PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

Pavir.3NG095200.1.p

Organism

Panicum virgatum

Taxonomic ID

38727

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.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	13.7	0.00019	1333	1356	1	22
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

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	2.1E-16	17	58	IPR003349	JmjN domain
PROSITE profile	PS51183	14.409	18	59	IPR003349	JmjN domain
Pfam	PF02375	4.6E-14	19	52	IPR003349	JmjN domain
PROSITE profile	PS51184	35.472	200	369	IPR003347	JmjC domain
SMART	SM00558	1.3E-45	200	369	IPR003347	JmjC domain
SuperFamily	SSF51197	1.51E-24	215	365	No hit	No description
Pfam	PF02373	3.9E-36	233	352	IPR003347	JmjC domain
SMART	SM00355	8.1	1333	1355	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.45	1356	1385	IPR007087	Zinc finger, C2H2
SMART	SM00355	15	1356	1380	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1358	1380	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	6.6E-9	1384	1410	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.002	1386	1410	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	11.344	1386	1415	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1388	1410	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	4.14E-9	1396	1439	No hit	No description
Gene3D	G3DSA:3.30.160.60	2.9E-9	1411	1439	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.845	1416	1447	IPR007087	Zinc finger, C2H2
SMART	SM00355	1.1	1416	1442	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1418	1442	IPR007087	Zinc finger, C2H2

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003676	Molecular Function	nucleic acid binding
GO:0046872	Molecular Function	metal 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*

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

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	1e-67	10	390	7	353	Transcription factor jumonji (Jmj) family protein
6ip4_A	1e-67	10	390	7	353	Arabidopsis JMJ13
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	988	1004	RRKELDSVEKSRAKKKR

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Pvr.28580	0.0	callus\| leaf

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE 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
UniProt	Histone 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
Source	Link
PlantRegMap	Pavir.3NG095200.1.p

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_025807104.1	0.0	lysine-specific demethylase JMJ705-like
Swissprot	Q9STM3	1e-163	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A2S3HD45	0.0	A0A2S3HD45_9POAL; Uncharacterized protein
STRING	Pavir.Cb01041.1.p	0.0	(Panicum virgatum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP6718	30	35

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G48430.1	1e-158	relative of early flowering 6

Link Out ? help Back to Top
Phytozome	Pavir.3NG095200.1.p

Publications ? help Back to Top
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] 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] 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] 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] 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] 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] Qiu Q, et al. DNA methylation repels targeting of Arabidopsis REF6. Nat Commun, 2019. 10(1): p. 2063 [PMID:31048693]