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 Bostr.28354s0001.1.p
Organism
Boechera stricta
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Boechereae; Boechera
Family C2H2
Protein Properties Length: 1245aa    MW: 139145 Da    PI: 6.6079
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Bostr.28354s0001.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H211.80.0007412011226123
                            EEET..TTTEEESSHHHHHHHHHH.T CS
               zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                            y+C    C++sFs+  +L  H r+ +
  Bostr.28354s0001.1.p 1201 YQCDmeGCTMSFSSEKQLALHKRNrC 1226
                            99********************9877 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF511978.79E-2879125No hitNo description
SMARTSM005581.4E-52159328IPR003347JmjC domain
PROSITE profilePS5118434.33162328IPR003347JmjC domain
SuperFamilySSF511978.79E-28177346No hitNo description
PfamPF023732.5E-38192311IPR003347JmjC domain
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
Sequence ? help Back to Top
Protein Sequence    Length: 1245 aa     Download sequence    Send to blast
EEASRYGICK ILPPVPPPSK KTLISNLNRS LAARAAARVR DGGESSCDYD GGPTFASRQQ  60
QIGFCPRKQR PVQRPVWQSG EHYSFGEFEA KARSFEKAYL KKCGKKSQLS ALEIETLYWR  120
ATVDKPFSVE YANDMPGSAF IPLSLAAARR RESGSDGGTV GETAWNMRAM ARAEGSLLKF  180
MKEEIPGVTS PMVYIAMMFS WFAWHVEDHD LHSLNYLHMG ASKTWYGVPK DAASAFEEVV  240
RVHGYGGELN PLVTFSTLGE KTTVMSPEVF VKAGIPCCRL VQNPGEFVVT FPGAYHSGFS  300
HGFNFGEASN IATPQWLRMA KNAAIRRAAI NYPPMVSHLQ LLYDFALALG SRVPTSINAK  360
PRSSRLKDKK RSEGERLTKN LFVENIIHNN ELLSSLGKGS PVALLPQSSS DISVCSDLRI  420
GSDLTTNQEN PIQLKSEDLS SDGVMVGLTN GLKDTVSVKE KFTSLCERNR NHLASRGKDT  480
QETLSDTERR NNDGAVGLSD QRLFSCVTCG VLSFDCVAIV QPKEAAARYI MSADSSFFND  540
WTAASGSENH GQAARSLHPQ STEKHDLNYF FNVPVQTTDH SMKTGDQRTS TTSLTNEHKD  600
NDALGLLATA YGDSSDSEEE DNEGLDASTS EGERKKYDQE SACAFKASSF DTDGNEDARD  660
GRTSDFNSQR LTSEQNSLSK GGNSSLLEIT LPFVPKSDDD PCRLHVFCLE HAAEVEQQFC  720
PIGGIHIMLL CHPEYPRIEA EAKRVAEELA INHEWNDTEF RNVTREDEET IQAALDNVEA  780
KGGNSDWTVK LGINLSYSAI LSRSPLYSKQ MPYNSVIYNV FGRSSPATSS LLKPEVSGKR  840
SSRQRKYVVG KWCGKVWMSH QVHPFLLHQD LEGEESERNC HLRAAIDEDV TGKRLFPCNV  900
SRDATTMFGR KYCRKRKVRA KAIPRKKLTS FKREDGDSDD TSEDHSYKQQ WRASGNEEES  960
YCGTGNTASG DSSNQMSDQQ IKGIRRHRGV KEFESDDEVS DRSLGEEYAV REHAVSESST  1020
ENSFQLYRQS IDGNALEDSV YGHDDDNIYR HPRGSPRSKR TKLFRNPVSY DLEENDVYQQ  1080
RGNRPASRIG GEYDSAEDSL EEQDFCSIGK KQTRSTAKRK VKTEIVQSPR EKNEELDSYM  1140
EGPSTRLRVR NLKPSRGSSE TKPKKIGKKR SSNASFSRVV SEEYVEEHEE AENEEEECAV  1200
YQCDMEGCTM SFSSEKQLAL HKRNRCPVKG CGKNFFSHKY LVQHQ
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A1e-59241638413Transcription factor jumonji (Jmj) family protein
6ip4_A1e-59241638413Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1914926KRKVRAKAIPRKK
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
PlantRegMapBostr.28354s0001.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY6644990.0AY664499.1 Arabidopsis thaliana relative of early flowering 6 (REF6) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002875902.10.0lysine-specific demethylase REF6 isoform X2
RefseqXP_023637886.10.0lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLD7LRW50.0D7LRW5_ARALL; Uncharacterized protein
STRINGBostr.28354s0001.1.p0.0(Boechera stricta)
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]