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.9KG529700.1.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: 442aa    MW: 45962 Da    PI: 9.8525
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.9KG529700.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H221.27.5e-0780102123
                          EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                          y+C++Cg+ F r  nL+ H r+H
  Pavir.9KG529700.1.p  80 YVCEICGQGFQREQNLQMHRRRH 102
                          9*********************9 PP
2zf-C2H210.70.0016179201123
                          EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                          ++C  C k +  +s++k H++t+
  Pavir.9KG529700.1.p 179 WVCARCAKGYAVQSDYKAHLKTC 201
                          58*******************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.601.4E-579102IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576678.12E-779102No hitNo description
PROSITE profilePS5015711.75980102IPR007087Zinc finger, C2H2
SMARTSM003556.5E-480102IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028082102IPR007087Zinc finger, C2H2
SMARTSM00355110143173IPR015880Zinc finger, C2H2-like
SuperFamilySSF576678.12E-7174199No hitNo description
SMARTSM00355270179206IPR015880Zinc 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: 442 aa     Download sequence    Send to blast
MALLVKSHHQ MLASSSTSSS SPSASRQLAA AAAAPQPPSS CLTDQQPSPA KRKRRPPGTP  60
DPDAEVVALS PRTLLESDRY VCEICGQGFQ REQNLQMHRR RHKVPWRLVK RAPPGGGEDG  120
GGGGASGGAA AAGGGGAPRK RVFVCPEPSC LHHDPAHALG DLVGIKKHFR RKHGGRRQWV  180
CARCAKGYAV QSDYKAHLKT CGTRGHSCDC GRVFSRVESF IEHQDACNSS RMRGEVVAPP  240
VPSSALPAIR LAVPRPHPPA VAAPQPPELQ LLPASSTAAP PVTATTALSS STITAAATTT  300
VSSQAEPHAA ATKLQLSIGP TVTAAASNEE DAEELRRAVE EKAAADAARE RARAEAAAAE  360
RALEEARRAR QRARADLEKA CALRDHAARL LAQVTCHACR QRSSLVAMSM AAAVGEGHGH  420
GHGGPAVACD PMRGGGVGAG M*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C1e-16175229357Zinc finger protein JACKDAW
5b3h_F1e-16175229357Zinc finger protein JACKDAW
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.281860.0root
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.9KG529700.1.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
GenBankAK3761500.0AK376150.1 Hordeum vulgare subsp. vulgare mRNA for predicted protein, complete cds, clone: NIASHv3116F03.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025795974.10.0protein indeterminate-domain 16-like
SwissprotF4IPE31e-114IDD15_ARATH; Zinc finger protein SHOOT GRAVITROPISM 5
TrEMBLA0A3L6SAP50.0A0A3L6SAP5_PANMI; Protein indeterminate-domain 16
STRINGGRMZM2G074032_P011e-161(Zea mays)
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
AT2G01940.12e-87C2H2-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]