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 Solyc03g111590.2.1
Common NameLOC101257458
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: 1253aa    MW: 139814 Da    PI: 9.1879
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc03g111590.2.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H211.30.001111361161123
                          EEET..TTTEEESSHHHHHHHHHH.T CS
             zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                          y C    C++sFs+k +L+ H ++ +
  Solyc03g111590.2.1 1136 YHCDleGCSMSFSSKQELTLHKKNvC 1161
                          889999***************99866 PP

2zf-C2H2110.001411601183223
                          EET..TTTEEESSHHHHHHHHHHT CS
             zf-C2H2    2 kCp..dCgksFsrksnLkrHirtH 23  
                          +Cp   C+k F ++ +L++H r+H
  Solyc03g111590.2.1 1160 VCPveGCKKKFFSHKYLVQHRRVH 1183
                          69999*****************99 PP

3zf-C2H211.10.001312191245123
                          EEET..TTTEEESSHHHHHHHHHH..T CS
             zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                          y C+   Cg++F+  s++ rH r+  H
  Solyc03g111590.2.1 1219 YACSeiGCGQTFRFVSDFSRHKRKtgH 1245
                          889999****************99666 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005453.6E-161960IPR003349JmjN domain
PROSITE profilePS5118314.9912061IPR003349JmjN domain
PfamPF023752.1E-152154IPR003349JmjN domain
SMARTSM005585.8E-49184353IPR003347JmjC domain
PROSITE profilePS5118432.372187353IPR003347JmjC domain
SuperFamilySSF511978.79E-25199351No hitNo description
PfamPF023731.9E-36217336IPR003347JmjC domain
SMARTSM003558.611361158IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.57211591188IPR007087Zinc finger, C2H2
SMARTSM003550.01211591183IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.604.3E-511591187IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028011611183IPR007087Zinc finger, C2H2
SuperFamilySSF576671.39E-911751217No hitNo description
Gene3DG3DSA:3.30.160.603.0E-811881213IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.74111891218IPR007087Zinc finger, C2H2
SMARTSM003550.001411891213IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028011911213IPR007087Zinc finger, C2H2
SuperFamilySSF576673.56E-712071241No hitNo description
Gene3DG3DSA:3.30.160.602.7E-812141241IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.07412191250IPR007087Zinc finger, C2H2
SMARTSM003550.4812191245IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012211245IPR007087Zinc 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:0010228Biological Processvegetative to reproductive phase transition of meristem
GO:0033169Biological Processhistone H3-K9 demethylation
GO:0035067Biological Processnegative regulation of histone acetylation
GO:0048366Biological Processleaf development
GO:0005634Cellular Componentnucleus
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 1253 aa     Download sequence    Send to blast
MAEASGNIEV FSWLKTLPVA PEYHPTLEEF QDPIAYIFKI EKEASKYGIC KIVPPVPAPP  60
KKTALANLNR SLSARAGSNG PTFTTRQQQI GFCPRKHRPV KKPVWQSGET YTVQQFQVKA  120
KAFEKNYLRK NSKRALTPLE VETLYWKATV DKPFSVEYAN DMPGSAFAPK KASLAAGGIG  180
EVSTLADTEW NMRGVSRSKG SLLKFMKEEI PGVTSPMVYL AMMFSWFAWH VEDHDLHSLN  240
YLHMGSGKTW YGVPRDAAVA FEEVIRVQGY AGETNPLVTF ATLGEKTTVM SPEVLLSAGI  300
PCCRLVQNAG EFVVTFPRAY HSGFSHGFNC GEASNIATPE WLRVAKDAAI RRASINCPPM  360
VSHFQLLYDL ALSLCSRVPK NIRIEPRSSR LKDKKKSEGD MLVKELFVED LNANNYLLHI  420
LGEGSPVVLL PQNSPGISIC SNLVAGSQSK VNSRLFPSSS NSDHEVKSKK DSAYDDRKLG  480
RKQGMKQYAG ISLEKGKYSS WHTGNSLPDS GRKDDAQSSP ETEKVNLDAA RGMTYKCDTL  540
SEQGLFSCAT CGILCYTCVA IIRPTEAAAR HLMSSDYSDF NGWTGSVSGI TATGRDPNAA  600
ESDSSSGRFV KRAPALIDDP VESSDRIQKL NNGSVEELSR TNTRKETSSL GLLALAYANS  660
SDSDEDEIEV DIPVEACESR HTESEDEVFL RVIDPYGNHR QKRAVSQGRN CQKFDNSVQL  720
ENESYPSGES NTLFGRSSHQ PRSHQVPAKC ISNIREIAQN NAVAPFDNAR MQFTSTSDED  780
SFRIHVFCLQ HAVQVEEQLR RIGGAHISLL CHPDYPKLEA QAKQVAEELG SDHFWREISF  840
REASKEDEEM IQSALEIEEA IHGNGDWTVK LDINLFYSAN LSRSPLYSKQ MPYNFIIYNA  900
