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.3KG120200.1.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: 313aa    MW: 35635 Da    PI: 8.8866
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.3KG120200.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H220.99.8e-077799123
                         EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                         + C+ Cg++F+ + +Lk+H+++H
  Pavir.3KG120200.1.p 77 HDCKECGMRFKKPAHLKQHMQSH 99
                         56*******************99 PP
2zf-C2H219.62.5e-06105129123
                          EEET..TTTEEESSHHHHHHHHHHT CS
              zf-C2H2   1 ykCp..dCgksFsrksnLkrHirtH 23 
                          ++C+   C+ ++srk++L+rH+ tH
  Pavir.3KG120200.1.p 105 FVCHvdGCPLRYSRKDHLNRHLLTH 129
                          89*********************99 PP
3zf-C2H2157.1e-05134159123
                          EEET..TTTEEESSHHHHHHHHHH.T CS
              zf-C2H2   1 ykCp..dCgksFsrksnLkrHirt.H 23 
                          ++Cp   C++ F+ k n++rH +  H
  Pavir.3KG120200.1.p 134 FVCPieGCDRKFNIKGNMQRHVQEiH 159
                          89*******************99877 PP
4zf-C2H221.18.3e-07171195123
                          EEET..TTTEEESSHHHHHHHHHHT CS
              zf-C2H2   1 ykCp..dCgksFsrksnLkrHirtH 23 
                          + Cp  +Cgk+F+  s Lk+H  +H
  Pavir.3KG120200.1.p 171 FICPevNCGKTFKYASKLKKHEESH 195
                          78*******************9988 PP
5zf-C2H212.10.0006263285323
                          ET..TTTEEESSHHHHHHHHHHT CS
              zf-C2H2   3 Cp..dCgksFsrksnLkrHirtH 23 
                          C   dC+ sFs ksnL++H + +
  Pavir.3KG120200.1.p 263 CCfeDCKCSFSKKSNLEKHVKAC 285
                          6668***************9976 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM00355123053IPR015880Zinc finger, C2H2-like
SMARTSM003550.00377799IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015714.02577104IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.609.9E-977103IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS0002807999IPR007087Zinc finger, C2H2
SuperFamilySSF576671.98E-1190131No hitNo description
Gene3DG3DSA:3.30.160.602.2E-11104131IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.0043105129IPR015880Zinc finger, C2H2-like
PROSITE profilePS501578.954105134IPR007087Zinc finger, C2H2
PROSITE patternPS000280107129IPR007087Zinc finger, C2H2
SuperFamilySSF576672.28E-7116165No hitNo description
Gene3DG3DSA:3.30.160.602.6E-8132160IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003552.1E-4134159IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.699134164IPR007087Zinc finger, C2H2
PROSITE patternPS000280136159IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.1E-6167195IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576675.37E-5168197No hitNo description
SMARTSM003550.0032171195IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.281171195IPR007087Zinc finger, C2H2
PROSITE patternPS000280173195IPR007087Zinc finger, C2H2
SMARTSM003556.5203228IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280205228IPR007087Zinc finger, C2H2
SMARTSM0035515231252IPR015880Zinc finger, C2H2-like
SMARTSM0035599261283IPR015880Zinc 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: 313 aa     Download sequence    Send to blast
MGDGAETGGG DGARTTAARA GAPRRDIRRY KCEFCGVVRS KKSLIRAHVL QNHKDEVNGL  60
EDYQEGGDGA SRKEVSHDCK ECGMRFKKPA HLKQHMQSHS LERPFVCHVD GCPLRYSRKD  120
HLNRHLLTHQ GKLFVCPIEG CDRKFNIKGN MQRHVQEIHK DGSPCESKKE FICPEVNCGK  180
TFKYASKLKK HEESHVKLDY TEVICCEPGC MKTFTNVECL KAHNQSCHQH VQCDVCGTKQ  240
LKRNFKRHRQ MHEGSCITER VKCCFEDCKC SFSKKSNLEK HVKACPRAAP TFRVPVLWVW  300
QEVFLQACKG HP*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1tf6_A1e-178122519157PROTEIN (TRANSCRIPTION FACTOR IIIA)
1tf6_D1e-178122519157PROTEIN (TRANSCRIPTION FACTOR IIIA)
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.337840.0callus| root
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Both isoforms 1 and 2 transcripts are expressed in seedlings and both TFIIIA and TFIIIA-C are present at similar ratios in 10-day-old seedlings (at protein level). In correlation with the reorganization of 5S rDNA chromatin to a mature state, full-length isoform 1 protein TFIIIA with transcriptional activity accumulates and permits de novo transcription of 5S rRNA. Isoforms 1 and 2 transcripts accumulate in various tissues of the reproductive phase, including flowers and siliques, but only isoform 2 is present in mature seeds. In flowers, both TFIIIA and TFIIIA-C are present at similar ratios (at protein level). Very low amounts of TFIIIA are found in extracts from fresh siliques compared to TFIIIA-C. The amount of full-length TFIIIA protein progressively increases from fresh siliques to seeds concomitant with lower proportions of the shorter TFIIIA-C protein (at protein level) thus leading to 5S rRNA accumulation in the seed. {ECO:0000269|PubMed:22353599}.
UniprotTISSUE SPECIFICITY: Expressed in seedlings, flowers, siliques and seeds. {ECO:0000269|PubMed:22353599}.
Functional Description ? help Back to Top
Source Description
UniProtEssential protein (PubMed:22353599). Isoform 1 is a transcription activator the binds both 5S rDNA and 5S rRNA and stimulates the transcription of 5S rRNA gene (PubMed:12711688, PubMed:22353599). Isoform 1 regulates 5S rRNA levels during development (PubMed:22353599). {ECO:0000269|PubMed:12711688, ECO:0000269|PubMed:22353599}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.3KG120200.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025805294.10.0transcription factor IIIA-like
RefseqXP_025805295.10.0transcription factor IIIA-like
SwissprotQ84MZ44e-86TF3A_ARATH; Transcription factor IIIA
TrEMBLA0A2T7E7G60.0A0A2T7E7G6_9POAL; Uncharacterized protein
STRINGPavir.Ca00708.1.p0.0(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP23823882
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G72050.24e-86transcription factor IIIA