PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID XP_004515844.1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Cicereae; Cicer
Family C2H2
Protein Properties Length: 1567aa    MW: 177565 Da    PI: 8.1359
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_004515844.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H212.80.0003614511476123
                      EEET..TTTEEESSHHHHHHHHHH.T CS
         zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                      y+C    C++sF +k +L++H r+ +
  XP_004515844.1 1451 YQCDieGCTMSFGSKQELVHHKRNiC 1476
                      99********************9877 PP

2zf-C2H212.80.0003514761498323
                      ET..TTTEEESSHHHHHHHHHHT CS
         zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                      Cp   Cgk F ++ +L++H r+H
  XP_004515844.1 1476 CPvkGCGKKFFSHKYLVQHRRVH 1498
                      9999*****************99 PP

3zf-C2H211.80.0007715341560123
                      EEET..TTTEEESSHHHHHHHHHH..T CS
         zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                      y+C    Cg++F+  s++ rH r+  H
  XP_004515844.1 1534 YVCAepGCGQTFRFVSDFSRHKRKtgH 1560
                      899999****************99666 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005453.0E-161657IPR003349JmjN domain
PROSITE profilePS5118314.1181758IPR003349JmjN domain
PfamPF023752.7E-131851IPR003349JmjN domain
SMARTSM005581.7E-47172341IPR003347JmjC domain
PROSITE profilePS5118432.784172341IPR003347JmjC domain
SuperFamilySSF511977.69E-26188339No hitNo description
PfamPF023732.3E-36205324IPR003347JmjC domain
Gene3DG3DSA:3.30.160.602.7E-414451473IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003556.714511473IPR015880Zinc finger, C2H2-like
SMARTSM003550.004514741498IPR015880Zinc finger, C2H2-like
SuperFamilySSF576676.72E-614741510No hitNo description
PROSITE profilePS5015712.50814741503IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.2E-514751502IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028014761498IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.602.5E-815031528IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.003615041528IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.82415041533IPR007087Zinc finger, C2H2
PROSITE patternPS00028015061528IPR007087Zinc finger, C2H2
SuperFamilySSF576672.65E-915141558No hitNo description
Gene3DG3DSA:3.30.160.602.4E-915291557IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.6215341560IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.03215341565IPR007087Zinc finger, C2H2
PROSITE patternPS00028015361560IPR007087Zinc 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: 1567 aa     Download sequence    Send to blast
MANSEEVFPW LKSLPVAPEY RPSIAEFQDP IGYIFKIEKE ASKYGICKII PPVSPSSKKT  60
AISNMNRSQP RFTTRQQQIG FCPRKPQPVR RPVWHSGHHY SLREFEAKAK SFEKSYFKKG  120
KKLSQLSPLE IETIYWKVTA DKPFSVEYAN DMPGSAFGVL NDGGYGGDGV LTVGETGWNM  180
RGVSRANGSL LRFMKEEIPG VTSPMVYVAM LFSWFAWHVE DHDLHSLNYL HMGASKTWYG  240
VPRDAAVAFE DVVRVHGYGG EINPLVTFAI LGEKTTVMSP EVFVGAGIPC CRLVQNAGEF  300
VVTFPRAYHT GFSHGFNCAE AANIATPEWL KVAKDAAIRR ASINYPPMVS HSQLLYDLGL  360
ALCSRVSGGI SVGPRSSRLK DKKRKGVGET VIKELFARDV LHNNDLLHAL GKGASVVLLP  420
RSSSDDLSVC TKLRVGSQQL KLNTEFSLNV CNSEGSNSSK SFISDDLVFN RNHGIKKVKG  480
FSSVKEKFAT LCERNRVCSF GENGDTCTSS SKTLQRDIEN DTNQGDALSD QRLFSCVTCG  540
ILCFSCVAIV QPRQPAARYL MSADCSFFND SIVGSGVARN MFTVAHEDAY ISKQSTYTGW  600
TKQNARNDLY DVPVESVEQR TQIADQNYIE ASNIERKKGN TALALLASAY GNSSDSEDDQ  660
GDSDIAVDGN DLNTMKHPSE SKSQEKSCLP SHFQDCQASP VNSINNYEYY MHKKVERIMS  720
SFDYSVKSED YDVTSGVAFK NTREGFHPTL NCSEDTHTEM PLLSKTVIPI ENKTLVPPCD  780
EDSSRMHVFC LEHAAEAERQ LRPFGGAHIL LLCHADYPKI EAEAKFVAEE MGIDYEWKNT  840
VYRHAEREDE ERIQSALDSE EAIPGNGDWA VKLGINLFYS ANLSRSPLYS KQMPYNSLMY  900
YAFGRSSPVN LPIEPKVCQR RTKRQKKVVA GKWCGKVWKS NQIHPLLAKR ELEDVQDEKS  960
LHGWPLPDEK SEVSERTHKS NTTNRKSGRK RKMTIENEGA WEGSSAEGDW LTDYSIEDKC  1020
NRSQRRALAS KRTRHIERDS TASEGDSSPL KHHKKHTSKH TKCMESDIVS DDSPDDNTHI  1080
QQWRKSVAKE AKSIDCDMVS DDTMDHASDW PHSEELSHKQ DVSEDSLGVD SLQQHRKTPK  1140
SNFDQYISEE DVISDGQTEV HFQNQKWRIS KNGQHKYLSE EDAVISDDQL EHSMLKQQLR  1200
NPNSRKELDN YHVEEDIISE DELECHSRKY QRRTPKDKQA KHVIGEDVTC DDQLEDHFQK  1260
PRRSIRMRKK NRHSDEEVMD DSAENNSHVL HRTPKRKQAK CTDEDNINSD DRMEDDCHQQ  1320
HSRPLRSKQT KSQILQQMKQ SNSLCVRSKT SRPVKCGSHM LTKSKSPRLM KQQPRVWNSQ  1380
SGNSKDEMSQ IEDDEGGGPP STRLRKRFLK VQSESEGKTT ERETKKKKVK NAIAAKVSAV  1440
RAKMKDDEEE YQCDIEGCTM SFGSKQELVH HKRNICPVKG CGKKFFSHKY LVQHRRVHED  1500
DRPLKCPWKG CKMAFKWAWA RTEHIRVHTG ARPYVCAEPG CGQTFRFVSD FSRHKRKTGH  1560
SVKKTRS
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A1e-78103558346Transcription factor jumonji (Jmj) family protein
6ip4_A1e-78103558346Arabidopsis JMJ13
Search in ModeBase
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_004515844.1
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_004515844.10.0lysine-specific demethylase REF6-like
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A1S2Z6B70.0A0A1S2Z6B7_CICAR; lysine-specific demethylase REF6-like
STRINGXP_004515844.10.0(Cicer arietinum)
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]