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 Pavir.3NG095200.1.p
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Panicinae; Panicum
Family C2H2
Protein Properties Length: 1453aa    MW: 161365 Da    PI: 7.4061
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.3NG095200.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H213.70.0001913331356122
                           EEET..TTTEEESSHHHHHHHHHH CS
              zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt 22  
                           ++C    C++sFs++ +L  H r 
  Pavir.3NG095200.1.p 1333 FTCDieGCDMSFSTQQDLALHKRD 1356
                           899999***************985 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005452.1E-161758IPR003349JmjN domain
PROSITE profilePS5118314.4091859IPR003349JmjN domain
PfamPF023754.6E-141952IPR003349JmjN domain
PROSITE profilePS5118435.472200369IPR003347JmjC domain
SMARTSM005581.3E-45200369IPR003347JmjC domain
SuperFamilySSF511971.51E-24215365No hitNo description
PfamPF023733.9E-36233352IPR003347JmjC domain
SMARTSM003558.113331355IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.4513561385IPR007087Zinc finger, C2H2
SMARTSM003551513561380IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028013581380IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.606.6E-913841410IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.00213861410IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.34413861415IPR007087Zinc finger, C2H2
PROSITE patternPS00028013881410IPR007087Zinc finger, C2H2
SuperFamilySSF576674.14E-913961439No hitNo description
Gene3DG3DSA:3.30.160.602.9E-914111439IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.84514161447IPR007087Zinc finger, C2H2
SMARTSM003551.114161442IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028014181442IPR007087Zinc 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: 1453 aa     Download sequence    Send to blast
MSPPAVETPE WLRNLPVAPE YRPTAAEFAD PIAYILKIEA EASRYGICKI VPPLAAPPRE  60
ATVERLRASF AANAAAGSGI DGAAPAPTFP TRLQQVGFST KNRRPASRRV WESGERYTLE  120
AFRAKARDID LPRHAVPPKH ASQLQLEALF WGACAARPFN VEYGNDMPGS GFAAPEELEL  180
DLEGGGGGGG GGNASLAARD VGETEWNMRL APRARGSLLR AMGRDVAGVT TPMLYVAMLY  240
SWFAWHVEDH ELHSLNYLHF GKPKTWYGVP RDAMLAFEDA VRVHGYADEL NAIMAFQTLN  300
EKTTVLSPEV LLSAGVPCCR LVQNPGEFII TFPGAYHSGF SHGFNCGEAT NIATPHWLQV  360
AKEAAVRRAS TNCGPLVSHY QLLYELALSL RPRELKNSND VPRSSRLRDK KKNESEIMIK  420
ETFVGSVIEN NNFLSILLDK SSCVIIPEIE FPLPSIPTMM VPEVTVKQAF IAGPCSNSQK  480
KDEDMFASAT TSSLCNGRKL YETKFGTVNS SAFLLNPEVQ SGVIEKGRSH QGGGLLDQGR  540
LPCVQCGILS YACVAIIQPK EAAVHVISQE CMSSSAKHGE IIKSDDTSNW ITIVPPQGHS  600
SETDDCTIPN VSSAHVSDRC RQLYTSSTHG GTSALGLLAS AYDSSDSDEE AETPNEIANI  660
TANNGAENVV TNIQSSGTSI QHQNTNLHLS EEECDPTATL SLLKPVDNRS IAMTQASIGT  720
DMTRPADLGE SLIANEQWSA YVDLDDDPNA SGAKTSLNTS FSRAKGAMEP DALTLLKYSK  780
DSCRMHVFCL EHALETWTQL QQIGGANIML LCHPEYPRAE SAAKVIAEEL GMKHAWKDIT  840
FKKATDEDIG RIRMALHDED AEPTSSDWAV KMGINIYYSA KQSKSPLYSK QVPYNSIIYK  900
AFAQENPDGD EERQRLRTTK KKVAGSWCGK VWMSNQVHPL LACEREEEDL DMVCSKAMVP  960
VSSYDRIQEE SSTRSTSLIN RSLSKRISRR KELDSVEKSR AKKKRYTTSD VATFDQPRNC  1020
DDHEKHEDGD ESESVDAQNT QQHQQYESQK INKKSSAKRR KDDKRNNNFY ERHNYHDDID  1080
YKLGLDWDNT PPQGLDIVEV KSGAQLQRSK KKSGKCKAND DLSNVEKKLQ KMGKKVSTKK  1140
HKNDKTNQQF QGNHNEDNNV NLLHEGNGDE ATQESWDEIP KQKTDDVKVK SRGKMHSGKK  1200
KASKCQTSDG LDNVDLLHED NGYEATQESW DEVPKQKTDD VRVKSRGKMH SGKKKASKCQ  1260
ISDGLDNGDN EAKFSCDTAL CYRDKATIDD WEEIPKEKAD DVKVKSNMQS GKKKTSKRPA  1320
SDGLRNGDKG AKFTCDIEGC DMSFSTQQDL ALHKRDICPV KGCKKKFFCH KYLLQHRKVH  1380
LDDRPLMCSF TGCKKTFKWP WARTEHMRVH TGVRPYACTE PGCTQTFRFV SDFSRHKRKT  1440
GHSSDKKKKN ST*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A1e-67103907353Transcription factor jumonji (Jmj) family protein
6ip4_A1e-67103907353Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
19881004RRKELDSVEKSRAKKKR
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.285800.0callus| leaf
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
PlantRegMapPavir.3NG095200.1.p
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_025807104.10.0lysine-specific demethylase JMJ705-like
SwissprotQ9STM31e-163REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A2S3HD450.0A0A2S3HD45_9POAL; Uncharacterized protein
STRINGPavir.Cb01041.1.p0.0(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP67183035
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G48430.11e-158relative 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]