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 676776928
Organism
Sisymbrium irio
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Sisymbrieae; Sisymbrium
Family C3H
Protein Properties Length: 1769aa    MW: 197839 Da    PI: 6.7846
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
676776928genomeVEGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H214.78.9e-0512311253323
                 ET..TTTEEESSHHHHHHHHHHT CS
    zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                 Cp   Cgk F ++ +L++H+r+H
  676776928 1231 CPvkGCGKNFFSHKYLVQHQRVH 1253
                 9999*****************99 PP
2zf-CCCH38.81.6e-1214331456326
                 S---SGGGGTS--TTTTT-SS-SS CS
    zf-CCCH    3 telCrffartGtCkyGdrCkFaHg 26  
                  e C f++rtG CkyG++CkF+H+
  676776928 1433 AEDCAFYMRTGSCKYGSTCKFNHP 1456
                 689********************9 PP
3zf-CCCH28.91.9e-0914851505525
                 --SGGGGTS--TTTTT-SS-S CS
    zf-CCCH    5 lCrffartGtCkyGdrCkFaH 25  
                 +C++++rtG CkyGd+C+F+H
  676776928 1485 ECKYYFRTGGCKYGDTCRFNH 1505
                 6******************** PP
4zf-CCCH406.7e-1315291552326
                 S---SGGGGTS--TTTTT-SS-SS CS
    zf-CCCH    3 telCrffartGtCkyGdrCkFaHg 26  
                 + +C++++rtG CkyG+ CkF+H+
  676776928 1529 EIECPYYMRTGSCKYGADCKFNHP 1552
                 568********************9 PP
5zf-CCCH18.14.7e-0616691694227
                 -S---SGGGGTS--TTTTT-SS-SSS CS
    zf-CCCH    2 ktelCrffartGtCkyGdrCkFaHgp 27  
                 ++++C ++++tG Ck+  +CkF+H++
  676776928 1669 DQPECAYYLKTGDCKFKFSCKFHHPK 1694
                 689*********************96 PP
6zf-CCCH31.62.9e-1017161739326
                 S---SGGGGTS--TTTTT-SS-SS CS
    zf-CCCH    3 telCrffartGtCkyGdrCkFaHg 26  
                 + +C +++r+G+Ck+G+ C+F H+
  676776928 1716 QNICTHYSRYGICKFGPACRFDHS 1739
                 679********************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005453.4E-71953IPR003349JmjN domain
PROSITE profilePS511838.7272061IPR003349JmjN domain
PfamPF023751.5E-92149IPR003349JmjN domain
SuperFamilySSF511973.02E-2651108No hitNo description
SMARTSM005583.5E-51133302IPR003347JmjC domain
PROSITE profilePS5118432.967136302IPR003347JmjC domain
SuperFamilySSF511973.02E-26151319No hitNo description
PfamPF023731.9E-37166285IPR003347JmjC domain
SMARTSM003559.612061228IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.17312291258IPR007087Zinc finger, C2H2
SMARTSM003550.0112291253IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.8E-612301257IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028012311253IPR007087Zinc finger, C2H2
SuperFamilySSF576676.56E-1012451287No hitNo description
Gene3DG3DSA:3.30.160.601.3E-812581282IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.92812591288IPR007087Zinc finger, C2H2
SMARTSM003550.001512591283IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012611283IPR007087Zinc finger, C2H2
SuperFamilySSF576677.83E-812771311No hitNo description
Gene3DG3DSA:3.30.160.606.3E-912831312IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.69912891320IPR007087Zinc finger, C2H2
SMARTSM003550.912891315IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012911315IPR007087Zinc finger, C2H2
SMARTSM003563.9E-714301457IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010315.27214301458IPR000571Zinc finger, CCCH-type
SuperFamilySSF902298.37E-614301459IPR000571Zinc finger, CCCH-type
PfamPF006424.6E-1014331456IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.106.1E-514361455IPR000571Zinc finger, CCCH-type
SMARTSM003569.5E-414801507IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010313.90114801508IPR000571Zinc finger, CCCH-type
SuperFamilySSF902291.7E-514831508IPR000571Zinc finger, CCCH-type
