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 BGIOSGA007250-PA
Common NameOsI_05578
Organism
Oryza sativa subsp. indica
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: 369aa    MW: 42765.7 Da    PI: 8.5261
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
BGIOSGA007250-PAgenomeRISView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H218.84.5e-066082123
                      EEETTTTEEESSHHHHHHHHHHT CS
           zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                      ++C+ Cg sF  + +Lk+H+++H
  BGIOSGA007250-PA 60 HTCQECGASFQKPAHLKQHMQSH 82
                      79*******************99 PP
2zf-C2H2224.3e-0788112123
                       EEET..TTTEEESSHHHHHHHHHHT CS
           zf-C2H2   1 ykCp..dCgksFsrksnLkrHirtH 23 
                       + Cp  dC+ s+ rk++L+rH+ +H
  BGIOSGA007250-PA  88 FICPleDCPFSYIRKDHLNRHMLKH 112
                       78*********************99 PP
3zf-C2H215.64.6e-05117142123
                       EEET..TTTEEESSHHHHHHHHHH.T CS
           zf-C2H2   1 ykCp..dCgksFsrksnLkrHirt.H 23 
                       ++C+   Cg+ Fs k n++rH +  H
  BGIOSGA007250-PA 117 FTCSmdGCGRKFSIKANMQRHVKEiH 142
                       89********************9988 PP
4zf-C2H215.83.9e-05154178123
                       EEET..TTTEEESSHHHHHHHHHHT CS
           zf-C2H2   1 ykCp..dCgksFsrksnLkrHirtH 23 
                       ++C+   C+k+F+  s +k+H  +H
  BGIOSGA007250-PA 154 FVCKeeGCNKVFKYASKMKKHEESH 178
                       89*******************9988 PP
5zf-C2H217.98.6e-06245269223
                       EET..TTTEEESSHHHHHHHHHH.T CS
           zf-C2H2   2 kCp..dCgksFsrksnLkrHirt.H 23 
                       kC+   C  sFs+ksnL++Hi+  H
  BGIOSGA007250-PA 245 KCSfeGCECSFSNKSNLTKHIKAsH 269
                       688899***************9888 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM00355241436IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.607.9E-65779IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015713.5476087IPR007087Zinc finger, C2H2
SMARTSM003550.00176082IPR015880Zinc finger, C2H2-like
PROSITE patternPS0002806282IPR007087Zinc finger, C2H2
SuperFamilySSF576672.34E-1172114No hitNo description
Gene3DG3DSA:3.30.160.605.1E-1280114IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003555.5E-488112IPR015880Zinc finger, C2H2-like
PROSITE profilePS501578.80888117IPR007087Zinc finger, C2H2
PROSITE patternPS00028090112IPR007087Zinc finger, C2H2
SuperFamilySSF576672.55E-898146No hitNo description
Gene3DG3DSA:3.30.160.601.0E-7115144IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003553.9E-4117142IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.154117147IPR007087Zinc finger, C2H2
PROSITE patternPS000280119142IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.0E-7151178IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.0038154178IPR015880Zinc finger, C2H2-like
PROSITE profilePS501579.764154178IPR007087Zinc finger, C2H2
PROSITE patternPS000280156178IPR007087Zinc finger, C2H2
SMARTSM003555.7186211IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280188211IPR007087Zinc finger, C2H2
SMARTSM0035515214235IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.608.2E-6226266IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576678.34E-8227282No hitNo description
SMARTSM003550.002244269IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.365244274IPR007087Zinc finger, C2H2
PROSITE patternPS000280246269IPR007087Zinc finger, C2H2
SMARTSM003555.8275301IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280277301IPR007087Zinc 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
Sequence ? help Back to Top
Protein Sequence    Length: 369 aa     Download sequence    Send to blast
MRVEATQHRD IRRYKCEFCT VVRSKKCLIR AHMVAHHKEE LDKSEIYKSN GEKVVHEGDH  60
TCQECGASFQ KPAHLKQHMQ SHSDERSFIC PLEDCPFSYI RKDHLNRHML KHQGKLFTCS  120
MDGCGRKFSI KANMQRHVKE IHEDETATKS NRQFVCKEEG CNKVFKYASK MKKHEESHVK  180
LDYVEVVCCE PGCMKTFTNV ECLRAHNQAC HQYVQCDICG EKHLKKNIKR HLRAHEEVPS  240
TERIKCSFEG CECSFSNKSN LTKHIKASHD QVKPFACRFT GCEKVFPYKH VRDNHEKSSA  300
HVYTQANFTE MDEQLLSCPR GGRKRKAVTV ETLTRKRVTM HGDASSLDNG TEYLRWLLSG  360
GDDDSSQTH
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1tf6_A8e-196425019174PROTEIN (TRANSCRIPTION FACTOR IIIA)
1tf6_D8e-196425019174PROTEIN (TRANSCRIPTION FACTOR IIIA)
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.180860.0callus| flower| leaf| panicle| stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329856820.0
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
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1004730.0AK100473.1 Oryza sativa Japonica Group cDNA clone:J023093M20, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015626855.10.0transcription factor IIIA isoform X1
SwissprotQ84MZ41e-105TF3A_ARATH; Transcription factor IIIA
TrEMBLA0A0D3EZT10.0A0A0D3EZT1_9ORYZ; Uncharacterized protein
TrEMBLA2X0370.0A2X037_ORYSI; Uncharacterized protein
TrEMBLA3A2F30.0A3A2F3_ORYSJ; Uncharacterized protein
STRINGORUFI02G01170.10.0(Oryza rufipogon)
STRINGORGLA02G0010700.10.0(Oryza glaberrima)
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
AT1G72050.21e-108transcription factor IIIA