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 mrna23255.1-v1.0-hybrid
Organism
Fragaria vesca
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Rosoideae; Potentilleae; Fragariinae; Fragaria
Family C2H2
Protein Properties Length: 1609aa    MW: 178488 Da    PI: 6.3622
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
mrna23255.1-v1.0-hybridgenomeGDRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H211.30.001115791605123
                               EEET..TTTEEESSHHHHHHHHHH..T CS
                  zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                               ykC+   Cg sF+  s++ rH r+  H
  mrna23255.1-v1.0-hybrid 1579 YKCKvdGCGLSFRFVSDFSRHRRKtgH 1605
                               99*********************9777 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005453.0E-151556IPR003349JmjN domain
PROSITE profilePS5118313.9381657IPR003349JmjN domain
PfamPF023751.4E-141750IPR003349JmjN domain
SMARTSM005585.4E-40295482IPR003347JmjC domain
SuperFamilySSF511971.02E-24297375No hitNo description
PROSITE profilePS5118432.198298482IPR003347JmjC domain
PfamPF023732.0E-31328465IPR003347JmjC domain
SuperFamilySSF511971.02E-24414479No hitNo description
SMARTSM003553514961518IPR015880Zinc finger, C2H2-like
SMARTSM003556.715191543IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.03215191548IPR007087Zinc finger, C2H2
SuperFamilySSF576677.25E-515201552No hitNo description
Gene3DG3DSA:3.30.160.601.2E-415201548IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028015211543IPR007087Zinc finger, C2H2
SuperFamilySSF576678.48E-1115471601No hitNo description
PROSITE profilePS5015712.75715491578IPR007087Zinc finger, C2H2
SMARTSM003555.4E-415491573IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.602.4E-1115491573IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028015511573IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.604.2E-1115741602IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.1915791605IPR015880Zinc finger, C2H2-like
PROSITE profilePS501579.6415791608IPR007087Zinc finger, C2H2
PROSITE patternPS00028015811605IPR007087Zinc 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: 1609 aa     Download sequence    Send to blast
MGDVKIPNWI EGLPLAPEFY PTHTEFADPI AYISKIEKEA SEFGICKIIP PLPRPSKRYV  60
FNNLNKSLAR RPELGCDLVP GSDGAVTKMG AADGSNDGEV RAVFTTRHQE LGQSVQRGKE  120
PTVQDLTSSG VAKQVWQSGE VYTLEQFESK ARTFARSILG TIRDVSPLVI EAMFWKAASE  180
KPIYIEYAND VPGSAFEEPE GVLFYSRRRR RKRNSYHRSG PNSDSKKSEV IRSCEKNSQN  240
GEVEEATPKN VSPTCLEVPK SSASPGIVST DETSQSSRKR SQNSSCDMEG TAGWMLSNSP  300
WNLQVIARSP GSLTRFMPDD IPGVTSPMVY IGMLFSWFAW HVEDHELHSM NFLHNGSAKT  360
WYSVPGNYAF AFEELIRTEA YGGTADRLVV NGSTNMFRMV QFLFLAAALS LLGNKTTLMS  420
PEVVIASGIP CCRLIQNPGE FVVTFPRAYH VGFSHGFNCG EAANFGTPQW LKVAKEAAVR  480
RAAMNYLPML SHQQLLYLST MSFISRVPRA LLPGVRSSRM RDRQKEDREL SVKKAFIEDI  540
LNENDVLSAL LGKESSCRAV LWNPDLLPYT SKESPIPTAG APVDTNSKEN ATDTQGGKST  600
NDQNSLVDEM SLYMENLNDL YLGSDDLSSD FQVDSGTLAC VACGILGFPF MSVMQPSEKA  660
STELQPEYIL SEELPGNSHF SPELHEAFKD SATEILSPIS NPCTTRFDNH WNIVNKFLRP  720
RSFCLEHAVE TLELLQCKGG ANMLVICHSD YQKIKAPAGA IAEEIGCPFN YKEVPLDTAS  780
KEDLNLIDLA VDDGRDECGE DWTSKLGINL RYCVKVRKSS SSKRVQHALA LGGALSTQSC  840
SAEFLTVDWK SRRSRTKKVY LDATYKQCQT IEKKKEEVVE AKSAAAASFK SEATIIQYSR  900
RNKRRPSTST GAGRVVEQPA TSEEFDKHGR RASDSSTHNN GKSTSLCARL DSYASKSMSE  960
VHPDVQMLEA TRDICLNSLP QVADRVALTA GSADKQIENH SLEERQMNSR GSSLAASESD  1020
MQHEIKILEE ARVNDPITPL AIACDERSEN REKQENRKLN KNDGNCNLVS ERQSQLWAEE  1080
DVLMDVGPVF TELTNVCTAD SIVTSSEEQM GNAVIDKSCV NSEICESITT ATDRSNNKAP  1140
ASYNSTLVSD PTSAASEGHV EFERETCIAE DFSNVVSSEF KPEEDIEIPQ GRNEDSSFSH  1200
ARRIRQPSPA CTDRLSGVPS TICAEADFHR GPTSHIQEFQ AADRSSEGEY ISTSVIQMEE  1260
THPSISLEES PEVPMGSSLE EGTSNGVILA TVVQQDAQTT NKAVEAPSQN FVIRVKNHPI  1320
PVYVEDDVPR VSCATEATLD DKEQWTNSYS NKELIASHDT SKCELSRVTI KTYFRVKRGS  1380
RAAEKLCNGS EDCISQPERE TGNIEPSLVD HRPGPETGSK RKRGLEQKMD DNFNINGYIR  1440
GPCEGLRRRA GKGVTVSEID IHDEVEEKPV AKKVKRPSDA SVHLKDKKKE QVKKTHSCNL  1500
GSCSMSFHTK EELMVHKRNR CPHEGCGKKF SCHKYAMVHS RVHENARPFK CPWKGCSMSF  1560
KWAWAQTEHI RVHTGEKPYK CKVDGCGLSF RFVSDFSRHR RKTGHYVS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A5e-56285496144346Transcription factor jumonji (Jmj) family protein
6ip4_A5e-56285496144346Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1206212RRRRRKR
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
PlantRegMapmrna23255.1-v1.0-hybrid
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAM4792524e-86AM479252.2 Vitis vinifera contig VV78X066822.6, whole genome shotgun sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004307375.10.0PREDICTED: probable lysine-specific demethylase ELF6
SwissprotQ6BDA00.0ELF6_ARATH; Probable lysine-specific demethylase ELF6
TrEMBLA0A2P6SJB80.0A0A2P6SJB8_ROSCH; Putative [histone H3]-lysine-36 demethylase
STRINGXP_004307375.10.0(Fragaria vesca)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF80313034
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]