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 Neem_1334_f_14
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Meliaceae; Azadirachta
Family C2H2
Protein Properties Length: 1641aa    MW: 185150 Da    PI: 8.8026
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Neem_1334_f_14genomeNGDView Nucleic Acid
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H211.40.0009915251550123
                      EEET..TTTEEESSHHHHHHHHHH.T CS
         zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                      y+C    C++sF +k +L+ H r+ +
  Neem_1334_f_14 1525 YQCDmeGCTMSFGSKQELVLHKRNiC 1550
                      99********************9877 PP

2zf-C2H212.80.0003715501572323
                      ET..TTTEEESSHHHHHHHHHHT CS
         zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                      Cp   Cgk F ++ +L++H r+H
  Neem_1334_f_14 1550 CPvkGCGKKFFSHKYLVQHRRVH 1572
                      9999*****************99 PP

3zf-C2H211.70.0008116081634123
                      EEET..TTTEEESSHHHHHHHHHH..T CS
         zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                      y+C    Cg++F+  s++ rH r+  H
  Neem_1334_f_14 1608 YVCAepGCGQTFRFVSDFSRHKRKtgH 1634
                      899999****************99666 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005451.5E-141960IPR003349JmjN domain
PROSITE profilePS5118313.7162061IPR003349JmjN domain
PfamPF023756.3E-152154IPR003349JmjN domain
SMARTSM005585.7E-19194334IPR003347JmjC domain
PROSITE profilePS5118419.123197334IPR003347JmjC domain
SuperFamilySSF511971.59E-13208354No hitNo description
PfamPF023731.1E-15227278IPR003347JmjC domain
SMARTSM003559.515251547IPR015880Zinc finger, C2H2-like
SuperFamilySSF576675.31E-615481584No hitNo description
PROSITE profilePS5015712.36215481577IPR007087Zinc finger, C2H2
SMARTSM003550.004515481572IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.602.6E-515491571IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028015501572IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.603.6E-915721600IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.74115781607IPR007087Zinc finger, C2H2
SMARTSM003550.001415781602IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028015801602IPR007087Zinc finger, C2H2
SuperFamilySSF576673.24E-915881632No hitNo description
Gene3DG3DSA:3.30.160.602.7E-916011631IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.03216081639IPR007087Zinc finger, C2H2
SMARTSM003550.6216081634IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028016101634IPR007087Zinc 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: 1641 aa     Download sequence    Send to blast
MAEAIQQQDI LPWLKTLPSA PEFHPTLAEF QDPIAYIFKI EKEASQYGIC KIVPPVPPAH  60
KKTAITNLNR SLAERAAATG PSSSSSSSSA PTFTTRQQQI GFCPRKPRPV QKPVWQSGEY  120
YTFQQFETKA KNFEKSYLKK CSNKKGPPSA LEIESLYWRA TVDKPFSVEY ANDMPGSAFV  180
PVKKNREVVG EGMTVGETAW NMRGVSRAKG SLLRFMKEEI PGVTSPMVYI AMMFSWFAWH  240
AEDHDLHSLN YLHMGASKTW YGVPMEAANA FEEVVRVHGY GGEINPLGFW LGSLLQILIR  300
LFEFFPLGFN CGEAANIATP EWLSIAKDAA IRRASINYPP MVSHFQLLYD LAIALHSSIP  360
MTISPKPRSS RLKDKKKDEG ETLVKELFVQ DVAQNNELLY ILGKGSPIVL LPESSLDALG  420
ANPRMPHGVC NYREAIKSPG GSVSNDLMIG RGNGVKPLKG FYPMKGKFTS LCERNSSLGG  480
TDNICTWSSQ MLPTDTEREE AGGQADRLSD QRLFSCVTCG ILSFSCVAVI QPREPTARYL  540
MSADCSFFND WIVGSGVTSA GFNVAGGDAV TSEQNSHRRS MGKSGPHSLY DVPVQSIDKI  600
QTVDHSNETI SGRSTERDTS ALNLLAMTYG NSSDSEEDQV EPNVAVCNDE ETNRPKCSLA  660
INYQQDFHGG ASGSLSLPRL DCRDKGPLQT IDCYVEPEFK SENFNDRNPE ISNCSVDFES  720
EKLDSSKANG LNGLLGDTDP ITISHASNCS PAVHGVENVE FSKAIVPIQN ADMSFTPRFD  780
EDSSRMHVFC LEHAVEVEQQ LRPIGGVHIL LLCHPDYPKI VAEAKLVAEE LEIDSFWNDI  840
SFRNATKEDE ERVQLALDSE DAIPGNGDWA VKLGINLFYS ANLSRSPLYS KQMAYNSVIY  900
NAFGRSSPAS SPTKSDYGRR PGRQRKVVAG KWCGKVWMSN QVHPFLSQKD PEEQEQERSF  960
LAWATPDEHL ERKPETTHHI QSTSETRKFS RKRKMPAESM SIKKVKCVDT EDAGSEDSEE  1020
DDTRIQQRRI LRSKPAKFME REDANSYDSP EDNSHVQKRS ASRRKVKCVE REVRVSNDLP  1080
PENSIKQYRR ISKSKQAKCA AREDVVLDDL PDDSSLKQYR KIPRSKLAKY ADRDDEVSDN  1140
SQGDSSYKQL KRIPRSKEAK WIGREDAVSD DSLEDNSRLL QYKRIPKRKQ AKWIEREAAA  1200
SDDSMEDNSQ QLQHKRITKS KKAKCIERED AVSEDSLEDN CRQLQHKRIS KSKQAKRIET  1260
EDVVSDDSLE NKSRQFHRRT PKSKQAEWVE REDAVSDDSL EDNSQQLCRR IPNSKRAKWI  1320
EREDAVSDNS LEDNAHQQHH RITRDKLAKC IEMEDAVSYD SAEDNSHQLR KIPRSKKAKF  1380
TERVDAVSYD SLEDNSLKKR GRILRSKQRK SETLRKMKQE TAWHMKTGKR SLTKQESPQQ  1440
MKQVTRQRSA KGVQNARQFD SFAEEELEGG PSTRLRKRIP KPVKAVVAKS KEKKQTTKKK  1500
VKNASAVKAP AGLSNAKVKD EEAGYQCDME GCTMSFGSKQ ELVLHKRNIC PVKGCGKKFF  1560
SHKYLVQHRR VHLDDRPLKC PWKGCKMTFK WAWARTEHIR VHTGARPYVC AEPGCGQTFR  1620
FVSDFSRHKR KTGHSTKKGR G
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A2e-701523163821136Lysine-specific demethylase REF6
6a58_A2e-701523163821136Lysine-specific demethylase REF6
6a59_A2e-701523163821136Lysine-specific demethylase REF6
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1989994SRKRKM
211821189KRIPKRKQ
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_006476948.10.0lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLV4TIR40.0V4TIR4_9ROSI; Uncharacterized protein
STRINGXP_006476948.10.0(Citrus sinensis)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM52592843
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]