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.0157s0065.1.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: 1292aa    MW: 143262 Da    PI: 8.9437
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Kalax.0157s0065.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H212.50.0004611991221323
                           ET..TTTEEESSHHHHHHHHHHT CS
              zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                           Cp   Cgk+F ++ +L +H r+H
  Kalax.0157s0065.1.p 1199 CPvtGCGKTFLSHKYLLQHRRVH 1221
                           9999*****************99 PP
2zf-C2H210.90.001412571283123
                           EEET..TTTEEESSHHHHHHHHHH..T CS
              zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                           y C    Cg++F+  s++ rH r+  H
  Kalax.0157s0065.1.p 1257 YMCAepGCGQTFRFVSDFSRHKRKtgH 1283
                           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
PfamPF023732.8E-37226345IPR003347JmjC domain
SMARTSM003552411741196IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.0511971226IPR007087Zinc finger, C2H2
SMARTSM003550.3311971221IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028011991221IPR007087Zinc finger, C2H2
SuperFamilySSF576677.69E-611991233No hitNo description
Gene3DG3DSA:3.30.160.603.6E-511991220IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
Gene3DG3DSA:3.30.160.602.0E-812211249IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.47112271256IPR007087Zinc finger, C2H2
SMARTSM003550.001412271251IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012291251IPR007087Zinc finger, C2H2
SuperFamilySSF576672.03E-912371282No hitNo description
Gene3DG3DSA:3.30.160.608.6E-912501280IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.84512571288IPR007087Zinc finger, C2H2
SMARTSM003551.112571283IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012591283IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 1292 aa     Download sequence    Send to blast
MSGKQQQAEV FQWLRALPVA PEYRPTLDEF QDPIAYIFKI EKEASRYGIC KIVPPLPPAP  60
RKTVVANFNK SVPNGSGARP 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
KDSNRLLQLL GEGLPVVLRP LSSVFSIYSK SRIQCLLKSR SSSHLGLCYQ KETVTSIRNN  480
LATSDINSGT NGRLPTVIGL PAVGSKFCST FDGNSCSLPN ESTEPQLSTS SRWVTDFENS  540
NAIQDNGASD KKLFSCVTCG ILCFSCVAII QPAEVAARYL MASDCSFFSD SENAAKKTSE  600
ELADSGRGVN TLDHTYSSGW MGRRAHNGTS NHIEEEYQSD EANSDREEQP RTTALDLLAS  660
AYGNSSDSEN DTRLDSDPVY ADGPNFSKIS SDSDFECNDS DIRDPLQEND FRWESSPRLH  720
SEGETTRFHI ADSDGENHYR RAFQNRNSTY DSPSFNLDKL ASMGSNLASL QSDKDSLRMH  780
VFCLEHAIEV KKKLKQIGGV NMLLLCHPDY PRVEAEAKSV QEELGLDHCW NDTAFRESSE  840
DDERCMAAAL ESAEDVSSNG DWTVKLGINL FYSASLSRSP LYSKQMPYNS IVYKAFGRVP  900
PLEAPAKSDG HTKGNSRKKK IVLAGKWCGK PWMSNQVHPL LLPPPPAALE EAQQEHLHAH  960
ASAKTDAADS DSIQPVKSSK ARRDDSSATT STPLAGSKRQ IVVYSRSNKK TKRAETGLSV  1020
SAGDGGDANA GENISHQQAK LHVRSKHKIE GNKKPLEEET RILYYSSKHV AKGDLKSTKE  1080
TTSLRNLYKP NFKPFGADLD DKREGGLSTR LRRRNTKPEL ELEGKVLVKK ERKPNKTPAN  1140
SKEAKIEKVD AKPRKSKVSE AARSRKKKDE EGEFQCDKDG CTMSFSLKQE LALHKRDICP  1200
VTGCGKTFLS HKYLLQHRRV HEDARPLKCP WKGCKMTFKW AWARTEHIRV HTGVRPYMCA  1260
EPGCGQTFRF VSDFSRHKRK TGHSVKRNIK C*
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}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
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]