FGRDSPDNTP EKSEYTGRGL GKQRRAIVAG KWCGKVWMSS QVHPLLAERT IDEEQEQNKS  960
ISALIKIEVK SERPRERTPT SKTVATTCKT GKKRSSTAAS RNASNAQLII ADDHDDSLLS  1020
SILQQHRRKT NLRSKRIKYE TPEPQKDVDK KKIFGSLIDD DPDGGPSTRL RKRIPKPSNE  1080
SPAKSVKAKP APTKQHESKK GPKVKLPFAN SIAKKEPVTK GPRSNIGKRM REEGEYHCDL  1140
EGCSMSFSSK QELTLHKKNV CPVEGCKKKF FSHKYLVQHR RVHMDDRPLK CPWKGCKMTF  1200
KWAWARTEHI RVHTGARPYA CSEIGCGQTF RFVSDFSRHK RKTGHISKKG RS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A3e-73133868366Transcription factor jumonji (Jmj) family protein
6ip4_A3e-73133868366Arabidopsis JMJ13
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Highly expressed in the shoot apical meristem and primary and secondary root tips, and lower expression in cotyledons, leaves and root axis along vascular tissues. Detected in inflorescences, stems and siliques. {ECO:0000269|PubMed:15377760, ECO:0000269|PubMed:18713399}.
Functional Description ? help Back to Top
Source Description
UniProtHistone demethylase that demethylates 'Lys-27' (H3K27me) of histone H3. Demethylates both tri- (H3K27me3) and di-methylated (H3K27me2) H3K27me (PubMed:21642989, PubMed:27111035). Demethylates also H3K4me3/2 and H3K36me3/2 in an in vitro assay (PubMed:20711170). Involved in the transcriptional regulation of hundreds of genes regulating developmental patterning and responses to various stimuli (PubMed:18467490). Binds DNA via its four zinc fingers in a sequence-specific manner, 5'-CTCTGYTY-3', to promote the demethylation of H3K27me3 and the regulation of organ boundary formation (PubMed:27111034, PubMed:27111035). Involved in the regulation of flowering time by repressing FLOWERING LOCUS C (FLC) expression (PubMed:15377760). Interacts with the NF-Y complexe to regulate SOC1 (PubMed:25105952). Mediates the recruitment of BRM to its target loci (PubMed:27111034). {ECO:0000269|PubMed:15377760, ECO:0000269|PubMed:18467490, ECO:0000269|PubMed:20711170, ECO:0000269|PubMed:21642989, ECO:0000269|PubMed:25105952, ECO:0000269|PubMed:27111034, ECO:0000269|PubMed:27111035}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00608ChIP-seqTransfer from AT3G48430Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapSolyc03g111590.2.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2385630.0Solanum lycopersicum chromosome 3 clone C03HBa0049N20, complete sequence
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004236313.10.0lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A3Q7FPK70.0A0A3Q7FPK7_SOLLC; Uncharacterized protein
STRINGSolyc03g111590.2.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA49882331
Representative plantOGRP44011217
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G48430.10.0relative of early flowering 6
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. Li C, et al.
    Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis.
    Nat. Genet., 2016. 48(6): p. 687-93
    [PMID:27111034]
  3. Cui X, et al.
    REF6 recognizes a specific DNA sequence to demethylate H3K27me3 and regulate organ boundary formation in Arabidopsis.
    Nat. Genet., 2016. 48(6): p. 694-9
    [PMID:27111035]
  4. Hyun Y, et al.
    Multi-layered Regulation of SPL15 and Cooperation with SOC1 Integrate Endogenous Flowering Pathways at the Arabidopsis Shoot Meristem.
    Dev. Cell, 2016. 37(3): p. 254-66
    [PMID:27134142]
  5. Cheng JZ,Zhou YP,Lv TX,Xie CP,Tian CE
    Research progress on the autonomous flowering time pathway in Arabidopsis.
    Physiol Mol Biol Plants, 2017. 23(3): p. 477-485
    [PMID:28878488]
  6. Li C, et al.
    Verification of DNA motifs in Arabidopsis using CRISPR/Cas9-mediated mutagenesis.
    Plant Biotechnol. J., 2018. 16(8): p. 1446-1451
    [PMID:29331085]
  7. Wang X, et al.
    The H3K27me3 demethylase REF6 promotes leaf senescence through directly activating major senescence regulatory and functional genes in Arabidopsis.
    PLoS Genet., 2019. 15(4): p. e1008068
    [PMID:30969965]
  8. Qiu Q, et al.
    DNA methylation repels targeting of Arabidopsis REF6.
    Nat Commun, 2019. 10(1): p. 2063
    [PMID:31048693]