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed constitutively during plant development. {ECO:0000269|PubMed:10524240}.
UniprotTISSUE SPECIFICITY: Expressed in roots rosette leaves, cauline leaves, stems, flowers and siliques. {ECO:0000269|PubMed:24335506}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a member of the Squamosa Binding Protein family of transcriptional regulators. SPL7 is expressed highly in roots and appears to play a role in copper homeostasis. Mutants are hypersensitive to copper deficient conditions and display a retarded growth phenotype. SPL7 binds to the promoter of the copper responsive miRNAs miR398b and miR389c.
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}.
Function -- GeneRIF ? help Back to Top
  1. SPL7 activates the transcription of multiple genes involved in copper homeostasis.
    [PMID: 19122104]
  2. Cu uptake into roots of Cu-deficient plants is dependent on FRO4/FRO5 and SPL7.
    [PMID: 22374396]
  3. COPT6 expression is regulated by copper availability that, in part, is controlled by a master regulator of copper homeostasis, SPL7
    [PMID: 22865877]
  4. SPL7 directly regulates miR408 expression.
    [PMID: 23289771]
  5. Data suggest that iron superoxide dismutase gene FSD1 and SPL7 transcriptional regulator SPL7 may associate withi copper homeostasis.
    [PMID: 23455955]
  6. Data indicate that cadmium (Cd) elicits SPL7-dependent copper (Cu) deficiency responses by altering expression of COPT1, COPT2, COPT6, CSD1, CSD2, miRNA398 b/c precursors and FSD1.
    [PMID: 23835944]
  7. The data presented here provide evidence for SPL7 and KIN17 protein interaction as a point of convergence in response to both Copper deficiency and oxidative stress.
    [PMID: 24335506]
  8. Cytological and biochemical approaches confirmed an operative transmembrane domain (TMD) and uncovered a dual localisation of SPL7 between the nucleus and an endomembrane system, most likely the endoplasmic reticulum (ER).
    [PMID: 25207797]
  9. The expression of SPL7 and its targets COPT2 and FSD1 was differently regulated in various light signalling mutants. Under copper deficiency, the expression of both targets decreased drastically in continuous darkness.
    [PMID: 26516126]
  10. CITF1 and SPL7 regulate Cu uptake and delivery to anthers, thereby influencing fertility, and highlight the relationship between Cu homeostasis, CITF1, SPL7, and the jasmonic acid metabolic pathway.
    [PMID: 29114014]
  11. In a series of grafting experiments using spl7 mutant and wild-type (WT) plants, expression of Cu-responsive microRNAs and the resulting suppression of CSD1 and CSD2 mRNAs were observed in leaves only when the aerial part was from WT plants, in which a low level of SPL7 was transcribed also in the vascular tissues.
    [PMID: 29635212]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00604PBM24477691Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT5G18830.2
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT1G23020(A), AT3G46900(A), AT3G56240(A), AT5G24380(A), AT5G59030(A), AT5G59520(A)
Interaction ? help Back to Top
Source Intact With
BioGRIDAT5G18830
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT5G18830
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY0638150.0AY063815.1 Arabidopsis thaliana putative squamosa promoter binding protein 7 (At5g18830) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_850850.10.0squamosa promoter binding protein-like 7
SwissprotQ8S9G80.0SPL7_ARATH; Squamosa promoter-binding-like protein 7
TrEMBLA0A178US840.0A0A178US84_ARATH; SPL7
STRINGAT5G18830.30.0(Arabidopsis thaliana)
Publications ? help Back to Top
  1. Cardon G, et al.
    Molecular characterisation of the Arabidopsis SBP-box genes.
    Gene, 1999. 237(1): p. 91-104
    [PMID:10524240]
  2. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  3. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  4. Kamada T, et al.
    Functional differentiation of peroxisomes revealed by expression profiles of peroxisomal genes in Arabidopsis thaliana.
    Plant Cell Physiol., 2003. 44(12): p. 1275-89
    [PMID:14701923]
  5. Yamasaki K, et al.
    A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors.
