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 GSBRNA2T00052497001
Common NameGSBRNA2T00052497001, LOC106365414
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: 491aa    MW: 54284.6 Da    PI: 8.4987
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSBRNA2T00052497001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H215.74.4e-057090323
                         ETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2  3 CpdCgksFsrksnLkrHirtH 23
                         C++Cgk F r  nL+ H r H
  GSBRNA2T00052497001 70 CEICGKGFQRDQNLQLHRRGH 90
                         *******************88 PP
2zf-C2H213.20.00027144166123
                          EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                          +kC++C+k++  +s+ k H +t+
  GSBRNA2T00052497001 144 WKCGKCSKRYAVQSDWKAHSKTC 166
                          58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576679.2E-76790No hitNo description
Gene3DG3DSA:3.30.160.604.3E-56790IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.4896890IPR007087Zinc finger, C2H2
PROSITE patternPS0002807090IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.607.8E-4132165IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576679.2E-7139164No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0005634Cellular Componentnucleus
GO:0044212Molecular Functiontranscription regulatory region DNA binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 491 aa     Download sequence    Send to blast
MTAEEHTISS SGGYVQNLSA TDHVDHRHEH EPFNPPLAKK KRNLPGNPDP EAEVIALSPK  60
TLMATNRFLC EICGKGFQRD QNLQLHRRGH NLPWKLKQRT SKEVRKRVYV CPEKSCVHHN  120
PTRALGDLTG IKKHFCRKHG EKKWKCGKCS KRYAVQSDWK AHSKTCGTRE YRCDCGTIFS  180
RRDSFITHRA FCDALAEETA RLNAASHLKS PTGNNLNYHY LMGTLIPSPQ PPPSFPFGAP  240
QPQHHHHPFP ITTTTFDQHH HQDSMQPASS LSLWMGGNVN HHQVTNEDCT QPQSPQEDYN  300
WVFGNANNSG ELSDSLITRE NINMAAHNEN ANAVTSLSVP SLFSNVDQMR QDANVAVANM  360
SATALLQKAA QMGVTSSTPT TTSDQSAFLQ SFKSKISDQS PNVEDGGSDK FFALFGSNSV  420
GLMSNNGLGH EIVNPRNGVT VVTGIDELQN YPLKRRRVEN GDALGGGQTR DFLGVGVQTM  480
CRSSSINGWI *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C1e-34140207370Zinc finger protein JACKDAW
5b3h_F1e-34140207370Zinc finger protein JACKDAW
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1453457KRRRV
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in the ground tissue and stele cells of embryos and 2-days post-germination roots but not in the quiescent center (PubMed:17785527). Detected only in cells that perform asymmetric cell divisions (PubMed:17785527). In roots, present in cortex, endodermis, and pericycle layer (PubMed:25829440). {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:25829440}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that regulates tissue boundaries and asymmetric cell division (PubMed:17785527, PubMed:25829440). Contributes to the sequestration of 'SHORT-ROOT' to the nucleus (PubMed:17785527, PubMed:25829440). Interacts with the SCR and MGP promoters (PubMed:21935722). Does not show transcription activity by itself, but regulates the transcription of downstream genes through interaction with other transcription factors (PubMed:21935722). Binds DNA via its zinc fingers (PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). Positively involved in gibberellic acid (GA) signaling (PubMed:24821766). {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:21935722, ECO:0000269|PubMed:24821766, ECO:0000269|PubMed:25829440}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00125DAPTransfer from AT1G03840Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapGSBRNA2T00052497001
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Up-regulated by the transcription factor JKD, and down-regulated by SHR, SCR and itself. {ECO:0000269|PubMed:21935722}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC1895090.0AC189509.2 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrB089B13, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009118688.10.0PREDICTED: zinc finger protein MAGPIE
RefseqXP_013660301.10.0zinc finger protein MAGPIE
SwissprotQ9ZWA60.0IDD3_ARATH; Zinc finger protein MAGPIE
TrEMBLA0A078H5460.0A0A078H546_BRANA; BnaA09g50820D protein
TrEMBLA0A3P5YLW50.0A0A3P5YLW5_BRACM; Uncharacterized protein
TrEMBLM4EUQ90.0M4EUQ9_BRARP; Uncharacterized protein
STRINGBra032541.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM37102660
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G03840.10.0C2H2 family protein
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]
  2. Muñoz-Strale D,León G
    Identification of two highly specific pollen promoters using transcriptomic data.
    Plant Physiol. Biochem., 2014. 83: p. 292-9
    [PMID:25208507]
  3. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]