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 Kalax.0327s0019.1.p
Organism
Kalanchoe marnieriana
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; Saxifragales; Crassulaceae; Kalanchoe
Family C2H2
Protein Properties Length: 1294aa    MW: 143713 Da    PI: 8.9723
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Kalax.0327s0019.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H213.90.0001612011223323
                           ET..TTTEEESSHHHHHHHHHHT CS
              zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                           Cp   Cgk+F ++ +L +H r+H
  Kalax.0327s0019.1.p 1201 CPvtGCGKTFFSHKYLLQHRRVH 1223
                           9999*****************99 PP
2zf-C2H210.90.001412591285123
                           EEET..TTTEEESSHHHHHHHHHH..T CS
              zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                           y C    Cg++F+  s++ rH r+  H
  Kalax.0327s0019.1.p 1259 YMCAepGCGQTFRFVSDFSRHKRKtgH 1285
                           789999****************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005451.7E-171960IPR003349JmjN domain
PROSITE profilePS5118314.4782061IPR003349JmjN domain
PfamPF023758.8E-152154IPR003349JmjN domain
SMARTSM005581.3E-46193362IPR003347JmjC domain
PROSITE profilePS5118433.078196362IPR003347JmjC domain
SuperFamilySSF511978.79E-26211378No hitNo description
PfamPF023732.9E-37226345IPR003347JmjC domain
SMARTSM003552611761198IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.0511991228IPR007087Zinc finger, C2H2
SMARTSM003550.2311991223IPR015880Zinc finger, C2H2-like
SuperFamilySSF576678.09E-612011235No hitNo description
Gene3DG3DSA:3.30.160.602.9E-512011222IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028012011223IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.7E-812231251IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.001412291253IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.47112291258IPR007087Zinc finger, C2H2
PROSITE patternPS00028012311253IPR007087Zinc finger, C2H2
SuperFamilySSF576672.05E-912391284No hitNo description
Gene3DG3DSA:3.30.160.609.3E-912521282IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.84512591290IPR007087Zinc finger, C2H2
SMARTSM003551.112591285IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012611285IPR007087Zinc 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: 1294 aa     Download sequence    Send to blast
MSGKQQQAEV FQWLRALPVA PEYRPTLDEF QDPIAYIFKI EKEASRYGIC KIVPPLPPAP  60
RKTVVANFNK SVPNGSGAKP TFTTRQQQIG FCPRRGRPVQ RPVWQSGEFY TFQEFEAKAR  120
AFERSYLKKC GKKAAVAAAA GAGLSALEIE TLYWKASADK PFSVEYANDM PGSAFAAASG  180
TGRRPREGGE GMTVGDTAWN MKGVARSTMS LLRFMKEDIA GVTSPMVYVA MLFSWFAWHV  240
EDHDLHSLNY LHTGAGKTWY GVPKEAAAGF EEVVRVHGYG GEINPLVTFA TLGEKTTVMS  300
PEVFVKAGIP CCRLVQNPGE FVVTFPRAYH SGFSHGFNCG EASNIATPYW LAVAKEAAVR  360
RASINYPPMV SHFQLLYDLA FALCSSLPMG VHSQPRSSRL KQKRKGVGET VVKQLFVEDI  420
KESNRLLQLL GEGLPVVLRP LSSAVFSIYS KSRIQCLLKS RSSSHLSLCY QKETVTSIRN  480
NLAASDINSG TNGRLPTVIG LPAVGSKFCS TFDGNSRSLP NESTEPQLST SSRWVTDYEN  540
SNAIQDDGAS DKKLFSCVTC GILCFSCVAI IQPAEVAARY LMASDCSFFS DSENAAKKTS  600
EELADSGRGV NTLDHTYSSG WMGRRAHNGK SNHIEEEYQS DEANSDREEQ PRTTALDLLA  660
SAYGNSSDSE NDTRLDSDPV YADGPNFSKI SSDSDFECND SDIRDPLQEN DFRWESSPRL  720
HSEGETTRFH IADSDGENHY RRAFQNRNST YDSPSFNLDK LASMGSNLAS LQSDKDSLRM  780
HVFCLEHAIE VKKKLKQIGG VNMLLLCHPD YPRVEAEAKS VQEELRLDHC WNDTAFRESS  840
EDDERCMAAA LESAEDVSSN GDWTVKLGIN LFYSASLSRS PLYSKQMPYN SIVYKAFGRV  900
PPLEAPAKSD GHTKGNSRKK KIVLAGKWCG KPWMSNQVHP LLLPPPPALE ETQQEHLHAH  960
ASASAKTDAA DSDSIQPVKS SKARRDDSSA TTSTPLAGSK RQIVVYSRSN KKTKRAETGL  1020
SVSASDGGDA DAGENLSNQQ AKLHVRSKHK IEGNKKPLEE ETRILYYSSK HVAKGDLKST  1080
KETTSLRDLY KPNFKPFGAD LDDKREGGLS TRLRRRNTKP ELEHEGKVLV KKERKPNKTP  1140
ANSKEAKIEK VDAKPRKSKV SEAARSRKKK DEEGEFQCDK EGCTMSFSLK QELALHKRDI  1200
CPVTGCGKTF FSHKYLLQHR RVHEDARPLK CPWKGCKMTF KWAWARTEHI RVHTGVRPYM  1260
CAEPGCGQTF RFVSDFSRHK RKTGHSVKRN IKC*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A3e-7673862356Transcription factor jumonji (Jmj) family protein
6ip4_A3e-7673862356Arabidopsis JMJ13
Search in ModeBase
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
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_010663055.10.0PREDICTED: lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLF6GTM20.0F6GTM2_VITVI; Uncharacterized protein
STRINGVIT_17s0000g09980.t010.0(Vitis vinifera)
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]