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.5NG265900.1.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: 422aa    MW: 44587.7 Da    PI: 9.3511
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.5NG265900.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H2193.8e-0678100123
                          EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                          ++C++Cgk F r  nL+ H r H
  Pavir.5NG265900.1.p  78 FVCEICGKGFQRDQNLQLHRRGH 100
                          89*******************88 PP
2zf-C2H2130.0003155177123
                          EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                          +kC +C+k++  +s+ k H +t+
  Pavir.5NG265900.1.p 155 WKCDKCSKRYAVQSDWKAHSKTC 177
                          58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576671.13E-777100No hitNo description
Gene3DG3DSA:3.30.160.601.1E-578100IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.61478100IPR007087Zinc finger, C2H2
SMARTSM003550.01278100IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028080100IPR007087Zinc finger, C2H2
SMARTSM00355260120150IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.9E-4143176IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576671.13E-7150175No hitNo description
SMARTSM00355140155175IPR015880Zinc 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: 422 aa     Download sequence    Send to blast
MASSEAASSI ISSNNPLVVA LAPLTNLQPS HQQAAAAAEQ PPPLPPPAKK KRNLPGTPDP  60
DAEVVALSPR TLLATNRFVC EICGKGFQRD QNLQLHRRGH NLPWKLRQRS GKAEPRKRVY  120
VCPEKSCVHH NPARALGDLT GIKKHFCRKH GEKKWKCDKC SKRYAVQSDW KAHSKTCGTR  180
EYRCDCGTLF SRRDSFITHR AFCDALAEET ARLSAAAPAP STAATSLCGQ GSSSYLFAGQ  240
AVRPNMMAAL KPAAGLSLWG GNTLPSMGDI NGGGGVLAGG GAPVPPHLYA DLFAPTAAQL  300
GCWLYGNGKP TTATTEAAFS GQQHAKPAAA TDMSATALLH KAAQMGAVTS MSDDAGGAMF  360
QHSANSKQLT GGNVAYDDDV LSAAARHIKD AVHVGREETR DFLGVSVQPL CSPSLPLQGW  420
I*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C4e-36151215367Zinc finger protein JACKDAW
5b3h_F4e-36151215367Zinc finger protein JACKDAW
Search in ModeBase
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.5NG265900.1.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
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1074681e-164AK107468.1 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-120IDD3_ARATH; Zinc finger protein MAGPIE
TrEMBLA0A2S3HZD50.0A0A2S3HZD5_9POAL; Uncharacterized protein
STRINGPavir.Eb00068.1.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
AT5G44160.11e-106C2H2-like zinc finger 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]