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.5KG000400.1.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: 428aa    MW: 45106.2 Da    PI: 8.8643
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.5KG000400.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H2193.9e-067496123
                         EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                         ++C++Cgk F r  nL+ H r H
  Pavir.5KG000400.1.p 74 FVCEICGKGFQRDQNLQLHRRGH 96
                         89*******************88 PP
2zf-C2H2130.00031150172123
                          EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                          +kC +C+k++  +s+ k H +t+
  Pavir.5KG000400.1.p 150 WKCDKCSKRYAVQSDWKAHSKTC 172
                          58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576671.57E-77396No hitNo description
PROSITE profilePS5015711.6147496IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.2E-57496IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.0127496IPR015880Zinc finger, C2H2-like
PROSITE patternPS0002807696IPR007087Zinc finger, C2H2
SMARTSM00355260115145IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.602.0E-4138171IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576671.57E-7145170No hitNo description
SMARTSM00355140150170IPR015880Zinc finger, C2H2-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0005634Cellular Componentnucleus
GO:0044212Molecular Functiontranscription regulatory region DNA binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 428 aa     Download sequence    Send to blast
MAASAAASSI ISNPLLAPLT NLQPSSHQQA AAADEQQPPL PPPAKKKRNL PGTPDPDAEV  60
IALSPRALLA TNRFVCEICG KGFQRDQNLQ LHRRGHNLPW KLRQRSGKEP RKRVYVCPEK  120
SCVHHNPARA LGDLTGIKKH FCRKHGEKKW KCDKCSKRYA VQSDWKAHSK TCGTREYRCD  180
CGTLFSRRDS FITHRAFCDA LAEETARLSA TAAPSAAQSS SNYLFAGAAG LANMMLPPAP  240
AAPHLKPAAG LSLWGPSSMA DIGIGGGAAP VPPHLYADLL APPTSDAAAQ LACCWLYGNS  300
NGELSSANNA SALTTEAQSV PSLFSGQQHA KPLAPTDMSA TALLHKAAQM GAVTSTMSDD  360
AGAAAMFQQS ANGNLTGGSV AYDDDVLSAA ARHIKDAVGR EETRDFLGVG VHPLCSSSLL  420
APLQGRI*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C2e-36146210367Zinc finger protein JACKDAW
5b3h_F2e-36146210367Zinc finger protein JACKDAW
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.316051e-152root
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in the ground tissue and stele cells of embryos and 2-days post-germination roots but not in the quiescent center (PubMed:17785527). Detected only in cells that perform asymmetric cell divisions (PubMed:17785527). In roots, present in cortex, endodermis, and pericycle layer (PubMed:25829440). {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:25829440}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that regulates tissue boundaries and asymmetric cell division (PubMed:17785527, PubMed:25829440). Contributes to the sequestration of 'SHORT-ROOT' to the nucleus (PubMed:17785527, PubMed:25829440). Interacts with the SCR and MGP promoters (PubMed:21935722). Does not show transcription activity by itself, but regulates the transcription of downstream genes through interaction with other transcription factors (PubMed:21935722). Binds DNA via its zinc fingers (PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). Positively involved in gibberellic acid (GA) signaling (PubMed:24821766). {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:21935722, ECO:0000269|PubMed:24821766, ECO:0000269|PubMed:25829440}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00125DAPTransfer from AT1G03840Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.5KG000400.1.p
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Up-regulated by the transcription factor JKD, and down-regulated by SHR, SCR and itself. {ECO:0000269|PubMed:21935722}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1074681e-178AK107468.1 Oryza sativa Japonica Group cDNA clone:002-129-B01, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025818706.10.0zinc finger protein MAGPIE-like
RefseqXP_025818707.10.0zinc finger protein MAGPIE-like
SwissprotQ9ZWA61e-126IDD3_ARATH; Zinc finger protein MAGPIE
TrEMBLA0A2S3HZD50.0A0A2S3HZD5_9POAL; Uncharacterized protein
STRINGPavir.Ea00021.1.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
AT1G03840.11e-113C2H2 family protein
Publications ? help Back to Top
  1. Muñoz-Strale D,León G
    Identification of two highly specific pollen promoters using transcriptomic data.
    Plant Physiol. Biochem., 2014. 83: p. 292-9
    [PMID:25208507]
  2. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]