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 GSBRNA2T00072972001
Common NameGSBRNA2T00072972001
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: 1124aa    MW: 125914 Da    PI: 7.2019
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSBRNA2T00072972001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H213.10.0002910351058223
                           EET..TTTEEESSHHHHHHHHHHT CS
              zf-C2H2    2 kCp..dCgksFsrksnLkrHirtH 23  
                           +C+   Cgk F+ + +L+ H+r+H
  GSBRNA2T00072972001 1035 RCTheGCGKKFRAHKYLVLHQRVH 1058
                           588889****************99 PP
2zf-C2H211.40.0009710941120123
                           EEET..TTTEEESSHHHHHHHHHH..T CS
              zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                           ykC+   Cg sF+  s++ rH r+  H
  GSBRNA2T00072972001 1094 YKCKveECGLSFRFVSDYSRHRRKtgH 1120
                           99*********************9777 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005451.1E-141757IPR003349JmjN domain
PROSITE profilePS5118314.3261859IPR003349JmjN domain
PfamPF023753.4E-161952IPR003349JmjN domain
SMARTSM005584.9E-46208377IPR003347JmjC domain
PROSITE profilePS5118435.171211377IPR003347JmjC domain
SuperFamilySSF511976.04E-26222375No hitNo description
PfamPF023731.1E-37241360IPR003347JmjC domain
SMARTSM0035517010111033IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.02710341063IPR007087Zinc finger, C2H2
SMARTSM003550.05710341058IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.606.2E-710351063IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028010361058IPR007087Zinc finger, C2H2
SuperFamilySSF576671.43E-1010501092No hitNo description
PROSITE profilePS5015712.09210641093IPR007087Zinc finger, C2H2
SMARTSM003550.009510641088IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.605.0E-1010641088IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028010661088IPR007087Zinc finger, C2H2
SuperFamilySSF576676.18E-910821116No hitNo description
Gene3DG3DSA:3.30.160.605.2E-1010891117IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003554.810941120IPR015880Zinc finger, C2H2-like
PROSITE profilePS501579.95110941123IPR007087Zinc finger, C2H2
PROSITE patternPS00028010961120IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009741Biological Processresponse to brassinosteroid
GO:0009826Biological Processunidimensional cell growth
GO:0033169Biological Processhistone H3-K9 demethylation
GO:0048577Biological Processnegative regulation of short-day photoperiodism, flowering
GO:0048579Biological Processnegative regulation of long-day photoperiodism, flowering
GO:0005634Cellular Componentnucleus
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 1124 aa     Download sequence    Send to blast
MGSSNVEIPN WLKAMPLAPV FRPTDTEFAD PIAYISKIEK QASAFGICKI VPPIPKPSKK  60
YVFCNLNKSL LRCPELASGV DVSKRLGQED RAVFTTRQQE LGQARKKTKE GSDVKQVWQS  120
GGVYTLEQFE SKSKAFYKSL LGTVKEVSPV VVEALFWRAA SEKPVYIEYA NDVAKASLAS  180
PSLSSQDPAK KKNMDVVVDE MEGTAGWKLS NSSWNLQMIA RSPGSVTRFM PDDIPGVTSP  240
MVYIGMLFSW FAWHVEDHEL HSMNYLHTGS PKTWYAVPSD YALDFEEVIR KNSYGRNIDQ  300
LAALTQLGEK TTLVSPEMIV SSDIPCCRLV QNPGEFVVTF PRSYHVGFSH GFNCGEAANF  360
GTPQWLNVAK EAAVRRAAMN YLPMLSHQQL LYLLTMSFFV LIVIVPRSLL PGGRSSRLRD  420
RQREEREFLV KKAFVEDILN ENKNLSVLLG EPGSRLVMWD PDLLPRHSAL ALAAAGVATT  480
PAVSSPAEAK SEIENKEENP SLLEELSLFM EKLKDVYYDD DDGQLNDFQI DSGTLPCVAC  540
GVLGFPFMSV VQPSEDALKD LSERQGEIDA LENKAESSET SDCEWNTSSR YVRPRIFCLE  600
HTIELQRLLQ SRGGLKFLVI CHKDFQKFKA HAAIVAEEVK VPFRYDDVLL ESASKEELSL  660
IDLAIEGEEN NEHGADWTSK LGINLRYCVK VRKNSPTNKI QHALSLGGLF SDSSHVLDMS  720
TIKWLQRKSR SKAKPCSTSC FTPRELGEKG RKDHPVLEKE EVESQGGRKE EKIIQYSRKK  780
KLNPNSNRSR HDRGVDSEMN NEVGDSADLT SVTREHQGHS VTSNNLRGVD EAAEMSDQGF  840
KEARTTNANI EEEEQSQVVL PTNREAHSSA QVGFEVAETN IASEKIVAGM VRDDEPLASN  900
GDQASSSGLQ AADNENSTES EVASSGDTKV VVEAKKKRKI EIDSETNDYH PESSIGFIKS  960
PCEGLRSRGK RKVTCEETSF NLNEASDEKK KHTAKRLKKT PNTGSTTTQH NLCYLEGCKM  1020
TFKSKADLAA HKRNRCTHEG CGKKFRAHKY LVLHQRVHND DRPFVCPWKG CSMNFKWQWA  1080
RTEHLRLHTG ERPYKCKVEE CGLSFRFVSD YSRHRRKTGH YVT*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A1e-73113918346Transcription factor jumonji (Jmj) family protein
6ip4_A1e-73113918346Arabidopsis 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
PlantRegMapGSBRNA2T00072972001
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_013611724.10.0PREDICTED: probable lysine-specific demethylase ELF6
SwissprotQ6BDA00.0ELF6_ARATH; Probable lysine-specific demethylase ELF6
TrEMBLA0A078HXB20.0A0A078HXB2_BRANA; BnaCnng10240D protein
STRINGBo9g181310.10.0(Brassica oleracea)
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]