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_016468899.1

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: 1240aa MW: 138758 Da PI: 9.1645

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_016468899.1	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	1124	1149	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 y C C++sFs+k +L H ++ + XP_016468899.1 1124 YHCDleGCSMSFSTKQELSLHKKNvC 1149 889999***************99866 PP
2	zf-C2H2	11	0.0013	1148	1171	2	23
EET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 2 kCp..dCgksFsrksnLkrHirtH 23 +Cp C+k F ++ +L++H r+H XP_016468899.1 1148 VCPveGCKKKFFSHKYLVQHRRVH 1171 69999*****************99 PP
3	zf-C2H2	12.2	0.00057	1207	1233	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C+ Cg++F+ s++ rH r+ H XP_016468899.1 1207 YVCTesGCGQTFRFVSDFSRHKRKtgH 1233 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	1.04E-24	194	338	No hit	No description
Pfam	PF02373	2.9E-37	213	332	IPR003347	JmjC domain
SMART	SM00355	11	1124	1146	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	6.6E-5	1145	1175	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.012	1147	1171	IPR015880	Zinc finger, C2H2-like
SuperFamily	SSF57667	1.85E-5	1147	1184	No hit	No description
PROSITE profile	PS50157	11.572	1147	1176	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1149	1171	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	2.8E-8	1176	1201	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.741	1177	1206	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0014	1177	1201	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1179	1201	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	2.78E-9	1187	1229	No hit	No description
Gene3D	G3DSA:3.30.160.60	2.0E-9	1202	1230	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.16	1207	1233	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.907	1207	1238	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1209	1233	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: 1240 aa Download sequence Send to blast
MAEASGNIEV FPWLKTLPVA PEYHPTLEEF QDPIAYIFKI EKEASKYGIC KIVPPVPAPP 60 KKTALAYLNR SLSARSGSNG GPTFTTRQQQ IGFCPRKHRP VKKPVWQSGE NYTVQEFQAK 120 AKAFEKNYLK KNFKKALTSP LEIETLYWKA TVDKPFSVEY ANDMPGSAFA PKKVGNAVTT 180 LADTEWNMRG VSRAKGSLLK FMKEEIPGVT SPMVYLAMMF SWFAWHVEDH DLHSLNYLHM 240 GAGKTWYGVP RDAAVAFEEV IRVHGYAGET NPLVTFATLG EKTTVMSPEV LLSAGIPCCR 300 LVQNAGDFVI TFPRAYHSGF SHGFNCGEAS NIATPGWLIV AKDAAIRRAS INCPPMVSHF 360 QLLYDLALSL CSRVPKNTRI EPRSSRLKDK KKSEGDMLVK ELFVEDLNCN NYLLHILGEG 420 SPVVLLPQHY SGISIGSNSV AGSQLKVNSR FPSISSPDHE VKSKTDSASD ALMLGRKQRM 480 KQLASVSLEK GKHSSWHAGN RLPESGRDEA ESSPETERGN LDPARGLTYR CDTLSEHGLF 540 SCVTCGILCY TCVAIIQPTE AAAHHLMSSD YRNFNDWTGN VGGVTATSRD DAAESDSSSG 600 WLVKRAPGGL IDVSIESSDR IRKLNNERVG VLSSTKARKE TSSLSLLALN YANSSDSDED 660 EVEANIPVEA CESRHMDFED EVSLRVIDPY ANHRQRRAVS DGRNCQSLDN SIHLESENPP 720 PGESNTLPDR SRHQLRSHQV GANCIPFSHR GEIANSDRVA PFDNGPMQFT STSDEDSFRI 780 HVFCLQHAVQ IEEQLRQVGG VHISLLCHPD YPKLEAQAKK MAEELGRDHF WREISFREAT 840 KEDEEMIQSA LEVEEAIHGN GDWTVKLDIN LFYSANLSRS PLYSKQMPCN FIIYNAFGRS 900 SPDEKSEYTG TGRGSGKQKR AVVAGKWCGK VWMSSQVHPL LAERRDTDEE QQQNNNIIST 960 RVKPEVKSER PCEMTPTGKT VARTGKKRKS RVENKRNSKL LIADDSSVSD VPQQQRKTNL 1020 RSKRIKYETP EPKEEDVDKK KRIGSPINDD PDGGPSTRLR KRMLKPSKES LVKSRPAPIK 1080 QQNESKKAEK GSKVKIPSAN SNSKKDPVMK ANTSKKMKDK EGEYHCDLEG CSMSFSTKQE 1140 LSLHKKNVCP VEGCKKKFFS HKYLVQHRRV HMDDRPLKCP WKGCKMTFKW AWARTEHIRV 1200 HTGARPYVCT ESGCGQTFRF VSDFSRHKRK TGHISKKGRG

