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.J062800.1.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: 966aa    MW: 105333 Da    PI: 5.6727
Description SBP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.J062800.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SBP131.92.1e-41151228178
                        --SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S--- CS
                SBP   1 lCqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkqa 78 
                        +CqvegC adls ak+yhrrhkvCe+h+ka++++v ++ qrfCqqCsrfh l+efDe+krsCrrrLa+hn+rrrk+++
  Pavir.J062800.1.p 151 ACQVEGCGADLSAAKDYHRRHKVCEMHAKASTAVVGNTVQRFCQQCSRFHLLQEFDEGKRSCRRRLAGHNRRRRKTRP 228
                        5**************************************************************************875 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:4.10.1100.102.2E-34144213IPR004333Transcription factor, SBP-box
PROSITE profilePS5114132.659149226IPR004333Transcription factor, SBP-box
SuperFamilySSF1036125.36E-39150230IPR004333Transcription factor, SBP-box
PfamPF031102.9E-30152225IPR004333Transcription factor, SBP-box
CDDcd002041.95E-9722852No hitNo description
SuperFamilySSF484035.6E-8746852IPR020683Ankyrin repeat-containing domain
SMARTSM002480.34747776IPR002110Ankyrin repeat
Gene3DG3DSA:1.25.40.203.2E-8749851IPR020683Ankyrin repeat-containing domain
SMARTSM00248710793823IPR002110Ankyrin repeat
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 966 aa     Download sequence    Send to blast
MEAARLGAQS SHLYGSGLGE LDLNRRENRV FGWDLNDWNW DSERFVATPV PTAAANGSGL  60
NSSPSSSEEA EAEVARNGGH RGDSDKRKRV VVIDDDDRED QDMIVNGGGS LSLRIGGSAV  120
GVGVMESSDV NEDDRNGKKI RVQGGSSNGP ACQVEGCGAD LSAAKDYHRR HKVCEMHAKA  180
STAVVGNTVQ RFCQQCSRFH LLQEFDEGKR SCRRRLAGHN RRRRKTRPDI AIGGTASIED  240
KVSNYLLLSL IGICANLNSD SVQHSNSQEL LSTLLKNLGS VAKSLEPKEL CKLLEAYQSL  300
QNGSNAGTSG TTNAAEEAAG PSNSKLPFGN GSHRGQASSS VVPVQSKATV VVTPEPASCK  360
LKDFDLNDTC NDMEGFEDGQ EGSPTPAFKA ADSPNCASWM QQDSTQSPPQ TSGNSDSTST  420
QSLSSSNGDA QCRTDKIVFK LFNKVPSDLP PVLRSQILGW LSSSPTDIES YIRPGCIILT  480
VYLRLVESAW RELSGNMSLH LDKLLNSSTD NFWASGLVFV MVRQQLAFMH NGQIMLDRPL  540
APSSHQYCKI LRVRPVAAPY SATINFRVEG FNLLSTSSRV ICSYEGCCIF QEDTDTVADD  600
AEDIECLSFC CSVPGSRGRG FIEVEDSGFS NGFFPFIIAE KDVCSEVSEL ESIFESSSDE  660
YAVVDDNARD QALEFLNELG WLLHRANRMS KQAETDTPLA AFNMWRFRKL GIFAMEREWC  720
AVVEMLLNFL FIGLVDLGSQ SPEEMVLSEN LLHAAVRRKS VKMVRFLLRY KPNKNSKGTA  780
QTYLFRPDAL GPLTITPLHI AAATSDAEDV LDALTDDPGL VGISAWSNAR DETGFTPEDY  840
ARQRGNDAYL NLVHKKIDKH LGKGHVVLGV PSSMCSVIPD GAKPGDVSLE ICRPMSASVP  900
RCLLCTQQAR VYPNSGARTF LYRPAMLTVM GVAVVCVCVG ILLHTFPRVY AAPTFRWELL  960
ERGPM*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1ul4_A3e-31145225484squamosa promoter binding protein-like 4
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.8350.0callus| leaf| root| stem
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
MP00633PBMTransfer from PK06791.1Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.J062800.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0388520.0BT038852.1 Zea mays full-length cDNA clone ZM_BFb0336G12 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025793312.10.0squamosa promoter-binding-like protein 6
SwissprotQ75LH60.0SPL6_ORYSJ; Squamosa promoter-binding-like protein 6
TrEMBLA0A2S3IGN30.0A0A2S3IGN3_9POAL; Uncharacterized protein
STRINGPavir.J01500.1.p0.0(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP19983892
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G60030.10.0squamosa promoter-binding protein-like 12
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]