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.6KG299300.1.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: 254aa    MW: 27264.7 Da    PI: 10.3092
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.6KG299300.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H220.61.2e-066688123
                         EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                         y+C +Cg+ F r  nL+ H r+H
  Pavir.6KG299300.1.p 66 YVCDICGQGFQRDQNLQMHRRRH 88
                         9*********************9 PP
2zf-C2H212.80.00036145166223
                          EETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2   2 kCpdCgksFsrksnLkrHirtH 23 
                           C  C+k +  +s++k H++t+
  Pavir.6KG299300.1.p 145 ACARCSKAYAVHSDYKAHLKTC 166
                          6*******************98 PP
3zf-C2H2120.00066174192523
                          TTTEEESSHHHHHHHHHHT CS
              zf-C2H2   5 dCgksFsrksnLkrHirtH 23 
                          dCg++Fsr +++  H+ t+
  Pavir.6KG299300.1.p 174 DCGRVFSRVESFIEHQDTC 192
                          9***************987 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576673.42E-66588No hitNo description
PROSITE profilePS5015711.5726688IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.608.5E-66688IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.00366688IPR015880Zinc finger, C2H2-like
PROSITE patternPS0002806888IPR007087Zinc finger, C2H2
SMARTSM00355110108138IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.605.3E-4135165IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576673.42E-6139164No hitNo description
SMARTSM00355230144171IPR015880Zinc finger, C2H2-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 254 aa     Download sequence    Send to blast
MLSSCAPTAL PPPEAGAAPP PEPPFRSLQI AATSSAKKKR RPAGTPDPDA EVVSLSPRTL  60
LESDRYVCDI CGQGFQRDQN LQMHRRRHKV PWKLLKREAG EAARKRVFVC PEPSCLHHDP  120
AHALGDLVGI KKHFRRKHSG HRQWACARCS KAYAVHSDYK AHLKTCGTRG HTCDCGRVFS  180
RVESFIEHQD TCNAGRQRAE TSSSPASGGA FGAAASTSRQ QQRRQMHATA AAAALSRTAS  240
SASPSSGGGG GDLG
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C4e-18140194357Zinc finger protein JACKDAW
5b3h_F4e-18140194357Zinc finger protein JACKDAW
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
13640KKKRR
23641KKKRRP
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.281861e-63root
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expression levels gradually decrease with aging in both the shoot and root vasculature. {ECO:0000269|PubMed:16813575}.
UniprotTISSUE SPECIFICITY: Mainly expressed in the endodermis, the gravity-sensing tissue in inflorescence stems. Mostly present in stems and flowers, and, to a lower extent, in seedlings, hypocotyls, roots and the shoot apical meristem (SAM). {ECO:0000269|PubMed:16813575}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor involved in inflorescence stems gravitropism, probably by regulating starch accumulation in amyloplasts of graviperceptive cells. Required for stem circumnutation movements. Regulates lateral organ morphogenesis and gravitropic responses (PubMed:24039602). Acts cooperatively with IDD16 to control silique and branche orientation (PubMed:24039602). Involved in the establishment of auxin gradients through the regulation of auxin biosynthesis and transport (PubMed:24039602). {ECO:0000269|PubMed:16813575, ECO:0000269|PubMed:18259878, ECO:0000269|PubMed:24039602, ECO:0000269|PubMed:9210330}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.6KG299300.1.p
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Not regulated by auxin. {ECO:0000269|PubMed:24039602}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1067960.0AK106796.1 Oryza sativa Japonica Group cDNA clone:002-116-B04, full insert sequence.
GenBankAK1195950.0AK119595.1 Oryza sativa Japonica Group cDNA clone:002-117-D09, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002444487.11e-136protein indeterminate-domain 14
SwissprotF4IPE31e-106IDD15_ARATH; Zinc finger protein SHOOT GRAVITROPISM 5
TrEMBLC5YM721e-134C5YM72_SORBI; Uncharacterized protein
STRINGPavir.Fa00691.1.p0.0(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP105138124
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G01940.11e-106C2H2-like zinc finger protein
Publications ? help Back to Top
  1. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  2. Kim JY,Ryu JY,Baek K,Park CM
    High temperature attenuates the gravitropism of inflorescence stems by inducing SHOOT GRAVITROPISM 5 alternative splicing in Arabidopsis.
    New Phytol., 2016. 209(1): p. 265-79
    [PMID:26256266]
  3. Ryu JY,Kim JY,Park CM
    Adaptive thermal control of stem gravitropism through alternative RNA splicing in Arabidopsis.
    Plant Signal Behav, 2015. 10(11): p. e1093715
    [PMID:26452406]
  4. Qu Y, et al.
    Peroxisomal CuAOζ and its product H2O2 regulate the distribution of auxin and IBA-dependent lateral root development in Arabidopsis.
    J. Exp. Bot., 2017. 68(17): p. 4851-4867
    [PMID:28992128]
  5. Shi H, et al.
    Zinc finger of Arabidopsis thaliana 6 is involved in melatonin-mediated auxin signaling through interacting INDETERMINATE DOMAIN15 and INDOLE-3-ACETIC ACID 17.
    J. Pineal Res., 2018. 65(2): p. e12494
    [PMID:29607541]