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 GSBRNA2T00136387001
Common NameGSBRNA2T00136387001
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: 1117aa    MW: 125525 Da    PI: 7.9915
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSBRNA2T00136387001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H213.20.0002610281051223
                           EET..TTTEEESSHHHHHHHHHHT CS
              zf-C2H2    2 kCp..dCgksFsrksnLkrHirtH 23  
                           +C+   Cgk F+ + +L+ H+r+H
  GSBRNA2T00136387001 1028 RCTheGCGKKFRAHKYLVLHQRVH 1051
                           588889****************99 PP
2zf-C2H211.40.0009710871113123
                           EEET..TTTEEESSHHHHHHHHHH..T CS
              zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                           ykC+   Cg sF+  s++ rH r+  H
  GSBRNA2T00136387001 1087 YKCKveECGLSFRFVSDYSRHRRKtgH 1113
                           99*********************9777 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005452.3E-141757IPR003349JmjN domain
PROSITE profilePS5118314.3261859IPR003349JmjN domain
PfamPF023754.0E-161952IPR003349JmjN domain
SMARTSM005588.7E-46211380IPR003347JmjC domain
PROSITE profilePS5118435.242214380IPR003347JmjC domain
SuperFamilySSF511979.06E-26214378No hitNo description
PfamPF023732.5E-37244363IPR003347JmjC domain
SMARTSM0035516010041026IPR015880Zinc finger, C2H2-like
SuperFamilySSF576677.99E-810151064No hitNo description
SMARTSM003550.05710271051IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.46410271056IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.1E-610281050IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028010291051IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.5E-910511078IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.06610571081IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.42710571086IPR007087Zinc finger, C2H2
PROSITE patternPS00028010591081IPR007087Zinc finger, C2H2
SuperFamilySSF576673.29E-1010681109No hitNo description
Gene3DG3DSA:3.30.160.605.3E-1010791110IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003554.810871113IPR015880Zinc finger, C2H2-like
PROSITE profilePS501579.95110871116IPR007087Zinc finger, C2H2
PROSITE patternPS00028010891113IPR007087Zinc 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: 1117 aa     Download sequence    Send to blast
MGSSNVEIPN WLKAMPLAPV FRPTDTEFAD PIAYISKIEK QASAFGICKI IPPIPKPSKK  60
YVFCNLNKSL LRCPELASGV DVSKRLGQED RAVFTTRQQE LGQARKKSRG GEGGDVKQVW  120
QSGGVYTLEQ FESKSKAFYK SQLGTVREVS PVVVEALFWR AASEKPMYIE YANDVPGSAF  180
GEPEGHFRHF RQRKRRGRGF YQRKNGTAGW KLSNSSWNLQ MIARSPGSVT RFMPDDIPGV  240
TSPMVYIGML FSWFAWHVED HELHSMNYLH TGSPKTWYAV PGDYALDFEE VIRKNSYGSN  300
LDQLAALTQL GEKTTLVSPE IIVSSDIPCC RLVQNPGEFV VTFPRSYHVG FSHGFNCGEA  360
ANFGTPQWLN VAKEAAVRRA AMNYLPMLSH QQLLYLLTMS FVSRQGNISI FPLVPRSLLP  420
GGRSSRLRDR QREEREFLVK KAFVEDILNE NKNLSVLLGE PGSRLVMWDP DLLPRHSVLA  480
LAATGVATTP AVSSPAEAKS EIENKEENPS LLEELSLFME KLKDVYYDDD DGQLNDFQID  540
SGTLPCVACG VLGFPFMSVV QPSENALKDL SERQGEIDAL EDKAESSEKS NCEWNTSSRY  600
IRPRIFCLEH TIELQRLLQS RGGLKFLVIC HKDFQKFKAH AAIVAEEVKV PFRYDDVLLE  660
SASKEELSLI DLAIEGEENN EYGADWTSKL GINLRYCVKV RKNSPTNKIQ HALSLGGLFS  720
DSSHVLDMST IKWLQRKSRS KAKPCSTTSG FTSRERLEVK AERRLGEKEE VESQGGRKEE  780
KIIQYSRKKK LNPNANRSRH ASAVDSEMNN EIGDSADLTS VTREHQGHSV ALEPRTTNAN  840
SEEEEQSQVV LPTNREAQTH SSAQVGLEVS ETNIASEKIV VDMVRDDDPL ASNGDEASSS  900
GLQAADDENS MESEVASSGN TKVIVEAKKK RKIELESETN DYHPESSIGF IKSPCEGLRS  960
RGKRKVTCEE TSSNLNEASD EEKKHTAKRL KKTPNTGSTT TQHNLCYQEG CKMTFKSKAD  1020
LAAHKRNRCT HEGCGKKFRA HKYLVLHQRV HNDERPLACP WKGCSMNFKW QWARTEHLRL  1080
HTGERPYKCK VEECGLSFRF VSDYSRHRRK TGHYVT*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A5e-76113948346Transcription factor jumonji (Jmj) family protein
6ip4_A5e-76113948346Arabidopsis JMJ13
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bna.147870.0leaf| seed
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed at low levels in cotyledons and leaves. Detected in inflorescences, stems, roots and siliques but not in shoot apical meristems or root tips. {ECO:0000269|PubMed:15377760, ECO:0000269|PubMed:18713399}.
Functional Description ? help Back to Top
Source Description
UniProtActs probably as a histone 'Lys-4' (H3K4me) demethylase. Involved in transcriptional gene regulation. Acts as a repressor of the photoperiodic flowering pathway and of FT. Binds around the transcription start site of the FT locus. {ECO:0000269|PubMed:15377760, ECO:0000269|PubMed:18467490, ECO:0000269|PubMed:19946624}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapGSBRNA2T00136387001
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY6645000.0AY664500.1 Arabidopsis thaliana early flowering 6 (ELF6) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009122623.10.0PREDICTED: probable lysine-specific demethylase ELF6 isoform X1
RefseqXP_009122624.10.0PREDICTED: probable lysine-specific demethylase ELF6 isoform X2
SwissprotQ6BDA00.0ELF6_ARATH; Probable lysine-specific demethylase ELF6
TrEMBLA0A3P6D2F60.0A0A3P6D2F6_BRACM; Uncharacterized protein
STRINGBra009474.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM115202731
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G04240.10.0C2H2 family protein
Publications ? help Back to Top
  1. Heidari B,Nemie-Feyissa D,Kangasjärvi S,Lillo C
    Antagonistic regulation of flowering time through distinct regulatory subunits of protein phosphatase 2A.
    PLoS ONE, 2013. 8(7): p. e67987
    [PMID:23976921]
  2. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  3. 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]
  4. Crevillén P, et al.
    Epigenetic reprogramming that prevents transgenerational inheritance of the vernalized state.
    Nature, 2014. 515(7528): p. 587-90
    [PMID:25219852]
  5. Yang H,Howard M,Dean C
    Physical coupling of activation and derepression activities to maintain an active transcriptional state at FLC.
    Proc. Natl. Acad. Sci. U.S.A., 2016. 113(33): p. 9369-74
    [PMID:27482092]