PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID PGSC0003DMP400026608
Common NameLOC102605874
Organism
Solanum tuberosum
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
Family C2H2
Protein Properties Length: 1252aa    MW: 139365 Da    PI: 9.1029
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
PGSC0003DMP400026608genomePGSCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H211.30.001111351160123
                            EEET..TTTEEESSHHHHHHHHHH.T CS
               zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                            y C    C++sFs+k +L+ H ++ +
  PGSC0003DMP400026608 1135 YHCDleGCSMSFSSKQELTLHKKNvC 1160
                            889999***************99866 PP
2zf-C2H2110.001411591182223
                            EET..TTTEEESSHHHHHHHHHHT CS
               zf-C2H2    2 kCp..dCgksFsrksnLkrHirtH 23  
                            +Cp   C+k F ++ +L++H r+H
  PGSC0003DMP400026608 1159 VCPveGCKKKFFSHKYLVQHRRVH 1182
                            69999*****************99 PP
3zf-C2H210.80.001512181244123
                            EEET..TTTEEESSHHHHHHHHHH..T CS
               zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                            y C+   Cg++F+  s++ rH r+  H
  PGSC0003DMP400026608 1218 YACTetGCGQTFRFVSDFSRHKRKtgH 1244
                            889999****************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005451.7E-151960IPR003349JmjN domain
PROSITE profilePS5118314.772061IPR003349JmjN domain
PfamPF023752.1E-152154IPR003349JmjN domain
SMARTSM005584.3E-48184353IPR003347JmjC domain
PROSITE profilePS5118432.071187353IPR003347JmjC domain
SuperFamilySSF511971.4E-24198367No hitNo description
PfamPF023732.3E-36217336IPR003347JmjC domain
SMARTSM003558.611351157IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.604.3E-511581186IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.57211581187IPR007087Zinc finger, C2H2
SMARTSM003550.01211581182IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028011601182IPR007087Zinc finger, C2H2
SuperFamilySSF576671.43E-911741216No hitNo description
Gene3DG3DSA:3.30.160.603.0E-811871212IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.74111881217IPR007087Zinc finger, C2H2
SMARTSM003550.001411881212IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028011901212IPR007087Zinc finger, C2H2
SuperFamilySSF576677.38E-812061240No hitNo description
Gene3DG3DSA:3.30.160.606.3E-912131240IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.15712181249IPR007087Zinc finger, C2H2
SMARTSM003550.3612181244IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012201244IPR007087Zinc 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: 1252 aa     Download sequence    Send to blast
MAEASGNIEV FSWLKTLPVA PEYHPTLEEF QDPIAYIFKI EKEASKYGIC KIVPPVPEPP  60
KKTALANLNR SLSARAGSNG PTFTTRQQQI GFCPRKHRPV KKPVWQSGET YTVQQFQAKA  120
KAFEKNYLRK NSKRALTPLE VETLYWKATV DKPFSVEYAN DMPGSAFAPK KASLAAGGIG  180
EVSTLADTEW NMRGVSRSKG SLLKFMKEEI PGVTSPMVYL AMMFSWFAWH VEDHDLHSLN  240
YLHMGSGKTW YGVPRDAAVA FEEVIRVQGY AGETNPLVTF ATLGEKTTVM SPEVLLSAGI  300
PCCRLVQNAG EFVVTFPQAY HSGFSHGFNC GEASNIATPE WLRVAKDAAI RRASTNCPPM  360
VSHFQLLYDL ALSLCSRVPK NIRIEPRSSR LKDKKKSEGD MLVKELFVED LNSNNYLLHI  420
LGEGSPVVLL PQNSTGISIC SNLVAGSQSK VNSRLFPSSS SSDHEVKSKK GSAYDDLKLG  480
RKQGMEQFAG ISLEKGKYSS WHTGNRLPDS GRKDDAQSSP DTERVNLDTA RGMTYKCDTL  540
SEQGLFSCAT CGILCYTCVA IIRPTEVAAH HLMSSDYSNF NDWTGSVSGV TATGRDPNAA  600
ESDSSSGRFV KRAPALIDVP VESSDRIQKL NNGSVEGFSR TKAHKETSSL GLLALAYANS  660
SDSDEDEVEA DIPVEACESR HTDSEDEVFL RVIDPYGNHR QKRAVSQGRN CQKTDNSVQL  720
ENESYPSGES NTLLGRSSHQ PRSHQVAAKC ISNIGEIVQN NAVAPFDHAR MQFTSTSDED  780
SFRIHVFCLQ HAVQVEEQLR RIGGARISLL CHPDYPKLEA QAKQVAEELG SDHFWREISF  840
REATKDDEEM IQSALEIEEA IHGNGDWTVK LDINLFYSAN LSRSPLYSKQ MPYNFIIYNA  900
FGRNSPDNTP EKSEYTGRGS GKQRRAIVAG KWCGKVWMSS QVHPLLAERT IDEEQEQNKS  960
ISAQIKIEVK SERPRERTPT GKTVSTACKT GKKRSSTAVS RNASNAQLII ADDHDDSLLS  1020
SILQQHRKTN LRSKRIKYET PEPQKDVDKK KIFGSIIDDD PDGGPSTRLR KRIPKPSNES  1080
PAKLVKVKPA PTKQHESKKG PKVKLPSANS NAKKEPVTKG PRSNIGKRMR EEGEYHCDLE  1140
GCSMSFSSKQ ELTLHKKNVC PVEGCKKKFF SHKYLVQHRR VHMDDRPLKC PWKGCKMTFK  1200
WAWARTEHIR VHTGARPYAC TETGCGQTFR FVSDFSRHKR KTGHVSKKGR S*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A8e-72134418413Transcription factor jumonji (Jmj) family protein
6ip4_A8e-72134418413Arabidopsis JMJ13
Search in ModeBase
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
PlantRegMapPGSC0003DMP400026608
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankHG9754420.0HG975442.1 Solanum pennellii chromosome ch03, complete genome.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006351452.10.0PREDICTED: lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLM1B7Y20.0M1B7Y2_SOLTU; Uncharacterized protein
STRINGPGSC0003DMT4000392240.0(Solanum tuberosum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA49882331
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. Xu X, et al.
    Genome sequence and analysis of the tuber crop potato.
    Nature, 2011. 475(7355): p. 189-95
    [PMID:21743474]
  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]