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.9NG659200.1.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 C2H2
Protein Properties Length: 541aa    MW: 56199.8 Da    PI: 9.1057
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.9NG659200.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H217.11.5e-055779123
                         EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                         ++C++C+k F r  nL+ H r H
  Pavir.9NG659200.1.p 57 FVCEICNKGFQRDQNLQLHRRGH 79
                         89*******************88 PP
2zf-C2H213.80.00017133155123
                          EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                          +kC +C+k +  +s+ k H +t+
  Pavir.9NG659200.1.p 133 WKCDKCSKKYAVQSDWKAHVKTC 155
                          58*******************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576672.63E-75679No hitNo description
Gene3DG3DSA:3.30.160.601.8E-55679IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.9495779IPR007087Zinc finger, C2H2
SMARTSM003550.0175779IPR015880Zinc finger, C2H2-like
PROSITE patternPS0002805979IPR007087Zinc finger, C2H2
SMARTSM0035521098128IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.3E-4121154IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.63E-7128153No hitNo description
SMARTSM0035590133153IPR015880Zinc finger, C2H2-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009937Biological Processregulation of gibberellic acid mediated signaling pathway
GO:0010029Biological Processregulation of seed germination
GO:0010431Biological Processseed maturation
GO:0005634Cellular Componentnucleus
GO:0044212Molecular Functiontranscription regulatory region DNA binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 541 aa     Download sequence    Send to blast
MEVEATPTTA VSSSGGAAQL PPPGPPAKKK RALPGMPDPD AEVIALSPKT LLATNRFVCE  60
ICNKGFQRDQ NLQLHRRGHN LPWKLRQRSG KEARKRVYVC PEPSCVHHDP SRALGDLTGI  120
KKHFCRKHGE KKWKCDKCSK KYAVQSDWKA HVKTCGSREY RCDCGTLFSR RDSFITHRAF  180
CDALAEESAK ARAEAPPADD DGGSSAAVGP PPAAPPTQAP VPAAPAPLRQ QPPPPPPAPH  240
RAEQRNEPET KAPEPTQLAP PLPSPAAAVP VLSHNSVTAA NVSARSSSSV AGTSQGLIGG  300
MFAPSSMAPA PQFPDLGGGV GRPERAMPGK PPSLCLATDA SSSIFSAPVA ADRQQFAPPP  360
PPSPSPHMSA TALLQKAAQM GATSSTSSFL RGLGLDASSP SPGASSSRQQ HHHDAMQVSL  420
PETSLQQWPP RLEQEPAPML SAGLGLSLPY DSTGAPVCLP ELMMGQSSLF GGKPATLDFL  480
GLGMSPTGAS AGRGLPTFML PIGGAVGMAG TGAGAAETFV AGRGPQATPW ERNPSTSPIL  540
*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C1e-35129190364Zinc finger protein JACKDAW
5b3h_F1e-35129190364Zinc finger protein JACKDAW
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.101610.0stem
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Strongly up-regulated during seed development. {ECO:0000269|PubMed:21571950}.
UniprotTISSUE SPECIFICITY: At 3 days post anthesis (DPA), expressed in the chalazal endosperm region. By 6 DPA, expressed in the endosperm and embryo. In fully germinated seed, strongest expression in the root tip and not detected in the cotyledons. In 4-days old seedlings, restricted to the vasculature of the cotyledons, the shoot apical meristem region, and the root tip. By 8 days, restricted to newly emerged leaves. {ECO:0000269|PubMed:21571950}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor promoting the transition to germination by regulating light and hormonal signaling during seed maturation (PubMed:21571950). Acts as a positive regulator of phytochrome and/or gibberellin action (PubMed:21571950, PubMed:25035403). {ECO:0000269|PubMed:21571950, ECO:0000269|PubMed:25035403}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00592DAPTransfer from AT5G66730Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.9NG659200.1.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
GenBankBT0545020.0BT054502.1 Zea mays full-length cDNA clone ZM_BFc0103M17 mRNA, complete cds.
GenBankBT0546180.0BT054618.1 Zea mays full-length cDNA clone ZM_BFb0032E02 mRNA, complete cds.
GenBankEU9555780.0EU955578.1 Zea mays clone 1537717 nucleic acid binding protein mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025798188.10.0protein indeterminate-domain 2-like isoform X1
SwissprotQ9LVQ71e-145IDD1_ARATH; Zinc finger protein ENHYDROUS
TrEMBLA0A2S3ITA10.0A0A2S3ITA1_9POAL; Uncharacterized protein
STRINGPavir.Ia04118.1.p0.0(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP20238320
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G50700.13e-96indeterminate(ID)-domain 2
Publications ? help Back to Top
  1. Fukazawa J, et al.
    DELLAs function as coactivators of GAI-ASSOCIATED FACTOR1 in regulation of gibberellin homeostasis and signaling in Arabidopsis.
    Plant Cell, 2014. 26(7): p. 2920-38
    [PMID:25035403]
  2. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]