PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID 30147.m013814
Common NameRCOM_1507500
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Euphorbiaceae; Acalyphoideae; Acalypheae; Ricinus
Family C2H2
Protein Properties Length: 1736aa    MW: 196560 Da    PI: 8.126
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
30147.m013814genomeJCVIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H212.40.0004816201645123
                     EEET..TTTEEESSHHHHHHHHHH.T CS
        zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                     y+C    C++sF +k +L +H r+ +
  30147.m013814 1620 YQCDieGCTMSFGSKQELAVHKRNiC 1645
                     99********************9877 PP

2zf-C2H212.70.000416451667323
                     ET..TTTEEESSHHHHHHHHHHT CS
        zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                     Cp   Cgk+F ++ +L++H r+H
  30147.m013814 1645 CPvkGCGKTFLSHKYLVQHRRVH 1667
                     9999*****************99 PP

3zf-C2H211.50.0009117031729123
                     EEET..TTTEEESSHHHHHHHHHH..T CS
        zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                     y+C    Cg++F+  s++ rH r+  H
  30147.m013814 1703 YVCAeeGCGQTFRFVSDFSRHKRKtgH 1729
                     89********************99666 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005454.7E-152970IPR003349JmjN domain
PROSITE profilePS5118314.523071IPR003349JmjN domain
PfamPF023751.9E-143164IPR003349JmjN domain
PROSITE profilePS5118433.863196365IPR003347JmjC domain
SMARTSM005581.3E-49196365IPR003347JmjC domain
SuperFamilySSF511974.12E-26210384No hitNo description
PfamPF023734.7E-37229348IPR003347JmjC domain
Gene3DG3DSA:3.30.160.601.9E-416111642IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003558.916201642IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.5716431672IPR007087Zinc finger, C2H2
SuperFamilySSF576671.58E-616431679No hitNo description
SMARTSM003550.003316431667IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.4E-516441671IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028016451667IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.609.1E-816721697IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.53316731702IPR007087Zinc finger, C2H2
SMARTSM003550.003816731697IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028016751697IPR007087Zinc finger, C2H2
SuperFamilySSF576673.35E-916831727No hitNo description
Gene3DG3DSA:3.30.160.603.2E-916981726IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.03217031734IPR007087Zinc finger, C2H2
SMARTSM003550.8517031729IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028017051729IPR007087Zinc 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: 1736 aa     Download sequence    Send to blast
MAAPSGLVTE PTASQQPQEV FQWLKNLPLA PEYHPTLAEF QDPIAYIFKI EKEASKYGIC  60
KIVPPVLAAP KKAAIANLNR SLAARSSSSK SAPTFTTRQQ QIGFCPRKPR PVQKPVWQSG  120
ENYTFQEFEA KAKSFEKSYF KKCPKKTAFS PLEVETLYWK ATVDKPFSVE YANDMPGSAF  180
SVKKMSGGKE IIEGVTVGET EWNMRGVSRA KGSLLRFMKE EIPGVTSPMV YVAMMFSWFA  240
WHVEDHDLHS LNYLHLGAGK TWYGVPKEAA VAFEEVVRDH GYGGEINPLV TFSVLGEKTT  300
VMSPEVFVTA GVPCCRLVQN AGEFVVTFPR AYHSGFSHGF NCGEAANIAT PEWLRVAKDA  360
AIRRASINYP PMVSHFQLLY DLALELCTRM PVSISAKPRS SRLKDKQKGE GETLVKEQFV  420
QNVIHNNELL HILGKGSSVV LLPRSSSDIS VCSDLQRNYG IDQSKGTISV KEKFASLCER  480
NRFSSLNGNE NKHTTNTRTE NKGTTHGDKL SDQRLFSCVT CGILSFDCIA VVQPTETAAR  540
YLMSADCSFF NDWIVGSGAT NNRLTTTNGD PNTCQLDQPT GWVENSVVDH LYDVPVQSVN  600
YQPQKIDKSK VNSNATMQGE SSALGLLALN YGNSSDSEED QDEPDVSDHA IDMPTCSSEN  660
KYKYQNCALP SFKQECHHDE TVSHTLSLVT LDCGDKVSLQ TDDCHKEHGD RAGNFKDGTP  720
DCFLDFGTDN MEPNGSECRF GDAVSISHIN SNCSPAVHDT EKMKFRRVVP RGNGDMPFAQ  780
RSDEDSSRMH VFCLEHAVEV EQQFRSIGGV HILLLCHPEY PRLEAEAKLV SEELGIDHLW  840
NDIAFRDATK NDEENIQSAL DSEEAIPGNG DWAVKLGINL FYSASLSHSS LYSKQMPYNS  900
VIYKAFGRVS PASSPTKLNV YGRRSGKQKK VVAGRWCGKV WMSNQVHNFL LKNASEDRDQ  960
EEEQDGSFHG WKMLDEKVER KLQNFYKTET ALAAAKSVRK RKLTTVTRPI KKVKSPETEA  1020
AASDDLEEDV SHKQHTKVYS RKQTKHIERE VSYDSLDNSH QQHGKTHRIK QAKSVERDDA  1080
VSDDSLGGNT HQQQHRRIPR SKQVKYIDSE NDVSDTLIGS NSQKQHSRIP KPRSKQVKYI  1140
RRKSEISDDS LEGDINEWHG RGPRSTQAGF YGREVAVSDD SLEESSHRPL GTVRRSKQAA  1200
YFESEDALSD DSVENSSLQQ NRRVSRGSLA KYFEREDEVS DDMLEENTFQ QCTGSHRSRK  1260
KKFVDREGEV SDNLLDESTQ LQHRRIFRSK QGRFVEREDE VSDDSLEDNS QQQRRIPTSK  1320
RAKFVESEDA VSDELEDDTH LKHWRIPRSK KAKIMEREAC SDDLQENDAQ WQPRKTPRGK  1380
PVKFIEREDV SDDLEEATHW QQRKTSRHKP VTSFEREDVS DDLQEENTRW QPRKTTRGKQ  1440
TKFFEKEDVS DDLQEDDTRW HPSKTPKSKQ AKYAELEDAV SDDLLEDNST KQHRRILRNK  1500
QKSGTLGKVN RESIQHVKQG TARAKKKENS KSIKKEKEVK QENPGFRNSK SGRLFESHVE  1560
EEVEGGPSTR LRKRPSKASK ESETKLKEKL QSNKKKVRGS ASAVKRASGQ KNNKDEDAEY  1620
QCDIEGCTMS FGSKQELAVH KRNICPVKGC GKTFLSHKYL VQHRRVHLDD RPLKCPWKGC  1680
KVTFKWAWAR TEHIRVHTGA RPYVCAEEGC GQTFRFVSDF SRHKRKTGHS VKKSRN
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A2e-78215136457Transcription factor jumonji (Jmj) family protein
6ip4_A2e-78215136457Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
19951001KSVRKRK
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
PlantRegMap30147.m013814
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_015580157.10.0lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLB9RAP00.0B9RAP0_RICCO; Nucleic acid binding protein, putative
STRINGXP_002511265.10.0(Ricinus communis)
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]