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 HL.SW.v1.0.G023714.1
Organism
Humulus lupulus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Cannabaceae; Humulus
Family C2H2
Protein Properties Length: 1494aa    MW: 167172 Da    PI: 8.831
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
HL.SW.v1.0.G023714.1genomeHOPBASEView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H212.90.0003314031425323
                            ET..TTTEEESSHHHHHHHHHHT CS
               zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                            Cp   Cgk F ++ +L++H r+H
  HL.SW.v1.0.G023714.1 1403 CPvkGCGKKFFSHKYLVQHRRVH 1425
                            9999*****************99 PP
2zf-C2H211.80.0007314611487123
                            EEET..TTTEEESSHHHHHHHHHH..T CS
               zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                            y+C    Cg++F+  s++ rH r+  H
  HL.SW.v1.0.G023714.1 1461 YVCAepGCGQTFRFVSDFSRHKRKtgH 1487
                            899999****************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005451.1E-172364IPR003349JmjN domain
PROSITE profilePS5118314.8532465IPR003349JmjN domain
PfamPF023753.1E-142558IPR003349JmjN domain
SMARTSM005583.1E-45196370IPR003347JmjC domain
PROSITE profilePS5118431.69199370IPR003347JmjC domain
SuperFamilySSF511979.89E-23210372No hitNo description
PfamPF023731.6E-33229352IPR003347JmjC domain
SMARTSM003552813781400IPR015880Zinc finger, C2H2-like
SuperFamilySSF576676.07E-614011437No hitNo description
PROSITE profilePS5015712.44514011430IPR007087Zinc finger, C2H2
SMARTSM003550.004514011425IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.2E-514031429IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028014031425IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.3E-714301455IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.63714311460IPR007087Zinc finger, C2H2
SMARTSM003550.001714311455IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028014331455IPR007087Zinc finger, C2H2
SuperFamilySSF576672.92E-914411485No hitNo description
Gene3DG3DSA:3.30.160.602.6E-914561484IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.03214611492IPR007087Zinc finger, C2H2
SMARTSM003550.6214611487IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028014631487IPR007087Zinc 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:0040010Biological Processpositive regulation of growth rate
GO:0045815Biological Processpositive regulation of gene expression, epigenetic
GO:0048366Biological Processleaf development
GO:0005634Cellular Componentnucleus
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
GO:0071558Molecular Functionhistone demethylase activity (H3-K27 specific)
Sequence ? help Back to Top
Protein Sequence    Length: 1494 aa     Download sequence    Send to blast
MAASALGSDP SPEVFSWLKT LPLAPEYHPT LTEFQDPISY IFKIEKEASK YGICKIVPPV  60
SPSPKKTVIA NLNKSLAARA GYSEGSNPKT PPTFTTRQQQ IGFCPRKPRP VQRPVWQSGE  120
QYTFQEFETK AKGFEKGFLK KCGKKGGGLS PLEIETLYWK ATVDKPFSVE YANDMPGSAF  180
VPVSAKKSRE AGESVTLGET AWNMRAVSRS KGSLLRFMKE EIPGVTSPMV YVAMLFSWFA  240
WHVEDHDLHS LNYLHMGASK TWYGVPKEAA VAFEEVIRVH GYGAEINPLV TFSILGEKTT  300
VMSPEVFVKE GVPCCRLVQN AGEFVVTFPR AYHTGFSHGE RPRRFNCAEA ANIATPEWLR  360
VANDAAIRRA SINYPPMVSH FQLLYDLALA LCSRIPVSIS SEPRSSRLKD KKKGEGETVV  420
KELFVQDVLK NNDILRVLGK GSPIVLLPRT SSDISVCSKL RVGSHLRLNT NVSLSPSISR  480
EEIKTSRSLI SDDLTIDRKQ EVDQEKVFYS VKGKLASLCE GSWVPSRGNK RTSTSNFKTP  540
IKNVEEKSNV DSDRLSEQRL FSCVTCGILS FACVAIVQPR DPAARYLMTA DCSFFNDWVV  600
NAGVASNVFP ISSVDQTASK QNTYTAWADN CAPLDSYEGP VPSISNQVQT EDQNNEVLSN  660
SEAHEATSAL GLLALHYGNS SDSEEDQARE DDSVYDKETN TTNCSPESKY RCESSSLSFQ  720
NSLSDAAGDD GRSPREIDLG EERASQNADF HKENGHNRDN VKYSSRQNFD CSVDASNNVA  780
STETNCLVGK IRDPMIVSQA CSADTYDAEA TRFCKATVPM KNDVVPFVPL SDEESSRMHV  840
FCLEHAVEVE QQLRQIGGVH ILLLCHPDYP KIETEAKSIA EELGINCPLN DTTFRDATKD  900
DQEKIQSALD SEEAMPKNGD WAVKLGINLF YSANLSRSPL YSKQMPYNSV IYNAFGRGSP  960
TSSSMKSDGF GRRSVKKKVV AGKWCGKVWM SNQVHPFLVK RNPEEEEERG ILAWAVPDEK  1020
PDRNHDSPHR NSNTMVTKKY VRKRKMKVEN ESIKKAKCIK GEDIVSENSM DGDSHEHHRR  1080
SLGNNQSTHT GVGSAKKGKH IQMEDAVSDD SMYVSLKQCK RTLRSKVTTS VETDDIVSDD  1140
SLGVISNYRN KKNPRREQAK QVKNLGIQDA VSDGSLDSES NQRRRRIPKS KQAKFMEEED  1200
SASDDFPGTN LYKQQTRIYK SKYAKSIERE DEVSDEPEEA YACHEDKRVL RSKQTKSTMQ  1260
PKMKQGTGRH VRQPSSQPVK QGTRQLAKKE TPKLKQQTPR LRNNQCDQNT SHICDDEEEE  1320
GGPSTRLRKR TPKPQKTAGP KKKEQQQQTS NKKAKNASAV KAQAGRGDAK FKDEEAEYVC  1380
DVEGCTMSFG VKHELVLHKR NICPVKGCGK KFFSHKYLVQ HRRVHMDDRP LRCPWKGCKM  1440
TFKWAWARTE HIRVHTGARP YVCAEPGCGQ TFRFVSDFSR HKRKTGHSTK KGR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A6e-74173918353Transcription factor jumonji (Jmj) family protein
6ip4_A6e-74173918353Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1971977RRSVKKK
210381044KYVRKRK
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_010101942.10.0lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A2P5EIB20.0A0A2P5EIB2_TREOI; TFIIH C1-like domain containing protein
STRINGXP_010101942.10.0(Morus notabilis)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF56483250
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]