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 676776926
Organism
Sisymbrium irio
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Sisymbrieae; Sisymbrium
Family C2H2
Protein Properties Length: 1422aa    MW: 159589 Da    PI: 7.2708
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
676776926genomeVEGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H2130.000313301352323
                 ET..TTTEEESSHHHHHHHHHHT CS
    zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                 Cp   Cgk F ++ +L++H r+H
  676776926 1330 CPvkGCGKNFFSHKYLVQHRRVH 1352
                 9999*****************99 PP
2zf-C2H210.70.001713881414123
                 EEET..TTTEEESSHHHHHHHHHH..T CS
    zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                 y+C    Cg++F+  s++ rH r+  H
  676776926 1388 YVCAepRCGQTFRFVSDFSRHKRKtgH 1414
                 899999****************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005452.5E-161960IPR003349JmjN domain
PROSITE profilePS5118313.9522061IPR003349JmjN domain
PfamPF023758.1E-142154IPR003349JmjN domain
SMARTSM005587.7E-52199368IPR003347JmjC domain
PROSITE profilePS5118433.593202368IPR003347JmjC domain
SuperFamilySSF511978.51E-27214386No hitNo description
PfamPF023738.1E-38232351IPR003347JmjC domain
SMARTSM003551213051327IPR015880Zinc finger, C2H2-like
SMARTSM003550.01613281352IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.96513281357IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.603.5E-613291356IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028013301352IPR007087Zinc finger, C2H2
SuperFamilySSF576676.35E-1013441386No hitNo description
Gene3DG3DSA:3.30.160.601.0E-813571381IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.001513581382IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.92813581387IPR007087Zinc finger, C2H2
PROSITE patternPS00028013601382IPR007087Zinc finger, C2H2
SuperFamilySSF576676.18E-813751410No hitNo description
Gene3DG3DSA:3.30.160.602.0E-813821411IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003559.513881414IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.28113881419IPR007087Zinc finger, C2H2
PROSITE patternPS00028013901414IPR007087Zinc 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: 1422 aa     Download sequence    Send to blast
MAVSEQSQDV FPWLKSLPVA PEFRPTLAEF QDPIAYIFKI EEEASRYGIC KILPPVPPSS  60
KKTAINNLNR SLAARAAARV REGGRASDYD DGPTFATRQQ QIGFCPRKQR PVQRPVWQSG  120
EHYTFGEFEF KAKSFEKNYL KKCGKKSSVS ALEMETLYWR ATVDKPFSVE YANDMPGSAF  180
IPLSLAAARR RESGGDGGTV GETGWNMRAM ARAEGSLLQF MKEEIPGVTS PMVYIAMMFS  240
WFAWHVEDHD LHSLNYLHMG ASKTWYGVPK DAAVAFEEVV RVHGYGEELN PLVTFSTLGE  300
KTTVMSPEVF VKAGIPCCRL VQNPGDFVVT FPGAYHSGFS HGFNFGEASN IATPQWLKIA  360
KDAAIRRAAI NYPPMVSHLQ LLYDYALALG SRVPVSIHTK PRSSRLKDKK RSEGEKLTKE  420
LFVQNIIHNN ELLHSLGKGS SIALLPQSSS DISVCSDLRI GSHLSDNQEK TIQLKSEDLS  480
SDSVTVGVSN VVKDAVSVKE KFTTLCERNR NHLVSKENET RGTSADSERR KSDRAVGLSD  540
QRLFSCVTCG VLSFDCVAIV QPKEAAARYL MSGDCSFFND WTVPSGSATL GQVAGSHHQQ  600
GTENPDVNNF YNVPGQTADH SMKTGDQITL SSSLTKANKD NGALGLLASA YGDSSDSEED  660
DHKGLDIPVS EEDACVLEAS SFDTDGKEET RDGLSSSFNS QRLTCEKGKE ADVSHATSSC  720
STLSCTSEQN RLSKGGNTSP LEITLPFISR SDDDSSRLHV FCLEHAAEVE QRLRPIGGIN  780
IMLLCHPEYP RIEAEGKIVA EELVLDHEWS DTEFRNVTRE DEETIQAALA NVEAKAGNSD  840
WAVKLGINLS YSAILSRSPL YSKQMPYNSV VYNAFGRSSL ATSSPTKSQV SGKRSSRQRK  900
YVAGKWCGKV WMSHQVHPFL LEEDLEEEES ERSHLRDEDV NGKRLFPCND SRDATTMFGR  960
KYCRKRKRRA KTVPRKKLSS FKREEGLSDD TSEDHSYKQQ WRASGNEEEL SDDSSNQMSD  1020
QQQLKEIVIH QEYHSDDEVS DRSLGQEYAV RECAASESSM ENGFQLYREK HPMYGDDDDD  1080
DDIYRHPRGI PRSKRTKVFR NRVSYDSEEN GVYQQRGRVY TSNAQTNRVV GEYDSVENSL  1140
EEHDFCSTGK RQTRSTAKRK VKTEIIQNLK DTRGRTLQQS GSRKKNQDLD SYMEGPSTRL  1200
RVRNLKPSRG SSETKPKKNG KRGSKISFFG VASEDDVEED EEEENEEPST RLRVRIMKSS  1260
RGSSETKPKK TCKKGSSLSF SGVASEDDVE ENEAEENEEE ECAAFQCDME GCTMSFNSEK  1320
QLSLHKRNIC PVKGCGKNFF SHKYLVQHRR VHSDDRPLKC PWKGCKMTFK WAWSRTEHIR  1380
VHTGARPYVC AEPRCGQTFR FVSDFSRHKR KTGHSVKKTK KR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A2e-771302142220140Lysine-specific demethylase REF6
6a58_A2e-771302142220140Lysine-specific demethylase REF6
6a59_A2e-771302142220140Lysine-specific demethylase REF6
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1963968RKRKRR
2964976KRKRRAKTVPRKK
3965976RKRRAKTVPRKK
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
PlantRegMap676776926
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
TrEMBLA0A1J3JIY40.0A0A1J3JIY4_NOCCA; Lysine-specific demethylase REF6
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]