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 Thhalv10010066m
Common NameEUTSA_v10010066mg
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Eutremeae; Eutrema
Family C2H2
Protein Properties Length: 1379aa    MW: 154581 Da    PI: 7.6615
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Thhalv10010066mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H211.40.0009612611286123
                       EEET..TTTEEESSHHHHHHHHHH.T CS
          zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                       y+C    C++sF++  +L  H r+ +
  Thhalv10010066m 1261 YQCDmeGCTMSFTSEKQLALHKRNiC 1286
                       99********************9877 PP

2zf-C2H213.10.0002812861308323
                       ET..TTTEEESSHHHHHHHHHHT CS
          zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                       Cp   Cgk F ++ +L++H r+H
  Thhalv10010066m 1286 CPvkGCGKNFFSHKYLVQHRRVH 1308
                       9999*****************99 PP

3zf-C2H2110.001313441370123
                       EEET..TTTEEESSHHHHHHHHHH..T CS
          zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                       y+C    Cg++F+  s++ rH r+  H
  Thhalv10010066m 1344 YVCAepSCGQTFRFVSDFSRHKRKtgH 1370
                       899999****************99666 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005451.6E-161960IPR003349JmjN domain
PROSITE profilePS5118314.0772061IPR003349JmjN domain
PfamPF023755.7E-142154IPR003349JmjN domain
SMARTSM005583.5E-52201370IPR003347JmjC domain
PROSITE profilePS5118434.061204370IPR003347JmjC domain
SuperFamilySSF511973.84E-27219388No hitNo description
PfamPF023732.8E-37234353IPR003347JmjC domain
Gene3DG3DSA:3.30.160.602.5E-412601283IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003558.512611283IPR015880Zinc finger, C2H2-like
SMARTSM003550.01612841308IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.96512841313IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.604.0E-612851307IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028012861308IPR007087Zinc finger, C2H2
SuperFamilySSF576676.55E-1013001342No hitNo description
Gene3DG3DSA:3.30.160.604.5E-1013081335IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.001513141338IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.92813141343IPR007087Zinc finger, C2H2
PROSITE patternPS00028013161338IPR007087Zinc finger, C2H2
SuperFamilySSF576678.38E-813321366No hitNo description
Gene3DG3DSA:3.30.160.601.2E-813361367IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003555.513441370IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.28113441375IPR007087Zinc finger, C2H2
PROSITE patternPS00028013461370IPR007087Zinc 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: 1379 aa     Download sequence    Send to blast
MAVSEQSPDV FPWLKSLPVA PEFRPTLAEF QDPIAYIFKI EEEASKYGIC KILPPVPPSS  60
KKTAINNLNR SLAARAAARV RDGADDGAWD YDGAPTFATR QQQIGFCPRK QRPVQRPVWQ  120
SGEHYSFGEF EFKAKNFEKN YLRKCGKRSQ LSALEIETLY WRATVDKPFS VEYANDMPGS  180
AFIPLSLAAA RRRESGGDGG TVGETAWNMR AMARAEGSLL KFMKEEIPGV TSPMVYIAMM  240
FSWFAWHVED HDLHSLNYLH MGAGKTWYGV PKDAAVAFEE VVRVHGYGGE LNPLVTFSTL  300
GEKTTVMSPE VFVRAGIPCC RLVQNPGEFV VTFPGAYHSG FSHGFNFGEA SNIATPQWLR  360
MAKDAAIRRA AINYPPMVSH LQLLYDFALA LGSRVPTSIN TKPRSSRLKD KKRSEGEKLT  420
KELFVQNIIH NNELLCSLGK GSPVALLPQS SSDVSVCSDL RIGSHLRTNQ EKPIQLKSED  480
LSSDSIMPGL NNGFKDAVSV KEKFTSLCER NRNHLASREN ETQGTSTDAE RKKNDRAVGL  540
SDQRLFSCVT CGILSFDCVA IVQPKEAAAR YLMSADCSFF NDWTVASGPA NLGQVAGSLH  600
PQSTGKHDVD YFYNVPVQTT DHSMKTGDQR TSSSSLTKEN KDDGALGLLA SAYGDSSDSE  660
EEDHKGSDIP ISEGITRQYD QEGACVSEAT SFDTDRNEEA RDGPSSDINS QRLTSGKGKE  720
IDVLHATSSC STLSCTSLQE IALPFIPRSD DDSSRLHVFC LEHAAEVEQQ LRPIGGIRIM  780
LLCHPEYPRI EAEAKIVSEE LGVNHEWNDT EFRNVSRVDE ETIQAALDNV EAKAGNSDWS  840
VKLGINLSYS AILSRSPLYS KQMPYNSVIY NAFGRGSPAT SSPTKPQVSG KRSSRQRKYV  900
VGKWCGKVWM SHQVHPFLLQ QDLEGDESER SCHLRGVLED DVIGKRLSPC NASRDATTMF  960
GRKYCRKRKM RAKALPRKKL TSFKREDVVS DDTSEDHSYK QQWRASGNEE ESYFETGNSV  1020
SGDSSNQMSD EQQEFVRHQG DKDFESDDEV SDRSLGEEYA VRECAASESS MENGSQLYRE  1080
NQSMYDHDDD DIYRHPRGLP RSKRTKFFRN PVSYDSEENG LYQQRGRVST SNAQISRMGG  1140
AYDSADNSLE EQEFCSAGKR QTRSTAKRKV KTEIVQSLRD TKRRALRQSG PRKKNQEVDI  1200
YMEGPSTRLR VRNLNPSIGS SETKPKKTGK KRNSNSFSRV ASEEELEEDE EENEQEECAP  1260
YQCDMEGCTM SFTSEKQLAL HKRNICPVKG CGKNFFSHKY LVQHRRVHSD DRPLKCPWKG  1320
CKMTFKWAWS RTEHIRVHTG ARPYVCAEPS CGQTFRFVSD FSRHKRKTGH SVKKTKKR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A2e-771258137820140Lysine-specific demethylase REF6
6a58_A2e-771258137820140Lysine-specific demethylase REF6
6a59_A2e-771258137820140Lysine-specific demethylase REF6
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1966978KRKMRAKALPRKK
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
PlantRegMapThhalv10010066m
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_006404261.10.0lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLV4LPK00.0V4LPK0_EUTSA; Uncharacterized protein
STRINGXP_006404261.10.0(Eutrema salsugineum)
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]