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 Kaladp0011s1015.1.p
Organism
Kalanchoe laxiflora
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: 1291aa    MW: 143280 Da    PI: 8.9324
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Kaladp0011s1015.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H213.90.0001611981220323
                           ET..TTTEEESSHHHHHHHHHHT CS
              zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                           Cp   Cgk+F ++ +L +H r+H
  Kaladp0011s1015.1.p 1198 CPvtGCGKTFFSHKYLLQHRRVH 1220
                           9999*****************99 PP
2zf-C2H210.90.001412561282123
                           EEET..TTTEEESSHHHHHHHHHH..T CS
              zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                           y C    Cg++F+  s++ rH r+  H
  Kaladp0011s1015.1.p 1256 YMCAepGCGQTFRFVSDFSRHKRKtgH 1282
                           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
PfamPF023758.7E-152154IPR003349JmjN domain
SMARTSM005581.3E-46195364IPR003347JmjC domain
PROSITE profilePS5118433.078198364IPR003347JmjC domain
SuperFamilySSF511979.06E-26213380No hitNo description
PfamPF023732.8E-37228347IPR003347JmjC domain
SMARTSM003552611731195IPR015880Zinc finger, C2H2-like
SMARTSM003550.2311961220IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.0511961225IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.602.9E-511981219IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028011981220IPR007087Zinc finger, C2H2
SuperFamilySSF576678.09E-611981232No hitNo description
Gene3DG3DSA:3.30.160.601.7E-812201248IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.001412261250IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.47112261255IPR007087Zinc finger, C2H2
PROSITE patternPS00028012281250IPR007087Zinc finger, C2H2
SuperFamilySSF576672.05E-912361281No hitNo description
Gene3DG3DSA:3.30.160.609.3E-912491279IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003551.112561282IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.84512561287IPR007087Zinc finger, C2H2
PROSITE patternPS00028012581282IPR007087Zinc 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: 1291 aa     Download sequence    Send to blast
MSGKQQQAEV FQWLRALPVA PEYRPTLDEF QDPIAYIFKI EKEASRYGIC KIVPPLPPAP  60
RKTVVANFNK SVPNGSGARP TFTTRQQQIG FCPRRGRPVQ RPVWQSGEFY TFQEFEAKAR  120
AFERSYLKKC GKKAAVAAAA AAGPGLSALE IETLYWKASA DKPFSVEYAN DMPGSAFAAA  180
SGTGRRPREG GEGMTVGDTA WNMKGVARST MSLLRFMKED IAGVTSPMVY VAMLFSWFAW  240
HVEDHDLHSL NYLHTGAGKT WYGVPKEAAA GFEEVVRVHG YGGEINPLVT FATLGEKTTV  300
MSPEVFVKAG IPCCRLVQNP GEFVVTFPRA YHSGFSHGFN CGEASNIATP YWLAVAKEAA  360
VRRASINYPP MVSHFQLLYD LAFALCSSLP MGVHSQPRSS RLKQKRKGVG ETVVKQLFVE  420
DIKESNRLLQ LLGEGLPVVL RPLSSAVFSI YSKSRIQCLL KSRSSSHLGL CYQKETVTSI  480
RNNLATSDIN SGTNGRLPTV IGLPAVGSKF CSTFDGNSRS LPNESTEPQL STSSRWVTDF  540
ENSNAIQDNG ASDKKLFSCV TCGILCFSCV AIIQPAEVAA RYLMASDCSF FSDSENAAKK  600
TSEELADSGR GVNTLDHTYS SGWMGRRAHN GTSNHIEEEY QSDEANSDRE EQPRTTALDL  660
LASAYGNSSD SENDTRLDSD PVYADGPNFS KISSDSDFEC NDSDIRDPLQ ENDFRWESSP  720
RLHSEGETTR FHIADSDGEN HYRRAFQNRN STYDSPSFNL DKLASMGSNL ASLQSDKDSL  780
RMHVFCLEHA IEVKKKLKQI GGVNMLLLCH PDYPRVEAEA KSVQEELGLD HCWNDTAFRE  840
SSEDDERCMA AALESAEDVS SNGDWTVKLG INLFYSASLS RSPLYSKQMP YNSIVYKAFG  900
RVPPLEAPAK SDGHTKGNSR KKKIVLAGKW CGKPWMSNQV HPLLLPPPPA LEETQQEHLH  960
AHASAKTDAA DSDSIQPVKS SKARRDDSSA TTSTPLAGSK RQIVVYSRSN KKTKRAETGL  1020
SVSASDGGDA DAGENLSNQQ AKLHVRSKHK IEGNKKPLEE ETRILYYSSK HVAKGDLKST  1080
KETTSLRDLY KPNFKPFGAD LDDKREGGLS TRLRRRNTKP ELEHEGKVLV KKERKPNKTP  1140
ANSKIEKVDA KPRKSKVSEA ARSRKKKDEE GEFQCDKEGC TMSFSLKQEL ALHKRDICPV  1200
TGCGKTFFSH KYLLQHRRVH EDARPLKCPW KGCKMTFKWA WARTEHIRVH TGVRPYMCAE  1260
PGCGQTFRFV SDFSRHKRKT GHSVKRNIKC *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A1e-7573882356Transcription factor jumonji (Jmj) family protein
6ip4_A1e-7573882356Arabidopsis 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]