    J. Mol. Biol., 2004. 337(1): p. 49-63
    [PMID:15001351]
  6. Kropat J, et al.
    A regulator of nutritional copper signaling in Chlamydomonas is an SBP domain protein that recognizes the GTAC core of copper response element.
    Proc. Natl. Acad. Sci. U.S.A., 2005. 102(51): p. 18730-5
    [PMID:16352720]
  7. Wang Y, et al.
    Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis.
    Plant Physiol., 2008. 148(3): p. 1201-11
    [PMID:18775970]
  8. Yamasaki H,Hayashi M,Fukazawa M,Kobayashi Y,Shikanai T
    SQUAMOSA Promoter Binding Protein-Like7 Is a Central Regulator for Copper Homeostasis in Arabidopsis.
    Plant Cell, 2009. 21(1): p. 347-61
    [PMID:19122104]
  9. Pilon M,Cohu CM,Ravet K,Abdel-Ghany SE,Gaymard F
    Essential transition metal homeostasis in plants.
    Curr. Opin. Plant Biol., 2009. 12(3): p. 347-57
    [PMID:19481497]
  10. Pe
    Regulation of copper transport in Arabidopsis thaliana: a biochemical oscillator?
    J. Biol. Inorg. Chem., 2010. 15(1): p. 29-36
    [PMID:19798519]
  11. Cohu CM, et al.
    Copper delivery by the copper chaperone for chloroplast and cytosolic copper/zinc-superoxide dismutases: regulation and unexpected phenotypes in an Arabidopsis mutant.
    Mol Plant, 2009. 2(6): p. 1336-50
    [PMID:19969519]
  12. Bernal M, et al.
    Transcriptome sequencing identifies SPL7-regulated copper acquisition genes FRO4/FRO5 and the copper dependence of iron homeostasis in Arabidopsis.
    Plant Cell, 2012. 24(2): p. 738-61
    [PMID:22374396]
  13. Ren L,Tang G
    Identification of sucrose-responsive microRNAs reveals sucrose-regulated copper accumulations in an SPL7-dependent and independent manner in Arabidopsis thaliana.
    Plant Sci., 2012. 187: p. 59-68
    [PMID:22404833]
  14. Jung HI, et al.
    COPT6 is a plasma membrane transporter that functions in copper homeostasis in Arabidopsis and is a novel target of SQUAMOSA promoter-binding protein-like 7.
    J. Biol. Chem., 2012. 287(40): p. 33252-67
    [PMID:22865877]
  15. Zhang H,Li L
    SQUAMOSA promoter binding protein-like7 regulated microRNA408 is required for vegetative development in Arabidopsis.
    Plant J., 2013. 74(1): p. 98-109
    [PMID:23289771]
  16. Andr
    Comparison of global responses to mild deficiency and excess copper levels in Arabidopsis seedlings.
    Metallomics, 2013. 5(9): p. 1234-46
    [PMID:23455955]
  17. Gayomba SR, et al.
    The CTR/COPT-dependent copper uptake and SPL7-dependent copper deficiency responses are required for basal cadmium tolerance in A. thaliana.
    Metallomics, 2013. 5(9): p. 1262-75
    [PMID:23835944]
  18. Garcia-Molina A,Xing S,Huijser P
    A conserved KIN17 curved DNA-binding domain protein assembles with SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE7 to adapt Arabidopsis growth and development to limiting copper availability.
    Plant Physiol., 2014. 164(2): p. 828-40
    [PMID:24335506]
  19. Garcia-Molina A,Xing S,Huijser P
    Functional characterisation of Arabidopsis SPL7 conserved protein domains suggests novel regulatory mechanisms in the Cu deficiency response.
    BMC Plant Biol., 2014. 14: p. 231
    [PMID:25207797]
  20. 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]
  21. Jin J, et al.
    An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.
    Mol. Biol. Evol., 2015. 32(7): p. 1767-73
    [PMID:25750178]
  22. 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]
  23. 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]
  24. 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]
  25. 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]
  26. Araki R, et al.
    SPL7 locally regulates copper-homeostasis-related genes in Arabidopsis.
    J. Plant Physiol., 2018.
    [PMID:29635212]