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 Lus10019482
Organism
Linum usitatissimum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Linaceae; Linum
Family C2H2
Protein Properties Length: 1582aa    MW: 178213 Da    PI: 8.2193
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Lus10019482genomeBGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H214.30.0001214901512323
                   ET..TTTEEESSHHHHHHHHHHT CS
      zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                   Cp   Cgk+F ++ +L++H r+H
  Lus10019482 1490 CPvkGCGKVFFSHKYLVQHRRVH 1512
                   9999*****************99 PP
2zf-C2H211.70.0008215481574123
                   EEET..TTTEEESSHHHHHHHHHH..T CS
      zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                   y+C    Cg++F+  s++ rH r+  H
  Lus10019482 1548 YVCAeeGCGQTFRFVSDFSRHKRKtgH 1574
                   89********************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005458.1E-162364IPR003349JmjN domain
PROSITE profilePS5118314.4372465IPR003349JmjN domain
PfamPF023751.7E-142558IPR003349JmjN domain
SuperFamilySSF511971.84E-22118178No hitNo description
PROSITE profilePS5118432.428194393IPR003347JmjC domain
SMARTSM005581.2E-39194393IPR003347JmjC domain
SuperFamilySSF511971.84E-22212386No hitNo description
PfamPF023735.4E-29227356IPR003347JmjC domain
SMARTSM003551114651487IPR015880Zinc finger, C2H2-like
SMARTSM003550.002514881512IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.50814881517IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.602.6E-514891511IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028014901512IPR007087Zinc finger, C2H2
SuperFamilySSF576672.0E-915041546No hitNo description
Gene3DG3DSA:3.30.160.601.7E-915121540IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.003615181542IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.82415181547IPR007087Zinc finger, C2H2
PROSITE patternPS00028015201542IPR007087Zinc finger, C2H2
SuperFamilySSF576674.94E-815361571No hitNo description
Gene3DG3DSA:3.30.160.603.5E-915411571IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.8515481574IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.0315481579IPR007087Zinc finger, C2H2
PROSITE patternPS00028015501574IPR007087Zinc 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: 1582 aa     Download sequence    Send to blast
MAASGGLAAE REDVLQWLRN LPLAPEYHPT LAEFQDPIAY IFKIEKEASK YGICKIVPPV  60
LQSPKKTAIA NLNRSLAARV VGGASSSSSS PPTFTTRQQQ IGFCPRKPRP VQKPVWQSGE  120
NYTFQEFESK AKSFEKSYFK KYAKKGTTLS PLEIETLYWK ATVDKPFSVE YANDMPGSAF  180
PVKKNSGIVV EGMSVGETEW NMRGVARAKG SLLRHMKEEI PGVTSPMLYI AMMFSWFAWH  240
VEDHDLHSLN YMHMGAGKTW YGVPKEAAVA FEEVVRVHGY GGEINPLREC SFQQNSCLSV  300
DHLARLITFA VLGEKTTVMS PEVFIRAGVP CCRLVQNAGE FVVTFPRAYH SGFSHGKVAV  360
YLQFPLWFNC GEASNIATPE WLRFAKEAAV RRASINYPPM VSHFQLLYDL ASELCSRFTT  420
NASAKPRSSR LKDKQKGESE MVTKEILVEN VMNNNNLLHN LGKGASVVLL PRSSSDISLC  480
SNYRFGSQFV KPSFGLRAHK GFMGQSKVSG YDDSKPDKID VINQVKDMYP LKAKFGSSYE  540
GQTCPVLGKS GNLHNPHPET EKIAMLDNKS PDQRLFSCVT CGILNYDCVA IIQPREAAAR  600
YLMSADCSFF NDWTVVSGAG KEAHVAADED AGGAGDSIAH GLHDVLESEN NHKQIIDQSS  660
GAVSGTKIKL EASALGLLAL NYGDSSDMDE EPGLSPDNND TYDRMNSLSE GNHQSQDSAS  720
PSLEEELPDG TSRHKFDYGN RVFLQGVENN MQQLESTDPL LAPTCDEDSS RMHVFCLEHA  780
VEVEQRLRQI GGVHVFLLCH PDYPGIEEQA KLVSEELRVD YLWKQTNYKD ASIDDEQRIQ  840
SVLDSEEAIP GNSDWAVKLG INLFYSANLS WSPLYSKQMA YNSVIYNAFG RTSPGSSPKK  900
SNNVSGRRNG RQRKAVVGKW CGKVWMSNQV HPFLINWDSQ YQDQEQEPEK LDVQQPHVFE  960
TETSRKSVKS VKKRKPKAKS VSVREVALAE IEEIASDDLG RVSRKPLGRL NNRKRTNSVE  1020
ERESLHRSKL ARSAVNEYVD SEDSLGDESL QQQQKKTISQ QTREFDCERA DFYDTVRKTS  1080
QKQRRTPRVC QAKYVQKESA SDDSLEENML QWHGRVPRSK QQMKLMNREE VSGLPLEESS  1140
QKSPKVYKRR KGKYAEKEYA APSESIENVY HRQNSLTPEG KQFEEAEFDD SLDESVKWQT  1200
ASFSREDLMS DDSVYNDDTH QQRGTARGKN PLSYSAEDAV SDDPLDTDTH QLERTIPRIG  1260
RSRSFGDEDA VSDDLLQEDD IEQNFRSIHQ NKRAKFSERQ AEITDELRNN STRRYPRKTP  1320
RGKHGRFIKG EIEDADSDHL VGEDFNEQQG RTLRSKQKRP RTPPSGKKSM QKETPLRPVK  1380
LETPRMRNKG NAYQFDDVPA DDDEEEGGPS SRLRRRPSKP TKVSVSKSKE IQQQQSSRIK  1440
VKSAPAGKAP AGRKSGKNKV EDGQFHCDID GCTMGFSSKQ ELNIHKRNIC PVKGCGKVFF  1500
SHKYLVQHRR VHVDDRPLKC PWKGCKMAFK WAWARTEHIR VHTGARPYVC AEEGCGQTFR  1560
FVSDFSRHKR KTGHSGRKDS E*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A8e-73134074346Transcription factor jumonji (Jmj) family protein
6ip4_A8e-73134074346Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1968974KSVKKRK
211431149PKVYKRR
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
PlantRegMapLus10019482
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_021614573.10.0lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A2C9VPX70.0A0A2C9VPX7_MANES; Uncharacterized protein
STRINGLus100194820.0(Linum usitatissimum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF56483250
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]