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 487204
Common NameARALYDRAFT_487204
Organism
Arabidopsis lyrata
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family C2H2
Protein Properties Length: 1337aa    MW: 149673 Da    PI: 6.8457
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
487204genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H2140.0001512481271223
               EET..TTTEEESSHHHHHHHHHHT CS
  zf-C2H2    2 kCp..dCgksFsrksnLkrHirtH 23  
               +C+   Cgk F+ + +L+ H+r+H
   487204 1248 RCTyeGCGKKFRAHKYLVLHQRVH 1271
               588889****************99 PP
2zf-C2H2110.001313071333123
               EEET..TTTEEESSHHHHHHHHHH..T CS
  zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
               ykC+   Cg sF+  s++ rH r+  H
   487204 1307 YKCKvdGCGLSFRFVSDYSRHRRKtlH 1333
               99*********************9777 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
PfamPF023757.3E-161750IPR003349JmjN domain
SMARTSM005584.0E-44262428IPR003347JmjC domain
PROSITE profilePS5118433.934262428IPR003347JmjC domain
SuperFamilySSF511972.36E-25264426No hitNo description
PfamPF023734.2E-37292411IPR003347JmjC domain
SMARTSM003557412241246IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.46412471276IPR007087Zinc finger, C2H2
SMARTSM003550.02312471271IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.603.3E-812481276IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028012491271IPR007087Zinc finger, C2H2
SuperFamilySSF576677.72E-1112631305No hitNo description
Gene3DG3DSA:3.30.160.601.0E-1012771301IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.003312771301IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.69512771306IPR007087Zinc finger, C2H2
PROSITE patternPS00028012791301IPR007087Zinc finger, C2H2
SuperFamilySSF576674.86E-912951330No hitNo description
Gene3DG3DSA:3.30.160.603.4E-1013021329IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS501579.86813071336IPR007087Zinc finger, C2H2
SMARTSM003550.113071333IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028013091333IPR007087Zinc 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: 1337 aa     Download sequence    Send to blast
MGNVEIPNWL KALPLAPVFR PTDTEFADPI AYISKIEKEA SAFGICKIIP PLPKPSKKYV  60
FYNLNKSLLK CPELVSDVDI SKVCKEDRAV FTTRQQELGQ TVKKTKGEKS KSNSQRSGVK  120
QVWQSGGVYT LEQFETKSRT FYKSQLGTIK EVSPVVVEAL FWKTASEKPI YIEYANDVPG  180
SAFGEPEGHF RHFRQRKRRG RGFYQRKTEI NDPSGKNGEN SSPEVEKAPL ASTSLSSQDS  240
SKQKNVDIVD EMEGTAGWKL SNSSWNLQTI ARSPGSVTRF MPDDIPGVTS PMVYIGMLFS  300
WFAWHVEDHE LHSMNYLHTG SPKTWYAVPC DYALDFEEII RKNSYGRNID QLAALTQLGE  360
KTTLVSPEMI VASGIPCCRL VQNPGEFVVT FPRSYHVGFS HGFNCGEAAN FGTPQWLNVA  420
KEAAVRRAAM NYLPMLSHQQ LLYLLTMSFV SRVPRSLLPG GRSSRLRDRQ REEREFLVKR  480
AFVEDILNEN KNLSVLLREP GSRLVTWDPD LLPRHNAVAL AAAAASAVLP PAVATNELEE  540
GHSELQNKEK TTLLEELSLF MEKLNDVYYD DDDGLLNDFQ VDSGTLPCVA CGVLGFPFMS  600
VVQPSEKALK DLPERQGDTD AQEITTLSSE KSDCEWKTSS RYIRPHIFCL EHTIELQRLL  660
QPRGGLKFLV ICHKDFQKFK AHAAIVAEEV KVPFRYDDVL LESASQEELS LIDLAIEDEE  720
NYEHGVDWTS ELGINLRYCV KVRKNSPTKK IQHALSLGGL FSDTSQMLDI STMRWLQRKS  780
RSKAKPISTS SFTPREHLEV KADGKLRDNM DSQAGKKEEK IIQYSRKKKL NPKPSAEHGQ  840
ELATLAKSKD FDKTCNKFTN RSHLDSAIRS EMNSEIGDSG RVIGVSFSIN PCSSSFTVGH  900
GQEHPEITVK FGSALDGNVT NSSSMGNTDS ADLTLTSISR EHQGHSLTSN NNGSNSGSHV  960
VASQTILVST DNNHGGPRKL SGDYVCSDVF VRGIQEAVEM SDQEFGEPRS TVTNIEDEQQ  1020
SKLVQPTKRE AVSGDHAQVE GAEAVCTIEN LCSEIILHTE HSSAQVGMEI PEINTASENI  1080
VVDMTHDGEP LESSDILSSS NGDQASSNGL QVLDDELSME SEVSSSENTE VIEAPNSMEE  1140
AKKKRKIESE CETNDNLERS IGFIRSPCEG LRSRGKRKET CETSLKPTET SDEERKPIAK  1200
RLKKTPKACS GSCHQEVPAT THPNRCYLEG CKMTFESKAK LQAHKRNRCT YEGCGKKFRA  1260
HKYLVLHQRV HNDERPFECS WKGCSMTFKW QWARTEHLRL HTGERPYKCK VDGCGLSFRF  1320
VSDYSRHRRK TLHYVT*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A2e-55242442137346Transcription factor jumonji (Jmj) family protein
6ip4_A2e-55242442137346Arabidopsis JMJ13
Search in ModeBase
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
PlantRegMap487204
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_002871082.10.0probable lysine-specific demethylase ELF6 isoform X2
SwissprotQ6BDA00.0ELF6_ARATH; Probable lysine-specific demethylase ELF6
TrEMBLD7LXG80.0D7LXG8_ARALL; Uncharacterized protein
STRINGfgenesh2_kg.6__338__AT5G04240.10.0(Arabidopsis lyrata)
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]