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 Itr_sc001303.1_g00003.1
Organism
Ipomoea trifida
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea
Family C2H2
Protein Properties Length: 1338aa    MW: 146920 Da    PI: 8.9616
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Itr_sc001303.1_g00003.1genomeKazusaView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H213.20.0002612501272323
                               ET..TTTEEESSHHHHHHHHHHT CS
                  zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                               Cp   Cgk F ++ +L++H r+H
  Itr_sc001303.1_g00003.1 1250 CPvkGCGKKFFSHKYLVQHRRVH 1272
                               9999*****************99 PP
2zf-C2H2120.0006413081334123
                               EEET..TTTEEESSHHHHHHHHHH..T CS
                  zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                               y+C    Cg++F+  s++ rH r+  H
  Itr_sc001303.1_g00003.1 1308 YVCAepGCGQTFRFVSDFSRHKRKtgH 1334
                               899999****************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005451.1E-161960IPR003349JmjN domain
PROSITE profilePS5118314.8252061IPR003349JmjN domain
PfamPF023759.8E-152154IPR003349JmjN domain
PROSITE profilePS5118429.684180393IPR003347JmjC domain
SMARTSM005582.4E-40180393IPR003347JmjC domain
SuperFamilySSF511974.39E-22195260No hitNo description
PfamPF023731.8E-14213264IPR003347JmjC domain
SuperFamilySSF511974.39E-22307411No hitNo description
PfamPF023738.9E-16320376IPR003347JmjC domain
SMARTSM003552512251247IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.44512481277IPR007087Zinc finger, C2H2
SMARTSM003550.004512481272IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.0E-512491276IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028012501272IPR007087Zinc finger, C2H2
SuperFamilySSF576671.62E-912641306No hitNo description
Gene3DG3DSA:3.30.160.603.1E-812771302IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.74112781307IPR007087Zinc finger, C2H2
SMARTSM003550.001412781302IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012801302IPR007087Zinc finger, C2H2
SuperFamilySSF576673.14E-812961330No hitNo description
Gene3DG3DSA:3.30.160.602.0E-913031331IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.38513081338IPR007087Zinc finger, C2H2
SMARTSM003550.6213081334IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028013101334IPR007087Zinc 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:0040010Biological Processpositive regulation of growth rate
GO:0045815Biological Processpositive regulation of gene expression, epigenetic
GO:0048366Biological Processleaf development
GO:0005634Cellular Componentnucleus
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
GO:0071558Molecular Functionhistone demethylase activity (H3-K27 specific)
Sequence ? help Back to Top
Protein Sequence    Length: 1338 aa     Download sequence    Send to blast
MGEGSSGVEV LSWLKTLPVA PEYHPTLEEF QDPIAYIFKI EGEASKYGIC KIVPPVGMPP  60
KKTAIANLNK SLAARPHSTF TTRQQQIGFC PRRHRPVQKP VWQSGENYTL QQFEAKAKGF  120
EKNYLKKGSK KGLLPLEVES LYWKATVDKP FSVEYANDIP GSAFAPKKAD SVGAVGEGAT  180
VAETEWNMRG VSRARGSLLK FMKEEIPGVT SPMVYIAMMF SWFAWHVEDH DLHSLNYLHM  240
GAGKTWYGVP RDAAVAFEEV IRLQGYGGEI NPLGSIPLLC VHSDDAELGF PKVQIASLLL  300
AMTYFAASDL PPNVRLGVTF ATLGEKTTVM SPEVLLNAGV PCCRLVQDVG EFVVTFPRAY  360
HSGFSHGFNC GEASNIATPG WLRVAKDAAI RRASINCPPM VSHFQLLYDL ALSFCSSDPG  420
LCTPSQNAAC SIFNLLFEKM MSKNIRTEPR SSRLKDKKKD EGEALVKDFF VQDLEQNNSL  480
LHMLGRGSSV ILLPRNSTEN FITANFQGSQ FKVKPGLFSS VDCPDDAVET GKDLDLDYPL  540
IGRKQGMKQT LGVCSNKGKS SPLCESTRLP ISGRDSNVSS AIAHANGNMN TASERAYYNC  600
DRSSEHGLFS CVTCGILCYT CVAIVQPTKA ASRCLMSTDY ASFSQWREAG GGTTAVDADT  660
NVTMIGSSSG LMVRRPPDSL FDVSIKHTSQ LSDESVGVVS TSRTHKVSSS LGLLASTYGD  720
SSDSEADEAE ADVSVKDSEG RSMDCSPEDE IPLQLVIDPY ADHRQRRAQR DSETANRTSI  780
LSCSLQDRRA VPSCAPSAQK PPERAVKNAL VAPFGDAPMP SDEDSSRMHV FCLQHAVEVE  840
KELQLIGGAH ISLLCHPDYP KLEAQAKKIA KESGSDYPWN DILFQEATKD DEKLIRSALD  900
SEDAIHGNGD WAVKLGINLF YSANLSRSTL YRKQMPYNSV IYSAFGCSSP GGSPTSSENN  960
MKVPGKHKRI VVAGKWCGKV WMSNQVHSLL AERVSDEQEI RRNASSRFVP DGKPPPMRSL  1020
ECNQITETAT PTCRTGKKRK SVTESRPPAN SKSVKTDDDD PDETLSVGFS QLKSKTNLRN  1080
KRIKREAAAE PQKDSDKKNK GGGVDFVSED EVEGGPSTRL RRRAPKPAKQ QLETKPAKQQ  1140
LETKPIKAKP ALKKPEPKKP KQQENKKAKK GGGGPAMKVP AGNSSNSKKS PAVKNPPISN  1200
SVNKKGVLNK APSNSAKARD EDGEYPCDLE GCVMSFDSKQ ELVMHKKNIC PVKGCGKKFF  1260
SHKYLVQHRR VHMDDRPLKC PWKGCKMTFK WAWARTEHIR VHTGARPYVC AEPGCGQTFR  1320
FVSDFSRHKR KTGHSTKK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A8e-74114176356Transcription factor jumonji (Jmj) family protein
6ip4_A8e-74114176356Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
111541161PEPKKPKQ
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
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_019160805.10.0PREDICTED: lysine-specific demethylase REF6 isoform X2
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A484N3860.0A0A484N386_9ASTE; 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. 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]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. Qiu Q, et al.
    DNA methylation repels targeting of Arabidopsis REF6.
    Nat Commun, 2019. 10(1): p. 2063
    [PMID:31048693]