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 Ciclev10018473m
Common NameCICLE_v10018473mg
Organism
Citrus clementina
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus
Family C2H2
Protein Properties Length: 1635aa    MW: 184227 Da    PI: 8.7
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Ciclev10018473mgenomeICGCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H212.80.0003615431565323
                       ET..TTTEEESSHHHHHHHHHHT CS
          zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                       Cp   Cgk F ++ +L++H r+H
  Ciclev10018473m 1543 CPvkGCGKKFFSHKYLVQHRRVH 1565
                       9999*****************99 PP
2zf-C2H211.70.0008116011627123
                       EEET..TTTEEESSHHHHHHHHHH..T CS
          zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                       y+C    Cg++F+  s++ rH r+  H
  Ciclev10018473m 1601 YVCAepGCGQTFRFVSDFSRHKRKtgH 1627
                       899999****************99666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005451.7E-161960IPR003349JmjN domain
PROSITE profilePS5118314.4372061IPR003349JmjN domain
PfamPF023756.3E-152154IPR003349JmjN domain
SMARTSM005584.9E-52191360IPR003347JmjC domain
PROSITE profilePS5118432.499191360IPR003347JmjC domain
SuperFamilySSF511971.73E-27209381No hitNo description
PfamPF023734.1E-37224343IPR003347JmjC domain
SMARTSM003551415181540IPR015880Zinc finger, C2H2-like
SMARTSM003550.004515411565IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.36215411570IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.603.7E-515421564IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028015431565IPR007087Zinc finger, C2H2
SuperFamilySSF576672.19E-915571599No hitNo description
Gene3DG3DSA:3.30.160.602.8E-915651593IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.001415711595IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.74115711600IPR007087Zinc finger, C2H2
PROSITE patternPS00028015731595IPR007087Zinc finger, C2H2
SuperFamilySSF576674.25E-815891623No hitNo description
Gene3DG3DSA:3.30.160.602.3E-915941624IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.46816011632IPR007087Zinc finger, C2H2
SMARTSM003550.6216011627IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028016031627IPR007087Zinc 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: 1635 aa     Download sequence    Send to blast
MAEPVQQQDI LPWLKTLPVA PEFHPTLAEF QDPIAYIFKI EKEASQYGIC KIVPPVPPPP  60
KKTAITFLNR SLAQRAAATG GATSSSGPTF TTRQQQIGFC PRKPRPVQKP VWQSGEYYTF  120
QEFETKAKNF EKSYLKKCGN KKAALSALEI ESLYWKASVD KPFSVEYAND MPGSAFVPVR  180
KIREAVGEGV TVGETPWNMR GVSRAKGSLL RFMKEEIPGV TSPMVYIAML FSWFAWHAED  240
HDLHSLNYLH MGASKTWYGV PMEAANAFEE VVRVHGYGEE INPLVTFATL GEKTTMISPE  300
VFVGAGVPCC RLVQNAGEFV VTFPRAYHMG FSHGFNCGEA ANIATPEWLN IAKDAAIRRA  360
SINYPPMVSH FQLLYDLAIA MHSSLPVAVS AKPRSSRLKD KNKDEGETLV KELFVQDVAQ  420
NNELLHVLGQ GSPIVLLPQS SSGALGANPW IPLGLCSYRE AIKSSGGLVS NDIMVGKNNG  480
INPVKGYCSV KGKFASLYAR NSSLSETDNI RNWNSQILST DTERQNTVQG DRSSDQRLFS  540
CVTCGILSFA CVAVIQPREP TARYLMSADC SFFNDWIVGS GVSGAFRAAG EDVIASEHNS  600
RSRWIGKSGR NSLYDVPVQS ANQIQAVDES NETISDRETK GDTSALNLLA ITYGNSSDSE  660
EEQVEPNVPM CDDKETKLTE CLLERKYQQN FHAAAAAAGS QDLSFISLDC EDEASLQISN  720
VQPEFRRDYL NDKNPQMSEC SVQFETDKHD CSKPNGFDGC FGDPIAASYA SKCAPVIHGG  780
ENVEFSKAIV PVMNAEMSFA PRSDEDSSRM HVFCLEHAVE VEQQLRPIGG VDIFLLCHPD  840
YPKMVAEAKL VAEELGIDSL CDEISFRVAT KEDEKRIHLS LDSEDAIPGN GDWAVKLGIN  900
LFYSANLSRS PLYSKQMPYN SIIYNAFGRS SPASSPNKYD NGRRPARQRK VVAGKWCGRV  960
WMSNQVHPFL VQKDPEEQEL ERSFHAWTTP DENFERKPES ICQTTSTLVT RKYSRKRKMV  1020
AESVSTKKAK CIDTEDAGSK YSLEGDTRIQ QRRILRNKPA KLMEKKDVDL PDSSEVSSYQ  1080
QKRSVSRRKQ AKCIQREVGD SNDALPGNSL IQYRRIPKRK HAKCIGREDA VLDDLTDDSS  1140
LKQYRRIPRS KLAKHVARED EVSDNSLRGT SDRQHTSIPK GKEFTCIDRD DAISDDSLQD  1200
NSRQLQFNRV PKSKQAEWIE REDAASDDSL EDYPHRLQHK KIPNIKQPKC IESEDPVLDN  1260
LLEKNTHRLH HQRILKSKRA KCVEREDAVS DDLLEDSSHM LPRRSQKSKQ AKWMREDAVS  1320
DDSLEDNCHQ QHKRIPRDKQ SKCTEMEDTV FYDSAEDKIR QFRRIARKRA NFTEREDAVL  1380
YDLLDNKSHR RHCRTLRSKQ LRTETLRKMK QETPSHMKPG KSRLTKQETS RLVKQVTSRQ  1440
HSVKSDQNAK LFDSVVEQEL EGGPSTRLRK RIPKPQKEFE TKPKEKNQAA KKKVKNASVV  1500
KAPAGLNNAK IKDEEAGYHC DMEGCTMSFG TKQELVLHKK NICPVKGCGK KFFSHKYLVQ  1560
HRRVHLDDRP LKCPWKGCKM TFKWAWARTE HIRVHTGARP YVCAEPGCGQ TFRFVSDFSR  1620
HKRKTGHSAK KSRG*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A1e-7473842356Transcription factor jumonji (Jmj) family protein
6ip4_A1e-7473842356Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
110131018SRKRKM
211131119RRIPKRK
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Highly expressed in the shoot apical meristem and primary and secondary root tips, and lower expression in cotyledons, leaves and root axis along vascular tissues. Detected in inflorescences, stems and siliques. {ECO:0000269|PubMed:15377760, ECO:0000269|PubMed:18713399}.
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_024044095.10.0lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLV4TIR40.0V4TIR4_9ROSI; Uncharacterized protein
STRINGXP_006440007.10.0(Citrus clementina)
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]