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 XP_010101942.1
Organism
Morus notabilis
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Moraceae; Morus
Family C2H2
Protein Properties Length: 1508aa    MW: 169200 Da    PI: 8.6449
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_010101942.1genomeBGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H213.40.0002213931418123
                      EEET..TTTEEESSHHHHHHHHHH.T CS
         zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                      y C    C++sFs+k +L+ H ++ +
  XP_010101942.1 1393 YMCDieGCTMSFSTKQELVLHKKNiC 1418
                      899999***************99866 PP
2zf-C2H213.10.0002814181440323
                      ET..TTTEEESSHHHHHHHHHHT CS
         zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                      Cp   Cgk F ++ +L++H r+H
  XP_010101942.1 1418 CPvkGCGKKFFSHKYLVQHRRVH 1440
                      9999*****************99 PP
3zf-C2H211.80.0007414761502123
                      EEET..TTTEEESSHHHHHHHHHH..T CS
         zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                      y+C    Cg++F+  s++ rH r+  H
  XP_010101942.1 1476 YVCAepGCGQTFRFVSDFSRHKRKtgH 1502
                      899999****************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005451.5E-142465IPR003349JmjN domain
PROSITE profilePS5118313.552566IPR003349JmjN domain
PfamPF023757.8E-142659IPR003349JmjN domain
PROSITE profilePS5118433.514186365IPR003347JmjC domain
SMARTSM005582.6E-50196365IPR003347JmjC domain
SuperFamilySSF511973.3E-26210379No hitNo description
PfamPF023732.0E-36229348IPR003347JmjC domain
SMARTSM003551013931415IPR015880Zinc finger, C2H2-like
SMARTSM003550.004514161440IPR015880Zinc finger, C2H2-like
SuperFamilySSF576677.21E-614161452No hitNo description
PROSITE profilePS5015712.44514161445IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.3E-514171444IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028014181440IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.3E-714451470IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.001714461470IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.63714461475IPR007087Zinc finger, C2H2
PROSITE patternPS00028014481470IPR007087Zinc finger, C2H2
SuperFamilySSF576672.68E-914561500No hitNo description
Gene3DG3DSA:3.30.160.602.3E-914711499IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.01114761507IPR007087Zinc finger, C2H2
SMARTSM003550.6214761502IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028014781502IPR007087Zinc 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:0032259Biological Processmethylation
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:0008168Molecular Functionmethyltransferase activity
GO:0046872Molecular Functionmetal ion binding
GO:0071558Molecular Functionhistone demethylase activity (H3-K27 specific)
Sequence ? help Back to Top
Protein Sequence    Length: 1508 aa     Download sequence    Send to blast
MAASGLTSEQ ASPEVFSWLK TLPQAPEYHP TLAEFQDPIS YIFKIEKEAS EYGICKIVPP  60
VPPSAKKTVI ANLNKSLAAR NGGFDASNPK NPPTFTTRQQ QIGFCPRKPR PVQRPVWQSG  120
ENYTFQQFEA KAKGFERSFF KRCAKKGALS PLEIETLYWK ATVDKPFSVE YANDMPGSAF  180
VPVSAKRSRE AGESATLGET AWNMRAVSRA KGSLLRFMKE EIPGVTSPMV YVAMMFSWFA  240
WHVEDHDLHS LNYLHMGAGK TWYGVPREAA VAFEEVVRVH GYGGEINPLV TFSILGEKTT  300
VMSPEVFVRA GVPCCRLVQN PGEFVVTFPR AYHTGFSHGF NCGEAANIAT PEWLRVAKDA  360
AIRRASINYP PMVSHFQLLY DLALALCSRI PESVGAEPRS SRLKDKKKGE GETVVKELFV  420
QNVLQNNDLL HVLGNGSPVV LLPRSSSDIS VCSKLRVGSH LRLNSSSPLA SCNSREEMKS  480
SRSLISDDLM IDRKQEVDQV KDFYSVKGKL ASLCDRSWVP SLRGNKITCA SNSKTSNMNV  540
EGESTVDNDG LSDQRLFSCV TCGILSFACV AIIQPREPAA RYLMSADCSF FNDWVVNAGV  600
ASNVFPVSNR YQTASKENTY TGWTDNSEPL ALCENPGQSV NFQAQMADQK NEIVSNTETQ  660
KAPSALGLLA LNYGNSSDSE EDQVQEDVSV DGNETNVSNC SLESKYRCES SSPSLRNCQG  720
DTVHGRSLVE LDSGDDFASQ NADSYMENGH NKDNTKYDSH QNFDCPVSFR TNNAAPAQSN  780
GLVPKFGDGM KASRTCSPDT YDAEATRFCK AIAPTKNENM PFVPICDEDS CRMHVFCLEH  840
AVEVEQQLRQ VGCVDIVLLC HPDYPKIETE AKAMAEELGI SHLWNDIEFR DATKDDENMI  900
QATLDSEEAI PKNGDWAVKL GINLFYSANL SRSPLYSKQM PYNSVIYDAF GRSSPASSSA  960
RSDGFERRPA KQKKVVAGKW CGKVWMSSQV HPFLAKKDPE EEEQERSFHT WATPDEKVER  1020
KYDGTRKSSN TMIAKKYVRK RKMTVESSST KKAKRVKRED AVSDNSMDDS HEHHRRSLRS  1080
KQAVSIGGGS AKKAKHTEIE GAASDDSLHD NSHRQHRRTF KSKQATYVES DGIVSDDSLE  1140
VDFRYQHKKI LRSKPSKHAG REDVVSDDSL DSDSHQLRGR VCRIKQAKHT EEEDVVSDDS  1200
LDSDSQLHRS IPRSKQAKYN EREDSSSDYF HRNNLQKLHR RISKSKPAKS IGREDEDLDE  1260
PLEDNARKSD ERILRSKRTK SALQQKMKQE TPHHVKQSTA RPVKQENRKL KQQTPRLRNS  1320
QCEQNILGSC AEEELEGGPS TRLRKRNPKP QKLTGAKRKE QQQPSRKKVK NAVVVKAQAG  1380
HNDAKSKDEE GEYMCDIEGC TMSFSTKQEL VLHKKNICPV KGCGKKFFSH KYLVQHRRVH  1440
MDDRPLRCPW KGCKMTFKWA WARTEHIRVH TGARPYVCAE PGCGQTFRFV SDFSRHKRKT  1500
GHSVKKAR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A1e-77183868353Transcription factor jumonji (Jmj) family protein
6ip4_A1e-77183868353Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
110351041KYVRKRK
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
PlantRegMapXP_010101942.1
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
TrEMBLW9S5V70.0W9S5V7_9ROSA; Lysine-specific demethylase REF6
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]