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 GSBRNA2T00116449001
Common NameGSBRNA2T00116449001
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: 402aa    MW: 46411.5 Da    PI: 8.2715
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSBRNA2T00116449001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H2120.000623557123
                         EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                         y C++Cg s s k++ ++Hi++H
  GSBRNA2T00116449001 35 YLCQYCGISRSKKYLITSHINSH 57
                         56********************6 PP
2zf-C2H220.21.6e-0682104123
                          EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                          ++C+ Cg  F+ + +Lk+H+++H
  GSBRNA2T00116449001  82 HTCQECGAEFKKPAHLKQHMQSH 104
                          79*******************99 PP
3zf-C2H2171.7e-05135159123
                          EEET..TTTEEESSHHHHHHHHHHT CS
              zf-C2H2   1 ykCp..dCgksFsrksnLkrHirtH 23 
                          ++C   dC+ s++rk++L+rH+ tH
  GSBRNA2T00116449001 135 FECYvdDCTSSYRRKDHLNRHLLTH 159
                          789999*****************99 PP
4zf-C2H222.14e-07204227223
                          EET..TTTEEESSHHHHHHHHHHT CS
              zf-C2H2   2 kCp..dCgksFsrksnLkrHirtH 23 
                          +C+   Cgk F+ +s+L++H+ +H
  GSBRNA2T00116449001 204 VCKekGCGKAFKYPSQLQKHQDSH 227
                          79999****************998 PP
5zf-C2H218.45.7e-06294319123
                          EEET..TTTEEESSHHHHHHHHHH.T CS
              zf-C2H2   1 ykCp..dCgksFsrksnLkrHirt.H 23 
                          +kC+   C+ +Fs  snL++H++  H
  GSBRNA2T00116449001 294 FKCEveGCSSTFSKASNLRKHLKAvH 319
                          89********************9877 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576679.26E-533104No hitNo description
SMARTSM00355253557IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.17582109IPR007087Zinc finger, C2H2
SMARTSM003550.001582104IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.603.4E-582105IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028084104IPR007087Zinc finger, C2H2
SuperFamilySSF576673.86E-6127161No hitNo description
Gene3DG3DSA:3.30.160.601.7E-8132161IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS501579.889135164IPR007087Zinc finger, C2H2
SMARTSM003550.2135159IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280137159IPR007087Zinc finger, C2H2
SuperFamilySSF576677.83E-5162190No hitNo description
PROSITE profilePS501579.473164194IPR007087Zinc finger, C2H2
SMARTSM003550.42164189IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280166189IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.3E-7189227IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.88E-6190228No hitNo description
PROSITE profilePS5015710.72203232IPR007087Zinc finger, C2H2
SMARTSM003550.0018203227IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280205227IPR007087Zinc finger, C2H2
SMARTSM003550.53235260IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.603.9E-4237258IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS000280237260IPR007087Zinc finger, C2H2
SMARTSM0035522263284IPR015880Zinc finger, C2H2-like
SuperFamilySSF576676.47E-9275332No hitNo description
Gene3DG3DSA:3.30.160.606.0E-8294319IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003555.2E-4294319IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.027294324IPR007087Zinc finger, C2H2
PROSITE patternPS000280296319IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.606.8E-5320348IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003555.5325351IPR015880Zinc finger, C2H2-like
PROSITE patternPS000280327351IPR007087Zinc 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: 402 aa     Download sequence    Send to blast
MQTNPDHRVE NQSEMAEEAA NVDAKPPKAK DIRHYLCQYC GISRSKKYLI TSHINSHHKM  60
EVEMERDEEA CEVDEEEVSG KHTCQECGAE FKKPAHLKQH MQSHSLEEMN VLFLFDNRRS  120
YLCYCFASVT LKRPFECYVD DCTSSYRRKD HLNRHLLTHK GKLFKCPVEN CKSEFSVHGN  180
ISRHVKKFHN SHHSESSTGQ KKLVCKEKGC GKAFKYPSQL QKHQDSHVKL DSIEAFCSEP  240
GCMKYFTNEE CLKAHIRSYH QHINCEICGS KHLKKNIKRH LRTHEEDSSS PGEFKCEVEG  300
CSSTFSKASN LRKHLKAVHE DIRPFVCGFS GCAKRFAYKH VRNNHEKSGS HIYTCGDFVE  360
ADEDFTSRPR GGVKRKHVTA EMLIRKRVMP PQFDSQEHET C*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5v3m_C3e-133535434309Zinc finger protein 568
5wjq_D2e-13353549284Zinc finger protein 568
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bna.45480.0flower| leaf| seed
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
PlantRegMapGSBRNA2T00116449001
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_013691614.10.0transcription factor IIIA-like
SwissprotQ84MZ40.0TF3A_ARATH; Transcription factor IIIA
TrEMBLA0A3P6AGH20.0A0A3P6AGH2_BRACM; Uncharacterized protein
STRINGBra008004.1-P0.0(Brassica rapa)
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]