Sequence ? help Back to Top

Protein Sequence Length: 1240 aa Download sequence Send to blast

MAEASGNIEV FPWLKTLPVA PEYHPTLEEF QDPIAYIFKI EKEASKYGIC KIVPPVPAPP  60
KKTALAYLNR SLSARSGSNG GPTFTTRQQQ IGFCPRKHRP VKKPVWQSGE NYTVQEFQAK  120
AKAFEKNYLK KNFKKALTSP LEIETLYWKA TVDKPFSVEY ANDMPGSAFA PKKVGNAVTT  180
LADTEWNMRG VSRAKGSLLK FMKEEIPGVT SPMVYLAMMF SWFAWHVEDH DLHSLNYLHM  240
GAGKTWYGVP RDAAVAFEEV IRVHGYAGET NPLVTFATLG EKTTVMSPEV LLSAGIPCCR  300
LVQNAGDFVI TFPRAYHSGF SHGFNCGEAS NIATPGWLIV AKDAAIRRAS INCPPMVSHF  360
QLLYDLALSL CSRVPKNTRI EPRSSRLKDK KKSEGDMLVK ELFVEDLNCN NYLLHILGEG  420
SPVVLLPQHY SGISIGSNSV AGSQLKVNSR FPSISSPDHE VKSKTDSASD ALMLGRKQRM  480
KQLASVSLEK GKHSSWHAGN RLPESGRDEA ESSPETERGN LDPARGLTYR CDTLSEHGLF  540
SCVTCGILCY TCVAIIQPTE AAAHHLMSSD YRNFNDWTGN VGGVTATSRD DAAESDSSSG  600
WLVKRAPGGL IDVSIESSDR IRKLNNERVG VLSSTKARKE TSSLSLLALN YANSSDSDED  660
EVEANIPVEA CESRHMDFED EVSLRVIDPY ANHRQRRAVS DGRNCQSLDN SIHLESENPP  720
PGESNTLPDR SRHQLRSHQV GANCIPFSHR GEIANSDRVA PFDNGPMQFT STSDEDSFRI  780
HVFCLQHAVQ IEEQLRQVGG VHISLLCHPD YPKLEAQAKK MAEELGRDHF WREISFREAT  840
KEDEEMIQSA LEVEEAIHGN GDWTVKLDIN LFYSANLSRS PLYSKQMPCN FIIYNAFGRS  900
SPDEKSEYTG TGRGSGKQKR AVVAGKWCGK VWMSSQVHPL LAERRDTDEE QQQNNNIIST  960
RVKPEVKSER PCEMTPTGKT VARTGKKRKS RVENKRNSKL LIADDSSVSD VPQQQRKTNL  1020
RSKRIKYETP EPKEEDVDKK KRIGSPINDD PDGGPSTRLR KRMLKPSKES LVKSRPAPIK  1080
QQNESKKAEK GSKVKIPSAN SNSKKDPVMK ANTSKKMKDK EGEYHCDLEG CSMSFSTKQE  1140
LSLHKKNVCP VEGCKKKFFS HKYLVQHRRV HMDDRPLKCP WKGCKMTFKW AWARTEHIRV  1200
HTGARPYVCT ESGCGQTFRF VSDFSRHKRK TGHISKKGRG

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	1e-71	13	370	8	353	Transcription factor jumonji (Jmj) family protein
6ip4_A	1e-71	13	370	8	353	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}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	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_016468899.1	0.0	PREDICTED: lysine-specific demethylase REF6-like isoform X1
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A1S3ZX21	0.0	A0A1S3ZX21_TOBAC; lysine-specific demethylase REF6-like isoform X1
STRING	XP_009791083.1	0.0	(Nicotiana sylvestris)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA4988	23	31

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]