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 Potri.012G092400.1
Common NamePOPTR_0012s09390g
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus
Family C2H2
Protein Properties Length: 1686aa    MW: 191195 Da    PI: 9.0985
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Potri.012G092400.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H2110.001315691594123
                          EEET..TTTEEESSHHHHHHHHHH.T CS
             zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                          y+C    C +sF +k +L  H r+ +
  Potri.012G092400.1 1569 YQCDidGCRMSFVSKQELALHKRNiC 1594
                          99********************9877 PP

2zf-C2H212.70.0003815941616323
                          ET..TTTEEESSHHHHHHHHHHT CS
             zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                          Cp   Cgk F ++ +L++H r+H
  Potri.012G092400.1 1594 CPvkGCGKKFFSHKYLVQHRRVH 1616
                          9999*****************99 PP

3zf-C2H211.60.0008816521678123
                          EEET..TTTEEESSHHHHHHHHHH..T CS
             zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                          y+C    Cg++F+  s++ rH r+  H
  Potri.012G092400.1 1652 YVCAeeGCGQTFRFVSDFSRHKRKtgH 1678
                          89********************99666 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005451.1E-132968IPR003349JmjN domain
PROSITE profilePS5118313.553071IPR003349JmjN domain
PfamPF023754.4E-143164IPR003349JmjN domain
SuperFamilySSF511973.3E-28117177No hitNo description
SMARTSM005583.6E-52196365IPR003347JmjC domain
PROSITE profilePS5118435.234196365IPR003347JmjC domain
SuperFamilySSF511973.3E-28214383No hitNo description
PfamPF023731.3E-36229348IPR003347JmjC domain
SMARTSM003558.915691591IPR015880Zinc finger, C2H2-like
SMARTSM003550.004515921616IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.38315921621IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.602.3E-515931620IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028015941616IPR007087Zinc finger, C2H2
SuperFamilySSF576672.5E-916081650No hitNo description
Gene3DG3DSA:3.30.160.604.0E-816211646IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.74116221651IPR007087Zinc finger, C2H2
SMARTSM003550.001416221646IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028016241646IPR007087Zinc finger, C2H2
SuperFamilySSF576676.38E-816401674No hitNo description
Gene3DG3DSA:3.30.160.602.9E-916471674IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.67916521683IPR007087Zinc finger, C2H2
SMARTSM003550.8516521678IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028016541678IPR007087Zinc finger, C2H2
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: 1686 aa     Download sequence    Send to blast
MAAPSGLSPE PPQPPTSTEV CQWLKNLPLA PEYRPTQAEF QDPIAYIFKI EKEASQYGIC  60
KIIPPVLPSA KKTTLSNLNR SLSARNGDSS APTFTTRQQQ IGFCPRKPRP VQKPVWQSGE  120
TYTFQEFETK AKSFEKNYLK KFSKKGGLSP LEIENLYWKA TLDKPFAVEY ANDMPGSAFS  180
PRKKEGQGGV VGEGMYVGET EWNMRSVSRA KGSLLRFMKE EIPGVTSPMV YIGMIFSWFA  240
WHVEDHDLHS LNYMHMGAGK TWYGVPREAA VAFEEVVRVH GYGGENNPLV TFAVLGEKTT  300
VMSPEVFISA GVPCCRLVQN AGEFVVTFPR AYHSGFSHGF NCGEAANIAT PEWLTVAKDA  360
AIRRASINYP PMVSHFQLLY DLALEFCTRI PVNISAKPRS SRLKDKQKGE GETLVKEQFV  420
KNMMQNNDLL HILGKGSSVV LLPRSSSDIS VCSNLRVGSQ LRDNPTLGLS SQKDFMKSSK  480
SSGSDDILMD ENQEINQVKG FFSVKAKFAS LCERNRFSTI NGNECTQSMN MSTERGSPIH  540
GDKLSDQRLF SCVTCGILSF DCLAIIQPKE AASRYLMSAD CSFFNDWVVG SGVTRDVFTV  600
AGGIANIPEQ NSSMRWVRKN TVAGLYDVPV QSLNYQIQMA DQSVEVASSS AKQMESSALG  660
LLALNYGNSS DSEDDQVEAG LSCHDETNFT NCSLESKYQG QSSACPSYKQ KYYDAETGGH  720
PLSPSKHDQR GDVPFKAIDM YPEHGDRPDN FKDRSDDTLG CSFGFPANNP ACIESNGLDG  780
RYRDPVSIPH MSLNCSPIVH DTEKTKFNRP TVPIENPDMP FTQRSDRDSS CLHVFCLEHA  840
VEIEQQLRQI GGVHIFLLCH PEYPRIEAEA KSVSEELGID HLWNDITFRD AAKEDEERIQ  900
SALDTEEAIP GNGDWAVKLG INLFYSANLS RSPLYSKQMP YNSVIYNAFG RASPVSSPPK  960
FKVYGRRSGK PKKVVAGKWC GKVWMSNQVH PFLVKRDFVY QNQEQEQERS FHALATPDEK  1020
LEKKPQTIHR NETSRKSGRK RKIIAGSRTV KKVKCLEAEE ADSEDSVGDN SHRQHMRIHN  1080
RKNTEDIERE ISYDLVEDSN QQHGSYRRKW AKSVESDDAV SDDPLAEHVR QQYRRMRRSK  1140
QAKSIKRENT VSYASVENKF RKQLRRVHRS DQAKCSERRC VASDDSLDDN SDQWHGRAPR  1200
STLAKYTERE DANSDDSPEE SSRWQHGRVS RSKLLRYVKK ESAISDDSLE NGFKQHNKRI  1260
SRGKRAQVIK RDDVVSDDSL DESAFQQLPR FSRIKLAKLI EREDAFSDGS LEENIHQQHG  1320
RILRSKQSKF VEREDAISDD SLEDSTHWQH RRIPRSKMAK FVESEDAASD DLQEDDGHQH  1380
HRRIPKRKKA NSIESEDVVS DDLWQNNIHR HLRKTPRGKQ PNIVEREEAV SDDLLENSSD  1440
QQDRIILRSK QKKSSMKQGI PRQLKQSAPK MIKKETPQLM KQERQIKPET PQLRFGKSDM  1500
NARQFDSHAE EERGGPRMRL RKRLSKAPKQ SLTRLKEKQN IKKKVKDATA VKAPAGRKNV  1560
KMKDEEAEYQ CDIDGCRMSF VSKQELALHK RNICPVKGCG KKFFSHKYLV QHRRVHIDDR  1620
PLKCPWKGCK MTFKWAWART EHIRVHTGAR PYVCAEEGCG QTFRFVSDFS RHKRKTGHLA  1680
KKGRG*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A4e-79183793346Transcription factor jumonji (Jmj) family protein
6ip4_A4e-79183793346Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
113811387RRIPKRK
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pth.124950.0bud| catkin
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPotri.012G092400.1
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_024438277.10.0lysine-specific demethylase REF6
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A2K1YB810.0A0A2K1YB81_POPTR; Uncharacterized protein
STRINGPOPTR_0012s09390.10.0(Populus trichocarpa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF56483250
Representative plantOGRP44011217
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]