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.9NG072500.3.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 TALE
Protein Properties Length: 274aa    MW: 30817.9 Da    PI: 6.3173
Description TALE family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.9NG072500.3.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox29.11.7e-091952302055
                          HHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHH CS
             Homeobox  20 eknrypsaeereeLAkklgLterqVkvWFqNrRake 55 
                          +k +yps++e+  LA+ +gL+++q+ +WF N+R ++
  Pavir.9NG072500.3.p 195 YKWPYPSETEKLALAETTGLDQKQINNWFINQRKRR 230
                          4679***************************99763 PP
2ELK43.37.2e-15150171122
                  ELK   1 ELKhqLlrKYsgyLgsLkqEFs 22 
                          ELKhqLlrKY+gyLg+L+qEFs
  Pavir.9NG072500.3.p 150 ELKHQLLRKYGGYLGGLRQEFS 171
                          9********************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM012553.3E-211761IPR005540KNOX1
PfamPF037902.5E-221859IPR005540KNOX1
SMARTSM012562.0E-2769120IPR005541KNOX2
PfamPF037913.2E-2374119IPR005541KNOX2
SMARTSM011884.2E-8150171IPR005539ELK domain
PROSITE profilePS5121311.575150170IPR005539ELK domain
PfamPF037892.7E-11150171IPR005539ELK domain
PROSITE profilePS5007112.957170233IPR001356Homeobox domain
SuperFamilySSF466895.99E-19171242IPR009057Homeodomain-like
SMARTSM003891.5E-10172237IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.601.9E-26175236IPR009057Homeodomain-like
CDDcd000862.37E-11182233No hitNo description
PfamPF059201.5E-16190229IPR008422Homeobox KN domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 274 aa     Download sequence    Send to blast
MAGAVLQREI SPVDHAETIK AKIMSHPQYS ALVAAYLDCQ KVGAPPDVSD RLSAMAAKLD  60
AQPGPSWRRH EPARADPELD QFMEAYCNML VKYQEELARP IHEAAEFFKS VERQLDSITD  120
SNYCEGAGSS EDDQDASCPE EIDPCAEDKE LKHQLLRKYG GYLGGLRQEF SKRKKKGKLP  180
KEARQKLLHW WELHYKWPYP SETEKLALAE TTGLDQKQIN NWFINQRKRR WKPTSEDMPF  240
AMVEAAGGFH APQGTAAAAA VLYMADGMYR LGS*
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in the embryo at 4 days after pollination (DAP) in the ventral and basal part of the embryo including the initial of the shoot apical meristem (SAM). At 5 DAP, expressed at the ventral side of the embryo, but the expression within SAM is down-regulated. At 7 DAP, expression is restricted to the boundaries between the embryonic organs, between the scutellum and the coleoptile, the coleoptile and the second leaf primordium, the shoot apical meristem and the first leaf primordium, the first leaf primordium and the coleoptile, the coleoptile and the epiblast and at the tip of the epiblast, but not in the leaf primordia. {ECO:0000269|PubMed:10080693}.
UniprotDEVELOPMENTAL STAGE: Expressed in the embryo at 4 days after pollination (DAP) in the ventral and basal part of the embryo, including the initial of the shoot apical meristem (SAM). At 5 DAP, expressed at the ventral side of the embryo, but the expression within SAM is down-regulated. At 7 DAP, expression is restricted to the boundaries between the embryonic organs, between the scutellum and the coleoptile, the coleoptile and the second leaf primordium, the shoot apical meristem and the first leaf primordium, the first leaf primordium and the coleoptile, the coleoptile and the epiblast and at the tip of the epiblast, but not in the leaf primordia. {ECO:0000269|PubMed:10080693, ECO:0000269|PubMed:10095070, ECO:0000269|PubMed:9869405}.
UniprotTISSUE SPECIFICITY: Expressed in stems, rachis and inflorescence. {ECO:0000269|PubMed:9869405}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor that may be involved in shoot formation during embryogenesis. {ECO:0000269|PubMed:10080693}.
UniProtProbable transcription factor that may be involved in shoot formation during embryogenesis. {ECO:0000269|PubMed:10080693, ECO:0000269|PubMed:9869405}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00671PBMTransfer from GRMZM2G135447Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.9NG072500.3.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankEU9663730.0EU966373.1 Zea mays clone 293957 homeobox protein rough sheath 1 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025795146.11e-174homeobox protein knotted-1-like 12 isoform X3
SwissprotO650341e-114KNOSC_ORYSI; Homeobox protein knotted-1-like 12
SwissprotO804161e-114KNOSC_ORYSJ; Homeobox protein knotted-1-like 12
TrEMBLA0A2T7C0H01e-175A0A2T7C0H0_9POAL; Uncharacterized protein
STRINGPavir.Ia00428.1.p0.0(Panicum virgatum)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G08150.12e-86KNOTTED-like from Arabidopsis thaliana
Publications ? help Back to Top
  1. Sato Y, et al.
    Loss-of-function mutations in the rice homeobox gene OSH15 affect the architecture of internodes resulting in dwarf plants.
    EMBO J., 1999. 18(4): p. 992-1002
    [PMID:10022841]
  2. Ito Y,Eiguchi M,Kurata N
    KNOX homeobox genes are sufficient in maintaining cultured cells in an undifferentiated state in rice.
    Genesis, 2001. 30(4): p. 231-8
    [PMID:11536429]
  3. Nagasaki H,Sakamoto T,Sato Y,Matsuoka M
    Functional analysis of the conserved domains of a rice KNOX homeodomain protein, OSH15.
    Plant Cell, 2001. 13(9): p. 2085-98
    [PMID:11549765]
  4. Postma-Haarsma AD, et al.
    Developmental regulation and downstream effects of the knox class homeobox genes Oskn2 and Oskn3 from rice.
    Plant Mol. Biol., 2002. 48(4): p. 423-41
    [PMID:11908517]
  5. Kuijt SJ, et al.
    Different subcellular localization and trafficking properties of KNOX class 1 homeodomain proteins from rice.
    Plant Mol. Biol., 2004. 55(6): p. 781-96
    [PMID:15604716]
  6. Yin H, et al.
    SUI-family genes encode phosphatidylserine synthases and regulate stem development in rice.
    Planta, 2013. 237(1): p. 15-27
    [PMID:22956125]