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 Rsa1.0_03664.1_g00008.1
Organism
Raphanus sativus
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: 796aa    MW: 89425.3 Da    PI: 7.6813
Description SBP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_03664.1_g00008.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SBP114.46.5e-36129205177
                              --SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S-- CS
                      SBP   1 lCqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkq 77 
                              +Cqv+gCe+d+ e+k yh+rh+vC ++++a++v+++g+ +r+CqqC++fh l +fDe+krsCrr+L++hn+rr++k 
  Rsa1.0_03664.1_g00008.1 129 RCQVPGCEVDIRELKGYHKRHRVCLTCANASSVVLDGEDKRYCQQCGKFHVLPDFDEGKRSCRRKLERHNNRRKRKD 205
                              6************************************************************************9986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:4.10.1100.105.1E-28123191IPR004333Transcription factor, SBP-box
PROSITE profilePS5114129.162127204IPR004333Transcription factor, SBP-box
SuperFamilySSF1036124.71E-33128206IPR004333Transcription factor, SBP-box
PfamPF031102.9E-27130203IPR004333Transcription 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: 796 aa     Download sequence    Send to blast
MSQSPPEMDI QPPALLDDDP SSSPMWDWGD LLDFAADDTL LFSPAPRPPP PPPMMMIATQ  60
QPPTQSESYP SPDESGSGSD RVRKRDPRLL CSNFVQGMVP CSCPELDQKL EEAELPKRKR  120
VRGGSGVVRC QVPGCEVDIR ELKGYHKRHR VCLTCANASS VVLDGEDKRY CQQCGKFHVL  180
PDFDEGKRSC RRKLERHNNR RKRKDKGGVS SKQQQVLSQN DNSVIDVDDG KADSTWPWYY  240
LQADNTCSSD QRVEQEASLI CEDWNIPTQG SVPCPGSINA DNFVPVTGSG EAQPDEGMND  300
TKFELSPSRG NNKSAYSTVC PTGRISFKLY DWNPAEFPRR LRHQIFQWLA NMPVELEGYV  360
RPGCTILTVF IAMPEIMWAK LSKDPVAYLD EFILKPGKML FGRGSMTVYL NSMIFRGSTL  420
KRVDVKLESP KLQFVYPTCF EAGKPIELIV CGLNLVQPKC RFLVSFAGKY LPHNYSVVPA  480
PDQNGKRSCN NKLYRINIVN SDPTLFGPAF VEVENESGLS NFIPLIIGDK TICSEMKLIE  540
QKFNAALLPE GQDVTACCCS LTCRCRDFKE RQNTFTGLLL DIAWSVKVPS AGCTELTVNR  600
CQIKRYNRVL DYLKQSNSPS ILGNILHNLE ILVKKMEPDS LIHSKCDCDV RLLHENMNLA  660
RKQQTHEDLK LDPVTSACCC ESSFQKDIPS RTLNFNQDPE AGLDRKERVQ ATSLDAGGKE  720
TDPLLNKEVV MNVSDIGNWP WKSCISRHTA QTFRSRQTAF LITTFVVCFA VCAVIYHPNK  780
VRQLSVAIRA RLAHKL
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1ul5_A3e-43127210388squamosa promoter binding protein-like 7
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1199204RRKRKD
2200205RKRKDK
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_03664.1_g00008.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018461585.10.0PREDICTED: squamosa promoter-binding-like protein 7
SwissprotQ8S9G80.0SPL7_ARATH; Squamosa promoter-binding-like protein 7
TrEMBLA0A0D2ZQ950.0A0A0D2ZQ95_BRAOL; Uncharacterized protein
STRINGBo00629s160.10.0(Brassica oleracea)
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]