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.3KG240000.1.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: 161834 Da    PI: 7.1575
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.3KG240000.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H213.30.0002513331356122
                           EEET..TTTEEESSHHHHHHHHHH CS
              zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt 22  
                           ++C    C++sFs++ +L  H r 
  Pavir.3KG240000.1.p 1333 FSCDieGCDMSFSTQQDLALHKRD 1356
                           899999***************985 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005451.7E-151758IPR003349JmjN domain
PROSITE profilePS5118314.2151859IPR003349JmjN domain
PfamPF023759.1E-141952IPR003349JmjN domain
PROSITE profilePS5118435.401200369IPR003347JmjC domain
SMARTSM005581.2E-46200369IPR003347JmjC domain
SuperFamilySSF511973.57E-24215365No hitNo description
PfamPF023733.9E-36233352IPR003347JmjC domain
SMARTSM003559.713331355IPR015880Zinc finger, C2H2-like
SMARTSM003551513561380IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.88713561385IPR007087Zinc finger, C2H2
PROSITE patternPS00028013581380IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.602.3E-913831410IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.00213861410IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.34413861415IPR007087Zinc finger, C2H2
PROSITE patternPS00028013881410IPR007087Zinc finger, C2H2
SuperFamilySSF576674.1E-913961439No hitNo description
Gene3DG3DSA:3.30.160.604.2E-914111439IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003551.114161442IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.84514161447IPR007087Zinc finger, C2H2
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 PIAYILKIEV EASRYGICKI VPPLAAPPRE  60
ATVERLRASF AANAAAASGI DGAAPAPTFP TRLQQVGFST KNRRPASRRV WESGERYTLE  120
AFRAKARDID LPRHAVPPKH ATQLQLEALF WGACAARPFN VEYGNDMPGS GFAAPQELEL  180
DLEGGGGGGG GGNAALAARD VGETEWNMRL APRARGSLLR AMGRDVAGVT TPMLYVAMLY  240
SWFAWHVEDH ELHSLNYLHF GKPKTWYGVP RDAMLAFEDA VRVHGYADEL NAIMAFQTLN  300
EKTTVLSPEV LLSAGVPCCR LVQNPGEFII TFPGAYHSGF SHGFNCGEAT NIATPRWLQV  360
AKEAAVRRAS TNCGPLVSHY QLLYELALSL RPRELKNSHD VPRSSRLRDK KKNESEIMIK  420
ETFVGSVIEN NNFLSILLDK SSCVIIPEIE FPLPSFPTMM VPEVTVKQAL IAGPCSNSQK  480
KDEDMLASAT TSSVCNGRKL YETKFGTVNT SAFLLNPEIQ SGVIEKGRSH QGGGLLDQGR  540
LPCVQCGILS YACGAIIQPK EAAVQYVISQ ECMSSSAKHG EIMKSDDTSN WITIVPPQGH  600
SSETDDYMIH SVSSAHISDR CRQLYTSSTH GCNSALGLLA SAYDSSDSDE EAEMPNEIAN  660
ISANNDAENG VTNVQSSGTS IQHQNTNLHL SEEECDPRAT LSQMKPVDDK IIAMTQASIG  720
TDMTRLADLG ESLIAYEQWS GYVDLDDDQT TSGAKTYLNT SFSRAKGAME PDALTLLKYS  780
KDSCRMHVFC LEHALETWTQ LQQIGGANIM LLCHPEYPRA ESAAKVIAEE LGMKHAWKDI  840
TFKKATDEDI GRIRLALQDE DAVPTSSDWA VKMGINIYYS AKQSKSPLYS KQVPYNSIIY  900
KAFAQENPDR DEERQQLRTT KKKVAGSWCG KVWMSNQVHP LLACEREEED LDLVCSKAMV  960
PVTSYDRIQE EPPTRSTILI NRNLSKRISR RKEVDSVEQS RSKKKKYTTS DVATFDQPRN  1020
CDDHDKYEDG DESESEDARN TQQHQQYESQ KINKKSSSKR QKDDKRNNFY ERHSYHDDID  1080
YRFGLDWDNT PPQGLDVVEV KSGAQLQGSK KKSSKCKAND DLLNVEKKLQ KMGKKVSTNK  1140
HKNDKTNQQF QGNHNEDNNV DLLPEDNGDE ATQESWDGIP KHKTNDVKVK SRGKMHSGKK  1200
KANKCQTSDG LDNVDLLHED NGYEVTQESL DEVPKQKTDD VRVKSRGKMH GGKKKASKCQ  1260
ISDVLDNGDN EAIFSCDTAL CDRDKATIDD WEEIPKEKAD DVKVKSNMQS GKKKASKRPA  1320
SDGLRNGDKG AKFSCDIEGC DMSFSTQQDL ALHKRDICPV KGCKKKFFCH KYLLQHRKVH  1380
LDERPLMCSF 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_A4e-67103907353Transcription factor jumonji (Jmj) family protein
6ip4_A4e-67103907353Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
19891005RRKEVDSVEQSRSKKKK
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: Expressed in leaves and flag leaves. Expressed at low levels in roots, shoots, stems and panicles. {ECO:0000269|PubMed:24280387}.
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}.
UniProtHistone demethylase that demethylates 'Lys-27' (H3K27me) of histone H3 with a specific activity for H3K27me3 and H3K27me2. No activity on H3K4me3, H3K9me3, H3K27me1 and H3K36me3. Involved in biotic stress response. May demethylate H3K27me3-marked defense-related genes and increase their basal and induced expression levels during pathogen infection. {ECO:0000269|PubMed:24280387}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.3KG240000.1.p
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By salt stress, abscisic acid (ABA), jasmonic acid (JA), the ethylene precursor ACC and infection by the bacterial pathogen Xanthomonas oryzae pv. oryzae. {ECO:0000269|PubMed:24280387}.
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
SwissprotQ5N7121e-164JM705_ORYSJ; Lysine-specific demethylase JMJ705
SwissprotQ9STM31e-163REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A2S3HD450.0A0A2S3HD45_9POAL; Uncharacterized protein
STRINGPavir.J05247.1.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-156relative of early flowering 6
Publications ? help Back to Top
  1. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. Qiu Q, et al.
    DNA methylation repels targeting of Arabidopsis REF6.
    Nat Commun, 2019. 10(1): p. 2063
    [PMID:31048693]