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 Solyc04g028560.2.1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon
Family C2H2
Protein Properties Length: 778aa    MW: 87641.4 Da    PI: 7.406
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc04g028560.2.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H211.50.00093686709223
                         EET..TTTEEESSHHHHHHHHHHT CS
             zf-C2H2   2 kCp..dCgksFsrksnLkrHirtH 23 
                         +Cp   C k F+++ + ++H+r+H
  Solyc04g028560.2.1 686 RCPveGCEKKFTSHKYAVVHQRVH 709
                         69999*****************99 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM0035517662684IPR015880Zinc finger, C2H2-like
SMARTSM003550.082685709IPR015880Zinc finger, C2H2-like
SuperFamilySSF576672.27E-5685722No hitNo description
PROSITE profilePS5015711.323685714IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.7E-5685713IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS000280687709IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.602.6E-9714739IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.0057715739IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.365715744IPR007087Zinc finger, C2H2
PROSITE patternPS000280717739IPR007087Zinc finger, C2H2
SuperFamilySSF576676.17E-10725767No hitNo description
Gene3DG3DSA:3.30.160.604.2E-10740768IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.6745771IPR015880Zinc finger, C2H2-like
PROSITE profilePS501579.037745776IPR007087Zinc finger, C2H2
PROSITE patternPS000280747771IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0045814Biological Processnegative regulation of gene expression, epigenetic
GO:0048579Biological Processnegative regulation of long-day photoperiodism, flowering
GO:0003676Molecular Functionnucleic acid binding
GO:0032452Molecular Functionhistone demethylase activity
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 778 aa     Download sequence    Send to blast
MSNNCYSHVW EVLQIYQNDW TCLWNTEFPL HAVDRIQRNG VHSLNHDEVP LYAQPSESAV  60
SPHEGQTSQS HHLSHTDNAA PTSKVDLEEE CDVSRGLVRP QIFCLEHAIQ TEELLHSKGG  120
ANVLVICHSD FQKIRGHAAV VAEEIGTAFK YNEIPLANAS QGHLSLIDLA IGQEEQNKCA  180
EDWTLKLNIN LRHCVKVQRN CPLKKLKHAL ILGGLFSDTT HSSDSLSLLK WRSRKVRSKR  240
KLNHSTESTL FANVQIAKVV SGSTVDMQNV RKGNITIQYS RKKYKPKDCS SAQISRVFMD  300
PFNVPKEVSL ADAKILGSTR RLRDENAGTA SLEERFFNSS DGKPRLRYEH EMLLQNKDRN  360
GDLLAPQEQN LLVTPSLMVE FDEAQAELCT TEKFSLKDKT CDTNSNSCHT ENKTMAAETS  420
GETDIAHVHT PACTSIYVVQ STAYNENLEE NDMTETVIRD KSDHPTEEDF ERYHHSGDDK  480
AIMTRSPMPV NSSGSCIDGP SRSCDKKIED QDSQQFGLGG ETSDGETLLK SMEQEIQIHN  540
SVKDIVVCDH VTSSTKHSQS GDDISEQHTK ESNNDTTSAV LLWPTGKNGG CELDLLTDYG  600
CSVSGFVRSP CEGLRPRVKK NVRGSRVESK EFLEKKPIGN KVKRSLYSSI IPKDKKEEKG  660
SHRCNLEGCW MSFQTKVELQ LHKQNRCPVE GCEKKFTSHK YAVVHQRVHK NDRPLKCPWK  720
GCTMTFKWAW ARTEHFRVHT GERPYKCKVE GCGLTFRFVS GYSRHRRKTG HYVDAAN*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A4e-5166077721138Lysine-specific demethylase REF6
6a58_A4e-5166077721138Lysine-specific demethylase REF6
6a59_A4e-5166077721138Lysine-specific demethylase REF6
Search in ModeBase
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
PlantRegMapSolyc04g028560.2.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_010319604.10.0probable lysine-specific demethylase ELF6
SwissprotQ6BDA02e-57ELF6_ARATH; Probable lysine-specific demethylase ELF6
TrEMBLA0A3Q7GUK70.0A0A3Q7GUK7_SOLLC; Uncharacterized protein
STRINGSolyc04g028560.2.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA48351721
Representative plantOGRP1198156
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G04240.17e-60C2H2 family protein
Publications ? help Back to Top
  1. Wang Y,van der Hoeven RS,Nielsen R,Mueller LA,Tanksley SD
    Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments.
    Theor. Appl. Genet., 2005. 112(1): p. 72-84
    [PMID:16208505]
  2. 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]
  3. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  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]