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

XP_016435657.1

Organism

Nicotiana tabacum

Taxonomic ID

4097

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; Nicotianeae; Nicotiana

Family

C2H2

Protein Properties

Length: 1241aa MW: 138728 Da PI: 9.2589

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_016435657.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	10.8	0.0016	1125	1150	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 y C C++sFs+k +L H ++ + XP_016435657.1 1125 YHCDleGCSMSFSTKQELSLHKKNvC 1150 889999***************99866 PP
2	zf-C2H2	11	0.0013	1149	1172	2	23
EET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 2 kCp..dCgksFsrksnLkrHirtH 23 +Cp C+k F ++ +L++H r+H XP_016435657.1 1149 VCPveGCKKKFFSHKYLVQHRRVH 1172 69999*****************99 PP
3	zf-C2H2	12.2	0.00055	1208	1234	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C+ Cg++F+ s++ rH r+ H XP_016435657.1 1208 YVCTetGCGQTFRFVSDFSRHKRKtgH 1234 99********************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	3.6E-16	19	60	IPR003349	JmjN domain
PROSITE profile	PS51183	14.991	20	61	IPR003349	JmjN domain
Pfam	PF02375	2.1E-15	21	54	IPR003349	JmjN domain
PROSITE profile	PS51184	31.698	180	349	IPR003347	JmjC domain
SMART	SM00558	1.8E-49	180	349	IPR003347	JmjC domain
SuperFamily	SSF51197	1.07E-24	194	338	No hit	No description
Pfam	PF02373	3.0E-37	213	332	IPR003347	JmjC domain
SMART	SM00355	11	1125	1147	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	6.6E-5	1146	1176	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	11.572	1148	1177	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.012	1148	1172	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1150	1172	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	3.41E-9	1164	1204	No hit	No description
Gene3D	G3DSA:3.30.160.60	2.8E-8	1177	1202	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.741	1178	1207	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0014	1178	1202	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1180	1202	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	5.76E-8	1196	1230	No hit	No description
Gene3D	G3DSA:3.30.160.60	3.7E-9	1203	1231	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.907	1208	1239	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.19	1208	1234	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1210	1234	IPR007087	Zinc finger, C2H2

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009741	Biological Process	response to brassinosteroid
GO:0009826	Biological Process	unidimensional cell growth
GO:0010228	Biological Process	vegetative to reproductive phase transition of meristem
GO:0033169	Biological Process	histone H3-K9 demethylation
GO:0035067	Biological Process	negative regulation of histone acetylation
GO:0048366	Biological Process	leaf development
GO:0005634	Cellular Component	nucleus
GO:0003676	Molecular Function	nucleic acid binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 1241 aa Download sequence Send to blast
MAEASGNIEV FPWLKTLPVA PEYHPTLEEF QDPIAYIFKI EKEASKYGIC KIVPPVPAPP 60 KKTALAYLNR SLSARSGSNG GPTFTTRQQQ IGFCPRKHRP VKKPVWQSGE NYTVQEFQAK 120 AKAFEKNYLK KNFKKALTSP LEIETLFWKA TVDKPFSVEY ANDMPGSAFA PKKVGNVVTT 180 LADTEWNMRG VSRAKGSLLK FMKEEIPGVT SPMVYLAMMF SWFAWHVEDH DLHSLNYLHM 240 GAGKTWYGVP RDAAVAFEEV IRVHGYAGET NPLVTFATLG EKTTVMSPEV LLSAGIPCCR 300 LVQNAGDFVI TFPRAYHSGF SHGFNCGEAS NIATPGWLIV AKDAAIRRAS INCPPMVSHF 360 QLLYDLALSL CSRVPKNIRI EPRSSRLKDK KKSEGDMLVK ELFVEDLNCN NYLLHILGEG 420 SPVVLLPRHY SGISIGSNSV AGSQLKVNSR FPSLSSPDHE VKSKTDSASD ALMLGRKQRM 480 KQLASVSLEK GKHSSWHTGN RLPESGRDEA ESSPETEREN LDPERGMTYR CDTLSEHGLF 540 SCVTCGILCY TCVAIIQPTE AAAHHLMSSD YRNFNDWTGN VGGVTANSRD ANAAESDSSS 600 GWLVKRAPGG LINVPIESSD RIRKLNNESV GVLSSTKARK ETSSLGLLAL NYANSSDSDE 660 DEVEANIPVE ACESRQMDFE DEVSLRVIDP YANHRQRRAV SGGRNCQSLD NSVHLESGNL 720 PSGESNTLPD RSRHQLRSHQ VGANCIPFAH RGEIANSDGV APFDNGPMQF TSTSDEDSFR 780 IHVFCLQHAV QVEEQLRQVG GVHISLLCHP DYPKLEAQAK KVAEELGRDH FWREISFREA 840 TKEDEEMIQS ALEVEEAIHG NGDWTVKLDI NLFYSANLSR SPLYSKQMPC NFIIYNAFGR 900 SSPDEKSEYT GTGRGSGKQR RAVVAGKWCG KVWMSSQVHP LLAERRDTDE EQQQNNNSIS 960 ARVKPEVKSE RPCEMTPTVK IVARTGKKRK SRVENKRNSK LLIADDSSVS NVPQQQRKTN 1020 LRSKRIKYET PEPKEEDVDK KKRFGSPIND DPDGGPSTRL RKRMPKPSKE SLVKPKPAPI 1080 KQQNESKKAE KGSKVKIPSS NSNSKKDPVM KANTSKKMKD KEGEYHCDLE GCSMSFSTKQ 1140 ELSLHKKNVC PVEGCKKKFF SHKYLVQHRR VHMDDRPLKC PWKGCKMTFK WAWARTEHIR 1200 VHTGARPYVC TETGCGQTFR FVSDFSRHKR KTGHISKKGR G

