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 Pavir.9KG301000.1.p
Organism
Panicum virgatum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Panicinae; Panicum
Family SBP
Protein Properties Length: 850aa    MW: 93514.7 Da    PI: 6.3345
Description SBP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.9KG301000.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SBP111.26.2e-35172246276
                          -SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S- CS
                  SBP   2 CqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkk 76 
                          Cqv+gCead+ e+k yhrrh+vC  +++a++v+++g+++r+CqqC++fh l +fDe+krsCrr+L++hn+rrr+k
  Pavir.9KG301000.1.p 172 CQVPGCEADIRELKGYHRRHRVCLRCAHASAVMLDGVHKRYCQQCGKFHVLLDFDEDKRSCRRKLERHNKRRRRK 246
                          ************************************************************************997 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:4.10.1100.103.6E-26169233IPR004333Transcription factor, SBP-box
PROSITE profilePS5114129.47169246IPR004333Transcription factor, SBP-box
SuperFamilySSF1036123.27E-33170249IPR004333Transcription factor, SBP-box
PfamPF031101.1E-26172246IPR004333Transcription 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: 850 aa     Download sequence    Send to blast
MDASDSGGGA AADAGEPLWD WGNLLDFVQD DDSLVLPWDN AAGIGAADPT EAVAPMLPAP  60
LPQPSEPEPE PEPEPGPVLP PPPLRVQGIG RRVRKRDPRL VCPNYLAGRV PCACPEVDEM  120
VAAAEVEDVA TEFLAGARKK TKTAARRGKA GAAGGSGAAG GTVRAVAMEM KCQVPGCEAD  180
IRELKGYHRR HRVCLRCAHA SAVMLDGVHK RYCQQCGKFH VLLDFDEDKR SCRRKLERHN  240
KRRRRKPDSK GILDKEIDEQ LDLSADVSGD GELREGIENM EGTTSEMLET VLSNKVLDRG  300
TPAGSEDVLS PTCTQPSLQN EQSKSVVTFA ASVEACIGAK QENAKLTTNS PMHDTKSGYS  360
SSCPTGRISF KLYDWNPAEF PRRLRHQIFE WLASMPVELE GYIRPGCTIL TVFVAMPQHM  420
WDKLSDDAAN LLRNLVNSPS SLLLGKGAFF IHVHNMIFQV LKDGATLMST RLDVQSPKID  480
YVHPTWFEAG KPVELILCGS FLDQPKFRSL LSFDGDYLKH DCCRLTSCDA IDCVENGDLI  540
LDSQHEIFRI NITQTRPEIH GPSFVEVENM FGLSNFVPIL FGSKQLCSEL ERIQDVLCGS  600
SNSNLFGELP GASSDPYERR KVQKAAMSGF LIDIGWLIRK PTHDDLKNVL SSTNIERWIC  660
ILKFLIQNDF INVLEIIVKS MENIMGSEVL SNLERGRLEG HVTAFLGYVK HAQNIINSRA  720
NNDKKTKLET RWTNQPSLGT SDPPAIENSG TDVDKNLHSA NAAYEEETVP LVTRDVSHRH  780
CCQPDMNARW LKPSLVVKYP GGATRMRLGM TVIVAAVLCF TACLVLFHPH GVGALASPVK  840
RYLSSDSTL*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1ul5_A2e-37171251585squamosa promoter binding protein-like 7
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1228246KRSCRRKLERHNKRRRRKP
2232244RRKLERHNKRRRR
3239246NKRRRRKP
4240245KRRRRK
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.445791e-156leaf
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Ubiquitous. {ECO:0000269|PubMed:16861571}.
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
MP00604PBMTransfer from AT5G18830Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.9KG301000.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025805456.10.0squamosa promoter-binding-like protein 9
SwissprotQ6I5760.0SPL9_ORYSJ; Squamosa promoter-binding-like protein 9
TrEMBLA0A3L6T0780.0A0A3L6T078_PANMI; Squamosa promoter-binding-like protein 9
STRINGGRMZM2G109354_P010.0(Zea mays)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP69223344
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G18830.21e-139squamosa promoter binding protein-like 7
Publications ? help Back to Top
  1. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]
  2. Cheng CH, et al.
    A fine physical map of the rice chromosome 5.
    Mol. Genet. Genomics, 2005. 274(4): p. 337-45
    [PMID:16261349]