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 XP_013584045.1
Organism
Brassica oleracea
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: 479aa    MW: 53015.4 Da    PI: 8.5583
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_013584045.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H2130.000317090323
                    ETTTTEEESSHHHHHHHHHHT CS
         zf-C2H2  3 CpdCgksFsrksnLkrHirtH 23
                    C++C k F r  nL+ H r H
  XP_013584045.1 70 CEICRKGFQRDQNLQLHRRGH 90
                    *******************88 PP
2zf-C2H213.50.00022144166123
                     EEETTTTEEESSHHHHHHHHHHT CS
         zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                     +kC++C+k++  +s+ k H +t+
  XP_013584045.1 144 WKCEKCSKRYAVQSDWKAHSKTC 166
                     58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576672.42E-56790No hitNo description
Gene3DG3DSA:3.30.160.601.4E-46790IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.4926890IPR007087Zinc finger, C2H2
PROSITE patternPS0002807090IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.6E-4132165IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.42E-5139164No hitNo description
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: 479 aa     Download sequence    Send to blast
MTAEDRTISS SGGYVQSSST TGHVDHHHEL ESFNPPPAKK KRNLPGNPDP EAEVIALSPT  60
TLMATNRFLC EICRKGFQRD QNLQLHRRGH NLPWKLKQRT TKEVRKRVYV CPEKSCVHHH  120
PTRALGDLTG IKKHFCRKHG EKKWKCEKCS KRYAVQSDWK AHSKTCGTRE YRCDCGTIFS  180
RRDSFITHRA FCDALAEETA RLNAASHLKS LTSNNLNYHY LMGTLIPSPP PFPFGPPQPL  240
QQHHFPITTN TFDHHHHDVM KPASSLSLWM GGNNNHHQVT VDEGIAPQED YNWVFGNANN  300
RGELITTSDS LITHENINIV SSKENANAAT SLSVPSLFSS VDHITQDANA ASSAVANMSA  360
TALLQKAAQM GVTSSTPTTI TTKQSTFHQT VEEGGSDKFF ALFGPNSVGL MSNNGLQHEI  420
ENPRSGVTVA SGIDELQNYP LKRRRVESVD AGGGGQTRDF LGVGVQTMCH HSSSINGWI
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C5e-36140215372Zinc finger protein JACKDAW
5b3h_F5e-36140215372Zinc finger protein JACKDAW
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1441445KRRRV
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_013584045.1
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
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB4934280.0AB493428.1 Arabidopsis thaliana At1g03840 mRNA for hypothetical protein, partial cds, clone: RAAt1g03840.
GenBankAK2278370.0AK227837.1 Arabidopsis thaliana mRNA for putative DNA-binding protein, complete cds, clone: RAFL14-40-M12.
GenBankBT0062090.0BT006209.1 Arabidopsis thaliana At1g03840 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_013584045.10.0PREDICTED: zinc finger protein MAGPIE
SwissprotQ9ZWA60.0IDD3_ARATH; Zinc finger protein MAGPIE
TrEMBLA0A0D3C7E30.0A0A0D3C7E3_BRAOL; Uncharacterized protein
TrEMBLA0A3P6FED50.0A0A3P6FED5_BRAOL; Uncharacterized protein
STRINGBo5g004120.10.0(Brassica oleracea)
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. 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]
  2. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]