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.3KG240000.1.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: 161834 Da PI: 7.1575

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Pavir.3KG240000.1.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	13.3	0.00025	1333	1356	1	22
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

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	1.7E-15	17	58	IPR003349	JmjN domain
PROSITE profile	PS51183	14.215	18	59	IPR003349	JmjN domain
Pfam	PF02375	9.1E-14	19	52	IPR003349	JmjN domain
PROSITE profile	PS51184	35.401	200	369	IPR003347	JmjC domain
SMART	SM00558	1.2E-46	200	369	IPR003347	JmjC domain
SuperFamily	SSF51197	3.57E-24	215	365	No hit	No description
Pfam	PF02373	3.9E-36	233	352	IPR003347	JmjC domain
SMART	SM00355	9.7	1333	1355	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	15	1356	1380	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.887	1356	1385	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1358	1380	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	2.3E-9	1383	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	4.1E-9	1396	1439	No hit	No description
Gene3D	G3DSA:3.30.160.60	4.2E-9	1411	1439	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	1.1	1416	1442	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.845	1416	1447	IPR007087	Zinc finger, C2H2
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 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*

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

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	4e-67	10	390	7	353	Transcription factor jumonji (Jmj) family protein
6ip4_A	4e-67	10	390	7	353	Arabidopsis JMJ13
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	989	1005	RRKEVDSVEQSRSKKKK

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: Expressed in leaves and flag leaves. Expressed at low levels in roots, shoots, stems and panicles. {ECO:0000269\|PubMed:24280387}.
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}.
UniProt	Histone 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
Source	Link
PlantRegMap	Pavir.3KG240000.1.p

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: 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
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	Q5N712	1e-164	JM705_ORYSJ; Lysine-specific demethylase JMJ705
Swissprot	Q9STM3	1e-163	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A2S3HD45	0.0	A0A2S3HD45_9POAL; Uncharacterized protein
STRING	Pavir.J05247.1.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-156	relative of early flowering 6

Link Out ? help Back to Top
Phytozome	Pavir.3KG240000.1.p

Publications ? help Back to Top
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] 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]