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.3KG117800.1.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: 299aa    MW: 34201.5 Da    PI: 8.7951
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.3KG117800.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H220.99.6e-072751123
                         EEET..TTTEEESSHHHHHHHHHHT CS
              zf-C2H2  1 ykCp..dCgksFsrksnLkrHirtH 23
                         ++C+   C+ s+srk++L+rH+ tH
  Pavir.3KG117800.1.p 27 FVCHvdGCPLSYSRKDHLNRHLLTH 51
                         89*********************99 PP
2zf-C2H212.20.000575681123
                         EEET..TTTEEESSHHHHHHHHHH.T CS
              zf-C2H2  1 ykCp..dCgksFsrksnLkrHirt.H 23
                         ++Cp   C+  F+ k n++rH +  H
  Pavir.3KG117800.1.p 56 FVCPieGCDCKFNIKGNMQRHVQEiH 81
                         89*******************99877 PP
3zf-C2H221.27.8e-0793117123
                          EEET..TTTEEESSHHHHHHHHHHT CS
              zf-C2H2   1 ykCp..dCgksFsrksnLkrHirtH 23 
                          + Cp  +Cgk+F+  s Lk+H  +H
  Pavir.3KG117800.1.p  93 FICPevNCGKTFKYASKLKKHEESH 117
                          78*******************9988 PP
4zf-C2H216.81.9e-05184208223
                          EET..TTTEEESSHHHHHHHHHH.T CS
              zf-C2H2   2 kCp..dCgksFsrksnLkrHirt.H 23 
                          kC   dC+ sFs ksnL++H +  H
  Pavir.3KG117800.1.p 184 KCRfdDCKCSFSKKSNLEKHVKAvH 208
                          69999***************99877 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576671.64E-72353No hitNo description
Gene3DG3DSA:3.30.160.601.9E-102553IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS501579.2242756IPR007087Zinc finger, C2H2
SMARTSM003550.0032751IPR015880Zinc finger, C2H2-like
PROSITE patternPS0002802951IPR007087Zinc finger, C2H2
SuperFamilySSF576672.78E-55482No hitNo description
Gene3DG3DSA:3.30.160.601.2E-75482IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.00165681IPR015880Zinc finger, C2H2-like
PROSITE profilePS501579.5565686IPR007087Zinc finger, C2H2
PROSITE patternPS0002805881IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.0E-689117IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576673.53E-590118No hitNo description
SMARTSM003550.003293117IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.28193117IPR007087Zinc finger, C2H2
PROSITE patternPS00028095117IPR007087Zinc finger, C2H2
SMARTSM003556.5125150IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280127150IPR007087Zinc finger, C2H2
SMARTSM0035515153174IPR015880Zinc finger, C2H2-like
SuperFamilySSF576677.51E-6164219No hitNo description
SMARTSM003550.034183208IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.03183213IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.607.6E-5183208IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS000280185208IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.605.0E-6209237IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003552.9214240IPR015880Zinc finger, C2H2-like
PROSITE profilePS501579.016214243IPR007087Zinc finger, C2H2
PROSITE patternPS000280216240IPR007087Zinc finger, C2H2
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: 299 aa     Download sequence    Send to blast
MCFITVLSMY FKILKDPAVA CPSVRPFVCH VDGCPLSYSR KDHLNRHLLT HQGKLFVCPI  60
EGCDCKFNIK GNMQRHVQEI HKDGSPCESK KEFICPEVNC GKTFKYASKL KKHEESHVKL  120
DCTEVICCEP GCMKTFTNVE CLKAHNQSCH QHVQCDVCGT KQLKRNFKRH RQMHEGSCIT  180
ERVKCRFDDC KCSFSKKSNL EKHVKAVHEQ RRPFVCQFSG CGKKFSYKHV RDIHEKSSAH  240
VHTEGDFVEA DEQRLRSAGG RKRKPVSVET FMRKRVAAPD DAPAHVDGTE YLRWLLSG*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1tf6_A2e-13314717157PROTEIN (TRANSCRIPTION FACTOR IIIA)
1tf6_D2e-13314717157PROTEIN (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.3KG117800.1.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
SwissprotQ84MZ41e-89TF3A_ARATH; Transcription factor IIIA
TrEMBLA0A3L6RD090.0A0A3L6RD09_PANMI; Uncharacterized protein
STRINGPavir.J02126.1.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
AT1G72050.12e-91transcription factor IIIA