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 Tp5g13600
Organism
Thellungiella parvula
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassicaceae incertae sedis; Schrenkiella
Family C2H2
Protein Properties Length: 1361aa    MW: 152420 Da    PI: 8.4
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Tp5g13600genomethellungiellaView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H210.70.001612441269123
                 EEET..TTTEEESSHHHHHHHHHH.T CS
    zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                 y+C    C++sF++  +L  H r+ +
  Tp5g13600 1244 YQCDmeGCTMSFNSEKQLSLHKRNiC 1269
                 99********************9877 PP
2zf-C2H213.20.0002812691291323
                 ET..TTTEEESSHHHHHHHHHHT CS
    zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                 Cp   Cgk F ++ +L++H r+H
  Tp5g13600 1269 CPvkGCGKNFFSHKYLVQHRRVH 1291
                 9999*****************99 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005454.4E-151960IPR003349JmjN domain
PROSITE profilePS5118313.7722061IPR003349JmjN domain
PfamPF023751.5E-132154IPR003349JmjN domain
SMARTSM005582.8E-50199368IPR003347JmjC domain
PROSITE profilePS5118432.824202368IPR003347JmjC domain
SuperFamilySSF511971.07E-25217385No hitNo description
PfamPF023733.1E-37232351IPR003347JmjC domain
SMARTSM003559.612441266IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.96512671296IPR007087Zinc finger, C2H2
SMARTSM003550.01612671291IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.603.3E-612681295IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028012691291IPR007087Zinc finger, C2H2
SuperFamilySSF576677.69E-1012831325No hitNo description
Gene3DG3DSA:3.30.160.601.4E-812961320IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.92812971326IPR007087Zinc finger, C2H2
SMARTSM003550.001512971321IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012991321IPR007087Zinc finger, C2H2
SuperFamilySSF576677.0E-813151349No hitNo description
Gene3DG3DSA:3.30.160.601.8E-813211350IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.03213271358IPR007087Zinc finger, C2H2
SMARTSM003552.413271353IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028013291353IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0040010Biological Processpositive regulation of growth rate
GO:0045815Biological Processpositive regulation of gene expression, epigenetic
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: 1361 aa     Download sequence    Send to blast
MAVSEQSPDV LPWLKSLPVA PEFRPTPAEF QDPIAYIFKI EEEASRYGIC KILPPVPPPS  60
KKTAIYNLNR SLAERAAARV REGAGACDYD GAPTFATRQQ QIGFCPRKQR PVQRPVWQSG  120
ERYSFGEFEA KAKSFERNYL KKCGKKSQLS ALEIETLYWR ATVDKPFSVE YANDMPGSAF  180
IPLSLAAARR KEYGGDGGTV GETAWNMRAM ARAEGSLLKF MKEETPGVTS PMVYIAMMFS  240
WFAWHVEDHD LHSLNYLHMG AGKTWYGVPK DAAVAFEEVI RVHGYGEELN PLVTFSTLGE  300
KTTVMSPEVC VKAGIPCCRL VQNPGEFVVT FPRAYHSGFS HGFNCGEASN IATPEWLRVA  360
KDAAIRRAAI NYPPMVSHLQ LLYDYALALG SRVPASIHTK PRSSRLKDKK RSEGEKLTKE  420
LFVQNIIHNN ELLLSLGKGS PVALLPQSSS DISVCSDLRV GSHLSANEER PTQLKAEDLS  480
SDSVMIGLNN GVKDAVSVKE KFTSLCERNR NHLASKENET QGNSRDAEKW KNAGAVGLSD  540
QRLFSCVTCG ILSFGCVAIV QPKEAAARYL MSADCSFFND WTVGSRSSNL GQDARSPVVK  600
SHSQSTGKHD VGYLYNTPVQ TTNHSMKTGD QRTSTTSVTK ANKEDGALEL LASAYGNSSD  660
SEEEDHKGLD AIILEERKHN ENGASPYDAS SFGTDGNEEA ACGKGKGVAE RSNGGSPSIL  720
DIAFPFIPRF DDDSSRLHMF CLEHAAEVEQ QLSPIGGVNI ILLCHPEYPR IEAEGKIVAE  780
ELGVSHEWSN TEFRNVTRED EETIQAALAN VEAKAGNSDW AVKLGINLSY SAILSRSPLY  840
SKQMPYNSVI YKVFGRNSSA TSSPTKPQVS GKRSSRQRKY VVGKWCGKVW MSHQVHPFLL  900
QQDLEVEESE RSHLRLEDVT GRRSFPCNVS RDSTTMFGRK YSRKRKMRAK AVPRKQLTSF  960
KREDGVSDDT SEDHSYKQQW RASGNDDESY FETGNSVSGD SSNQMSDQQQ RKIIRRDKGV  1020
KEFESDDEVS DRSLGEEYAV RERAVSESSM ENSFQPYKQS MHRNALEDSV YGHNDDNIYR  1080
HPRGYPRSKR AKVFRNPVSY DSEENGVYQQ RGNIQASRIG GDYDSAEDSL EEQEFCSTRK  1140
RQTRSTAKRK VKTEIVQSPR DTRGRTLQQS GSKKKNQDLD YMEGPSTRLR VRNLKPSRGS  1200
SETKQKKTGK KGSGNASFSR VVSEEELEED EEEENEEEEC AAAYQCDMEG CTMSFNSEKQ  1260
LSLHKRNICP VKGCGKNFFS HKYLVQHRRV HSDDRPLKCP WKGCKMTFKW AWSRTEHIRV  1320
HTGARPYLCI EPGCGQTFRF VSDFSRHKRK TGHSAKKTKK S
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A1e-741241136020139Lysine-specific demethylase REF6
6a58_A1e-741241136020139Lysine-specific demethylase REF6
6a59_A1e-741241136020139Lysine-specific demethylase REF6
6ip0_A1e-7294654422Transcription factor jumonji (Jmj) family protein
6ip4_A1e-7294654422Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1941946SRKRKM
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapTp5g13600
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006404260.10.0lysine-specific demethylase REF6
RefseqXP_024013589.10.0lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLV4M0K30.0V4M0K3_EUTSA; Uncharacterized protein
STRINGXP_006404260.10.0(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]