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.5KG779600.1.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 MYB_related
Protein Properties Length: 505aa    MW: 55320.7 Da    PI: 8.3144
Description MYB_related family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.5KG779600.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding248.7e-08411460147
                          TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHT...TTS-HHHHHHHHHHH CS
      Myb_DNA-binding   1 rgrWTteEdellvdavkqlGggtWktIartmg...kgRtlkqcksrwqky 47 
                          r++++  E e lv+av+qlG+g+Wk I  +      +Rt  ++k++w ++
  Pavir.5KG779600.1.p 411 RMPFSVGEVEALVEAVEQLGTGRWKDIKMHGFdgaDHRTYVDLKDKWKTL 460
                          7899999*******************96664469999**********986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS500538.829221293IPR000626Ubiquitin domain
SuperFamilySSF542362.73E-6225293IPR029071Ubiquitin-related domain
PROSITE profilePS5129414.95406465IPR017930Myb domain
Gene3DG3DSA:1.10.10.603.8E-9407462IPR009057Homeodomain-like
SMARTSM007173.4E-6410463IPR001005SANT/Myb domain
CDDcd116601.48E-17413462No hitNo description
SuperFamilySSF466894.1E-15413493IPR009057Homeodomain-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 505 aa     Download sequence    Send to blast
MLVRDSSVRC TRPCEISHGL DIIREPGAFG VRHPGSSCSA EVVQAHQAEP IRRQTDGHAA  60
ALDSLFDSVD LDGRPPALVS SDSSSRVLLC RHDKEHKALC KVEVHHTADR DNDENSSGCT  120
HPSTTGNEGY KPHYLGNHRI RKLLASKVRK AACKTCGGMS NKGSKLSFCG KKIPGTRQKV  180
RRTNFKRTKL TRGATKGMLT GACGTSFTTK GQNKLCGFED YQVNLKINSF NIPELFVEIP  240
ETATIGSLKR TVMDVVTSIM EDGLRVGVLL QGKSIQDDNK TLHQAGICHG EKLNNIDFTL  300
ECDRQQDSPS GVIIQEEMDF ASADIVEPLA RMKYEEPFPE TKGGCGNQQP MKAYLNGSLA  360
GCVHHPVEMA SQDTSASLQS VIRVAASDLN ALATVPICKA RRSEIGQRRA RMPFSVGEVE  420
ALVEAVEQLG TGRWKDIKMH GFDGADHRTY VDLKDKWKTL VHTASISPQQ RRGEPVPQEL  480
LDRVLSAQAY WSQQQEASWK GSCS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
2juh_A7e-533994955101Telomere binding protein TBP1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.336020.0callus| leaf| root
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Ubiquitous. {ECO:0000269|PubMed:10811811}.
Functional Description ? help Back to Top
Source Description
UniProtBinds the telomeric double-stranded 5'TTTAGGG-3' repeat and regulates telomere length and structure. {ECO:0000269|PubMed:10811811, ECO:0000269|PubMed:17586654}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.5KG779600.1.p
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_025818928.10.0telomere-binding protein 1-like isoform X1
RefseqXP_025818929.10.0telomere-binding protein 1-like isoform X1
SwissprotQ9LL451e-175TBP1_ORYSJ; Telomere-binding protein 1
TrEMBLA0A2T7DB210.0A0A2T7DB21_9POAL; Uncharacterized protein
STRINGPavir.Ea04142.1.p0.0(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP108241215
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G07540.13e-69TRF-like 2
Publications ? help Back to Top
  1. Yu EY, et al.
    Sequence-specific DNA recognition by the Myb-like domain of plant telomeric protein RTBP1.
    J. Biol. Chem., 2000. 275(31): p. 24208-14
    [PMID:10811811]
  2. Hong JP, et al.
    Suppression of RICE TELOMERE BINDING PROTEIN 1 results in severe and gradual developmental defects accompanied by genome instability in rice.
    Plant Cell, 2007. 19(6): p. 1770-81
    [PMID:17586654]
  3. Ko S, et al.
    Solution structure of the DNA binding domain of rice telomere binding protein RTBP1.
    Biochemistry, 2009. 48(5): p. 827-38
    [PMID:19152316]
  4. Mukherjee K,Pandey DM,Vidyarthi AS
    In silico characterization and analysis of RTBP1 and NgTRF1 protein through MD simulation and molecular docking - A comparative study.
    Interdiscip Sci, 2015.
    [PMID:25663113]
  5. Mukherjee K,Pandey DM,Vidyarthi AS
    In Silico Characterization and Analysis of RTBP1 and NgTRF1 Protein Through MD Simulation and Molecular Docking: A Comparative Study.
    Interdiscip Sci, 2015. 7(3): p. 275-86
    [PMID:26289405]