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 LOC_Os05g03020.1
Common NameLOC4337652, OJ1001_G01.7, Os05g0121400, OSNPB_050121400
Organism
Oryza sativa subsp. japonica
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
Family C2H2
Protein Properties Length: 381aa    MW: 43065.1 Da    PI: 8.6163
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os05g03020.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H220.41.4e-0680102123
                       EEETTTTEEESSHHHHHHHHHHT CS
           zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                       + C+ Cg sF+ + +L++H+++H
  LOC_Os05g03020.1  80 HDCKVCGASFKKPAHLRQHMQSH 102
                       56*******************99 PP
2zf-C2H219.72.3e-06108132123
                       EEET..TTTEEESSHHHHHHHHHHT CS
           zf-C2H2   1 ykCp..dCgksFsrksnLkrHirtH 23 
                       ++C+   C+ s+srk++L+rH+ tH
  LOC_Os05g03020.1 108 FSCHvdGCPFSYSRKDHLNRHLLTH 132
                       89*********************99 PP
3zf-C2H211.30.0011137162123
                       EEET..TTTEEESSHHHHHHHHHH.T CS
           zf-C2H2   1 ykCp..dCgksFsrksnLkrHirt.H 23 
                       + Cp   C++ F+ k n +rH +  H
  LOC_Os05g03020.1 137 FACPmeGCNRKFTIKGNIQRHVQEmH 162
                       78*******************98877 PP
4zf-C2H220.81e-06174198123
                       EEET..TTTEEESSHHHHHHHHHHT CS
           zf-C2H2   1 ykCp..dCgksFsrksnLkrHirtH 23 
                       + Cp  +Cgk+F+  s L++H  +H
  LOC_Os05g03020.1 174 FICPeeNCGKTFKYASKLQKHEESH 198
                       78*******************9988 PP
5zf-C2H216.91.8e-05265289223
                       EET..TTTEEESSHHHHHHHHHH.T CS
           zf-C2H2   2 kCp..dCgksFsrksnLkrHirt.H 23 
                       +C+  dC+ sFs ksnL +H +  H
  LOC_Os05g03020.1 265 RCHlkDCKLSFSKKSNLDKHVKAvH 289
                       7*******************99877 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM00355153355IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.602.8E-57799IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.001680102IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.73480107IPR007087Zinc finger, C2H2
PROSITE patternPS00028082102IPR007087Zinc finger, C2H2
SuperFamilySSF576671.05E-1093134No hitNo description
Gene3DG3DSA:3.30.160.608.6E-13100134IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS501579.349108137IPR007087Zinc finger, C2H2
SMARTSM003550.0016108132IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280110132IPR007087Zinc finger, C2H2
SuperFamilySSF576671.95E-6118168No hitNo description
Gene3DG3DSA:3.30.160.601.2E-6135163IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.866137167IPR007087Zinc finger, C2H2
SMARTSM003550.0019137162IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280139162IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.602.0E-7170198IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.47E-5171200No hitNo description
PROSITE profilePS5015711.24174198IPR007087Zinc finger, C2H2
SMARTSM003550.0018174198IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280176198IPR007087Zinc finger, C2H2
SMARTSM003557.8206231IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280208231IPR007087Zinc finger, C2H2
SMARTSM0035513234255IPR015880Zinc finger, C2H2-like
SuperFamilySSF576672.67E-7245306No hitNo description
PROSITE profilePS5015711.967264294IPR007087Zinc finger, C2H2
SMARTSM003550.031264289IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.602.0E-5265290IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS000280266289IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.606.5E-6291317IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003553.5295321IPR015880Zinc finger, C2H2-like
PROSITE profilePS501578.974295326IPR007087Zinc finger, C2H2
PROSITE patternPS000280297321IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0005730Cellular Componentnucleolus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0008097Molecular Function5S rRNA binding
GO:0046872Molecular Functionmetal ion binding
GO:0080084Molecular Function5S rDNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0020039anatomyleaf lamina
Sequence ? help Back to Top
Protein Sequence    Length: 381 aa     Download sequence    Send to blast
MGSVELGAEE REVAGGEGGS KGAAPPARDI RRYKCDFCSV VRSKKGLIRA HVLEHHKDEV  60
DDLDDYLGRG GGETCKEMDH DCKVCGASFK KPAHLRQHMQ SHSLERPFSC HVDGCPFSYS  120
RKDHLNRHLL THQGKLFACP MEGCNRKFTI KGNIQRHVQE MHKDGSPCES KKEFICPEEN  180
CGKTFKYASK LQKHEESHVK LDYSEVICCE PGCMKAFTNL ECLKAHNKSC HRHVVCDVCG  240
TKQLKKNFKR HQRMHEGSCV TERVRCHLKD CKLSFSKKSN LDKHVKAVHE QKRPFVCGFS  300
GCGKSFSYKH VRDNHEKSSA HVYVQANFEE IDGERPRQAG GRKRKAIPVE SLMRKRVAAP  360
DDDAPACDDG TEYLRWLLSG *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1tf6_A9e-198522820157PROTEIN (TRANSCRIPTION FACTOR IIIA)
1tf6_D9e-198522820157PROTEIN (TRANSCRIPTION FACTOR IIIA)
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.331400.0callus| flower| leaf| panicle| stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329868400.0
Expression AtlasQ60F45-
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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00229DAPTransfer from AT1G72050Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os05g03020.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs05g03020
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK0995280.0AK099528.1 Oryza sativa Japonica Group cDNA clone:J013031H23, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015637660.10.0transcription factor IIIA isoform X1
SwissprotQ84MZ41e-115TF3A_ARATH; Transcription factor IIIA
TrEMBLA0A0E0H8T00.0A0A0E0H8T0_ORYNI; Uncharacterized protein
TrEMBLQ60F450.0Q60F45_ORYSJ; Os05g0121400 protein
STRINGOS05T0121400-020.0(Oryza sativa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP23823882
Representative plantOGRP29811627
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G72050.21e-115transcription factor IIIA