PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Cagra.9217s0004.1.p
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella
Family C2H2
Protein Properties Length: 1309aa    MW: 146660 Da    PI: 7.2305
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cagra.9217s0004.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H212.90.0003312201243223
                           EET..TTTEEESSHHHHHHHHHHT CS
              zf-C2H2    2 kCp..dCgksFsrksnLkrHirtH 23  
                           +C+   Cgk F+ + +L+ H+r+H
  Cagra.9217s0004.1.p 1220 RCTheGCGKKFRAHKYLVLHQRVH 1243
                           588889****************99 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005451.9E-151555IPR003349JmjN domain
PROSITE profilePS5118314.161657IPR003349JmjN domain
PfamPF023757.2E-161750IPR003349JmjN domain
PROSITE profilePS5118433.22259425IPR003347JmjC domain
SMARTSM005584.1E-43259425IPR003347JmjC domain
SuperFamilySSF511973.84E-25262423No hitNo description
PfamPF023735.5E-37289408IPR003347JmjC domain
SMARTSM003557311961218IPR015880Zinc finger, C2H2-like
SMARTSM003550.05712191243IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.02712191248IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.606.6E-712201248IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028012211243IPR007087Zinc finger, C2H2
SuperFamilySSF576671.61E-1012351277No hitNo description
Gene3DG3DSA:3.30.160.601.9E-1012491273IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.003512491273IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.69512491278IPR007087Zinc finger, C2H2
PROSITE patternPS00028012511273IPR007087Zinc finger, C2H2
SuperFamilySSF576671.59E-812671301No hitNo description
Gene3DG3DSA:3.30.160.607.9E-1012741302IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003551.112791305IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012811305IPR007087Zinc 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: 1309 aa     Download sequence    Send to blast
MGSVEIPNWL KALPLAPVFR PTDTEFADPI AYISKIEKEA SAFGICKIIP PLPKPSKKYV  60
FHNLNKSLLK CPELVSDVDI SREDRAVFTT RQQELGQTVK KTKGEKSKSI SQRTGVKQVW  120
QSGGVYTLEQ FEAKSKTFYK SQLGTVKEVS PVVVEALFWK AASQKPIYIE YANDVPGSAF  180
GEPEGHFRHF RQRKRRGRGF YQRKTEINDP SDKIGENSSP EVEKAPLAST SLSPQDSSKQ  240
KNTDIVDEME GTAGWKLSNS SWNLQTIARS PGSVTRFMPD DIPGVTSPMV YIGMLFSWFA  300
WHVEDHELHS MNYLHTGSPK TWYAVPCDYA LEFEEVIRKN SYGKNIDQLA ALTQLGEKTT  360
LVSPEMIVAS GIPCCRLVQN HGEFVVTFPR SYHVGFSHGF NCGEAANFGT PQWLNVAKEA  420
AVRRAAMNYL PMLSHQQLLY LLTMSFVSRV PRSFLPGGRS SRLRDRQREE REFLVKKAFV  480
EDILNENKNL SVLLREPGSR LVMWDPDLLP RHSALALAAV GGAATSAVLP PSVATNIPEE  540
GHSELQNKEK TTLLEELSLF MEKLNDVYYD DDDGLLNDFQ VDSGTLPCVA CGVLGFPFMS  600
VVQPSEKALK DLLEGQGKID AQEIMTLSSE KSHCEWKTSS RYIRPRIFCL EHTIELQRLL  660
QSKGGMKFLI ICHKDFQKFK AHAATVAEEV KVPFSYDDVL LEGASQEELS LIDLAIEDEE  720
NYKHAIDWTS ELGINLRYCV KVRKNSSTKK IQHALSLGGL FSDRSHMLDF STIRWLQRKS  780
RSKAKPSSTS SFTHREQLQV KVDGKLGENL DSQTEKKEKK IIQYSRKKKL NSKPSVEQGQ  840
DLAPLAESRE FGKTCNKLAN MSHLDSSIRF DGAHDQEHPE ITIKFGSALD GNVTNSVSMV  900
NGYSADLSSV SREQQGHSMT SNNNGSNAGS HVVASQTVLI STGDNHVRPR KFSGDYVCSD  960
VSVRDLQEVV EMSDQEFGGP RSTVTNIEDE QQSQMVQPTK REAVSGDHGQ MEGAEAVCTR  1020
EILCSDIILQ TEHSSAQVGM EIPEINTASE NMVVDMTHDG EPLESSDILS SSNGDQASSN  1080
GLQVPDDELS MESEVSSSEN TEVIEAPNST GEAKKKMKID SVFETNDNLE SSIGFIRSPC  1140
EGLRSRGKRK SRSETWLKLT ETSGEAKRPI AKRGKKTPKA RSGSLQQEDP TTTHPNRCYL  1200
EGCKMTFDSK AKLQTHKRNR CTHEGCGKKF RAHKYLVLHQ RVHNDDRPFE CSWEGCSMTF  1260
KWQWARTEHL RLHTGERPYK CKVEGCELSF RFVSDYSRHR RKTGHYVA*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A5e-5494398346Transcription factor jumonji (Jmj) family protein
6ip4_A5e-5494398346Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1815829KKEKKIIQYSRKKKL
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
PlantRegMapCagra.9217s0004.1.p
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_006286906.10.0probable lysine-specific demethylase ELF6
SwissprotQ6BDA00.0ELF6_ARATH; Probable lysine-specific demethylase ELF6
TrEMBLR0GSE70.0R0GSE7_9BRAS; Uncharacterized protein
STRINGCagra.9217s0004.1.p0.0(Capsella grandiflora)
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. Crevillén P, et al.
    Epigenetic reprogramming that prevents transgenerational inheritance of the vernalized state.
    Nature, 2014. 515(7528): p. 587-90
    [PMID:25219852]
  4. 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]