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 GSBRNA2T00099570001
Common NameGSBRNA2T00099570001
Organism
Brassica napus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family C2H2
Protein Properties Length: 375aa    MW: 42631.8 Da    PI: 7.4258
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSBRNA2T00099570001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H211.10.00122143123
                         EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                         y C++Cg s s k++ ++Hi +H
  GSBRNA2T00099570001 21 YLCQYCGISRSKKYLITSHIESH 43
                         56*******************96 PP
2zf-C2H220.71.1e-066789123
                         EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                         ++C+ Cg  F+ + +Lk+H+++H
  GSBRNA2T00099570001 67 HTCNECGAEFKKPAHLKQHMQSH 89
                         79*******************99 PP
3zf-C2H217.98.6e-0695119123
                          EEET..TTTEEESSHHHHHHHHHHT CS
              zf-C2H2   1 ykCp..dCgksFsrksnLkrHirtH 23 
                          ++C   dC+ s++rk++L+rH+ tH
  GSBRNA2T00099570001  95 FTCYvdDCTASYRRKDHLNRHLLTH 119
                          899999*****************99 PP
4zf-C2H2201.8e-06177200223
                          EET..TTTEEESSHHHHHHHHHHT CS
              zf-C2H2   2 kCp..dCgksFsrksnLkrHirtH 23 
                          +C+   Cgk F+ +s+L++H  +H
  GSBRNA2T00099570001 177 VCKevGCGKAFKYPSQLQKHEDSH 200
                          79999***************9888 PP
5zf-C2H220.31.4e-06267292123
                          EEET..TTTEEESSHHHHHHHHHH.T CS
              zf-C2H2   1 ykCp..dCgksFsrksnLkrHirt.H 23 
                          +kC+   C+ +Fs +snL++H++  H
  GSBRNA2T00099570001 267 FKCEveGCSSTFSKPSNLQKHLKAvH 292
                          89********************9877 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM00355262143IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015714.0666794IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.9E-86794IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003559.7E-46789IPR015880Zinc finger, C2H2-like
PROSITE patternPS0002806989IPR007087Zinc finger, C2H2
SuperFamilySSF576679.3E-1179121No hitNo description
PROSITE profilePS501579.70295124IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.1E-995121IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.0795119IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028097119IPR007087Zinc finger, C2H2
SuperFamilySSF576673.13E-5122150No hitNo description
PROSITE profilePS501579.556124154IPR007087Zinc finger, C2H2
SMARTSM003551.2124149IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280126149IPR007087Zinc finger, C2H2
SuperFamilySSF576677.91E-5172202No hitNo description
Gene3DG3DSA:3.30.160.609.2E-6174200IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.471176205IPR007087Zinc finger, C2H2
SMARTSM003550.0055176200IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280178200IPR007087Zinc finger, C2H2
SMARTSM003550.52208233IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280210233IPR007087Zinc finger, C2H2
SMARTSM0035528236257IPR015880Zinc finger, C2H2-like
SuperFamilySSF576671.93E-8248302No hitNo description
PROSITE profilePS5015712.84267297IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.607.8E-8267292IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003553.6E-4267292IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280269292IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.608.1E-5293319IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003554.9298324IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280300324IPR007087Zinc 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: 375 aa     Download sequence    Send to blast
MSEEAANVDV NPTKTKDIRN YLCQYCGISR SKKYLITSHI ESHHKMEVEE ERNEEACEDE  60
EEISGKHTCN ECGAEFKKPA HLKQHMQSHS LERPFTCYVD DCTASYRRKD HLNRHLLTHK  120
GKLFKCPVEN CKSEFSIHGN ISKHVKKFHT DGDSNKDDTG SGDSQPSECS SGQKKLVCKE  180
VGCGKAFKYP SQLQKHEDSH VKLDSVEAFC SEIGCMKYFT NEECLKAHIR SSHQHVNCEI  240
CGSKHLKKNI KRHLKTHDED SSSPGEFKCE VEGCSSTFSK PSNLQKHLKA VHEDIRPFVC  300
GFPGCGMRFA YKHVRNNHEN SGSHVYTCGD FVEADEDFTS RPRGGLKRKQ VTAEMLVRKR  360
VMPPQFDSEE HETC*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5wjq_D4e-16213279284Zinc finger protein 568
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bna.94840.0leaf| seed| vegetative meristem
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
PlantRegMapGSBRNA2T00099570001
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_013589949.10.0PREDICTED: transcription factor IIIA-like
SwissprotQ84MZ40.0TF3A_ARATH; Transcription factor IIIA
TrEMBLA0A397YNU20.0A0A397YNU2_BRACM; Uncharacterized protein
TrEMBLA0A3P6BJ380.0A0A3P6BJ38_BRACM; Uncharacterized protein (Fragment)
STRINGBo6g092790.10.0(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM47142852
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G72050.20.0transcription factor IIIA
Publications ? help Back to Top
  1. Chalhoub B, et al.
    Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome.
    Science, 2014. 345(6199): p. 950-3
    [PMID:25146293]