PfamPF006425.0E-714851505IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.101.3E-414861506IPR000571Zinc finger, CCCH-type
SMARTSM003564.0E-715261553IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010315.54415261554IPR000571Zinc finger, CCCH-type
PfamPF006422.0E-1015291552IPR000571Zinc finger, CCCH-type
SuperFamilySSF902292.88E-515301553IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.108.4E-515321551IPR000571Zinc finger, CCCH-type
SMARTSM003560.5416671694IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010312.87816671695IPR000571Zinc finger, CCCH-type
SuperFamilySSF902291.57E-517111739IPR000571Zinc finger, CCCH-type
SMARTSM003562.8E-417131740IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010314.76517131741IPR000571Zinc finger, CCCH-type
PfamPF006421.6E-717161739IPR000571Zinc finger, CCCH-type
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: 1769 aa     Download sequence    Send to blast
MSVSEQSPDV FPWLKSLPVA PEFRPTLAEF QDPIAYIFKI EEEASRYGIL WQSGEHYSFG  60
EFEAKAKSFE KNYLKRYGKR SQLSALEIET LYWRATVDKP FSVEYANDMP GSAFIPLSLA  120
AARRREYGGD GGTVGETGWN MRAMARAEGS LLKFMKEEIP GVTSPMVYIA MMFSWFAWHV  180
EDHDLHSLNY LHMGAGKTWY GVPKDAAVAF EEVVRVHGYG GELNPLVTFS TLGEKTTVMS  240
PEVFVKAGIP CCRLVQNPGE FVVTFPRAYH SGFSHGFNCG EASNIATPEW LRVAKDAAIR  300
RAAINYPPMV SHLQLLYDYA LALGSRVPAS IHTKPRSSRL KDKKRSEGEK LTKELFVQNI  360
IHDNELLQSL GKGSPIALLP QSSSDISVCS ELRIGSHLSG NEEKPIQLKS EDLSSDSHSD  420
GVKDILSVKE KFTSLCESNR NHLATKEKET QRASEDSERR KNDGAVGLSD QRLFSCVTCG  480
VLSFDCVAIV QPKEAAARYL MSADCSFFNE WTVGSGSANP GQDVMKPYSQ STGKHDVGYL  540
YNASVQTTDH SMKTGDQRAS TTSATKAHKK DNALGLLASA YGDSSDSEEE DQKGVDAIIS  600
EERKYDQNGA SPYEASDGNE EATVGRTSDY SNQRFSRGKG KGVVEGINDI TLPFVPRSDD  660
DSSRLHVFCL EHAAEVEQQL RPIGGIHIML LCHPEYPRIE AEGKIVAGEL GVNHEWSDTE  720
FRNVTREDEE TIQAALANVE AKAGNSDWAA KLGVNLSYSA ILSRSPLYSK QMPCNSVIYN  780
AFGRGSPETS SPAKPQVSGK RSSRQKKYVV GKWCGKVWMS HQVHSFLLEQ EDGEESELRD  840
EDVSGKRLFP YSDSRDATTM FGRKYSRKRK MRAKAVPRKK LTSFKREDGV SDDTSEDHSY  900
KQQWRAPENE EEMSDDSSNQ MFDQQQQQRL KRIRRDKSVR EFDSDDEVSD RSLGEEYAVR  960
ECAVSDSSME DSFQPYKQSM GRNSLDSVYG HNDDNIYRHP RGYPRSKQAK VFRNPISYDS  1020
EDNDVYQQRG NIQASRIGCE YDSAEDYIEE QKICSIGKRQ TRSIAKRKVK TEIVQSRRGR  1080
TLQQSGSRKK NEDLDSYMEG PSTRLRVRNL KPSRGSLETK PKKTGKKSSK ISFFGSEDDV  1140
EEEEENEEPS TRLRVRILKS SRGSSVTKPK KTGKKGSKIS FPGVASEDDV EENEAEVNEE  1200
EECAAYQCDM EGCTMSFNSE KQLSLHKRNI CPVKGCGKNF FSHKYLVQHQ RVHSDDRPLK  1260
CPWKGCKMTF KWAWSRTEHI RVHTGARPYV CAEPGCDQTF RFVSDFSRHK RKTGHSAKKT  1320
KKRKNMTNSQ GLSGSIADGF ETKPVSLSLS GDSSADGSPS DLNHAVDDLS NEFKNVGLEE  1380
VEKEKSVMMM SVSESNGGLD LKQEEEEEDG DGDDDGGVSD NESVSTYPMR PGAEDCAFYM  1440
RTGSCKYGST CKFNHPLPNP RKIQIARDTN IRAKEEDGDQ QRLMECKYYF RTGGCKYGDT  1500
CRFNHTKPKS GLPSVQELNF LGLPIRPGEI ECPYYMRTGS CKYGADCKFN HPDPTTIGGT  1560
DSPSFHGNNG GSIGSFSPKT TFQPSSTSWS SPRHANGATP FIPSMLSQSR GLVSQTPEWN  1620
GYQASGYSSE RSVFTPSTTY LMNNPSAETN MFSQYQYQMT AEEFPERPDQ PECAYYLKTG  1680
DCKFKFSCKF HHPKNRLPKQ PAYALNDKGL PLRPDQNICT HYSRYGICKF GPACRFDHSI  1740
QVPDSTGSSN AGVEPPQVGA NGNESDGWN
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A8e-771203132320140Lysine-specific demethylase REF6
6a58_A8e-771203132320140Lysine-specific demethylase REF6
6a59_A8e-771203132320140Lysine-specific demethylase REF6
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1865870SRKRKM
2867879KRKMRAKAVPRKK
313091323KRKTGHSAKKTKKRK
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMap676776928
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_006404260.10.0lysine-specific demethylase REF6
RefseqXP_024013589.10.0lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A1J3JIY40.0A0A1J3JIY4_NOCCA; Lysine-specific demethylase REF6
STRINGXP_006404260.10.0(Eutrema salsugineum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM52592843
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]