Sequence ? help Back to Top

Protein Sequence Length: 1241 aa Download sequence Send to blast

MAEASGNIEV FPWLKTLPVA PEYHPTLEEF QDPIAYIFKI EKEASKYGIC KIVPPVPAPP  60
KKTALAYLNR SLSARSGSNG GPTFTTRQQQ IGFCPRKHRP VKKPVWQSGE NYTVQEFQAK  120
AKAFEKNYLK KNFKKALTSP LEIETLFWKA TVDKPFSVEY ANDMPGSAFA PKKVGNVVTT  180
LADTEWNMRG VSRAKGSLLK FMKEEIPGVT SPMVYLAMMF SWFAWHVEDH DLHSLNYLHM  240
GAGKTWYGVP RDAAVAFEEV IRVHGYAGET NPLVTFATLG EKTTVMSPEV LLSAGIPCCR  300
LVQNAGDFVI TFPRAYHSGF SHGFNCGEAS NIATPGWLIV AKDAAIRRAS INCPPMVSHF  360
QLLYDLALSL CSRVPKNIRI EPRSSRLKDK KKSEGDMLVK ELFVEDLNCN NYLLHILGEG  420
SPVVLLPRHY SGISIGSNSV AGSQLKVNSR FPSLSSPDHE VKSKTDSASD ALMLGRKQRM  480
KQLASVSLEK GKHSSWHTGN RLPESGRDEA ESSPETEREN LDPERGMTYR CDTLSEHGLF  540
SCVTCGILCY TCVAIIQPTE AAAHHLMSSD YRNFNDWTGN VGGVTANSRD ANAAESDSSS  600
GWLVKRAPGG LINVPIESSD RIRKLNNESV GVLSSTKARK ETSSLGLLAL NYANSSDSDE  660
DEVEANIPVE ACESRQMDFE DEVSLRVIDP YANHRQRRAV SGGRNCQSLD NSVHLESGNL  720
PSGESNTLPD RSRHQLRSHQ VGANCIPFAH RGEIANSDGV APFDNGPMQF TSTSDEDSFR  780
IHVFCLQHAV QVEEQLRQVG GVHISLLCHP DYPKLEAQAK KVAEELGRDH FWREISFREA  840
TKEDEEMIQS ALEVEEAIHG NGDWTVKLDI NLFYSANLSR SPLYSKQMPC NFIIYNAFGR  900
SSPDEKSEYT GTGRGSGKQR RAVVAGKWCG KVWMSSQVHP LLAERRDTDE EQQQNNNSIS  960
ARVKPEVKSE RPCEMTPTVK IVARTGKKRK SRVENKRNSK LLIADDSSVS NVPQQQRKTN  1020
LRSKRIKYET PEPKEEDVDK KKRFGSPIND DPDGGPSTRL RKRMPKPSKE SLVKPKPAPI  1080
KQQNESKKAE KGSKVKIPSS NSNSKKDPVM KANTSKKMKD KEGEYHCDLE GCSMSFSTKQ  1140
ELSLHKKNVC PVEGCKKKFF SHKYLVQHRR VHMDDRPLKC PWKGCKMTFK WAWARTEHIR  1200
VHTGARPYVC TETGCGQTFR FVSDFSRHKR KTGHISKKGR G

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	4e-72	13	382	8	366	Transcription factor jumonji (Jmj) family protein
6ip4_A	4e-72	13	382	8	366	Arabidopsis JMJ13
Search in ModeBase

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}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00608	ChIP-seq	Transfer from AT3G48430	Download

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	HG975442	0.0	HG975442.1 Solanum pennellii chromosome ch03, complete genome.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009613169.1	0.0	PREDICTED: lysine-specific demethylase REF6 isoform X2
Refseq	XP_016435657.1	0.0	PREDICTED: lysine-specific demethylase REF6-like isoform X2
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A1S3X714	0.0	A0A1S3X714_TOBAC; lysine-specific demethylase REF6-like isoform X2
STRING	XP_009613168.1	0.0	(Nicotiana tomentosiformis)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G48430.1	0.0	relative of early flowering 6

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]