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_016468900.1

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: 1223aa MW: 137026 Da PI: 9.2468

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_016468900.1	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	1107	1132	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 y C C++sFs+k +L H ++ + XP_016468900.1 1107 YHCDleGCSMSFSTKQELSLHKKNvC 1132 889999***************99866 PP
2	zf-C2H2	11	0.0013	1131	1154	2	23
EET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 2 kCp..dCgksFsrksnLkrHirtH 23 +Cp C+k F ++ +L++H r+H XP_016468900.1 1131 VCPveGCKKKFFSHKYLVQHRRVH 1154 69999*****************99 PP
3	zf-C2H2	12.2	0.00056	1190	1216	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C+ Cg++F+ s++ rH r+ H XP_016468900.1 1190 YVCTesGCGQTFRFVSDFSRHKRKtgH 1216 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
SMART	SM00558	3.6E-39	180	348	IPR003347	JmjC domain
PROSITE profile	PS51184	26.069	180	347	IPR003347	JmjC domain
SuperFamily	SSF51197	6.04E-21	194	322	No hit	No description
Pfam	PF02373	6.4E-33	213	322	IPR003347	JmjC domain
SMART	SM00355	11	1107	1129	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	6.5E-5	1128	1158	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamily	SSF57667	1.81E-5	1130	1167	No hit	No description
PROSITE profile	PS50157	11.572	1130	1159	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.012	1130	1154	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1132	1154	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	2.8E-8	1159	1184	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.741	1160	1189	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0014	1160	1184	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1162	1184	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	2.78E-9	1170	1212	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.9E-9	1185	1213	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.907	1190	1221	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.16	1190	1216	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1192	1216	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: 1223 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 SHVAKDAAIR RASINCPPMV SHFQLLYDLA LSLCSRVPKN 360 TRIEPRSSRL KDKKKSEGDM LVKELFVEDL NCNNYLLHIL GEGSPVVLLP QHYSGISIGS 420 NSVAGSQLKV NSRFPSISSP DHEVKSKTDS ASDALMLGRK QRMKQLASVS LEKGKHSSWH 480 AGNRLPESGR DEAESSPETE RGNLDPARGL TYRCDTLSEH GLFSCVTCGI LCYTCVAIIQ 540 PTEAAAHHLM SSDYRNFNDW TGNVGGVTAT SRDDAAESDS SSGWLVKRAP GGLIDVSIES 600 SDRIRKLNNE RVGVLSSTKA RKETSSLSLL ALNYANSSDS DEDEVEANIP VEACESRHMD 660 FEDEVSLRVI DPYANHRQRR AVSDGRNCQS LDNSIHLESE NPPPGESNTL PDRSRHQLRS 720 HQVGANCIPF SHRGEIANSD RVAPFDNGPM QFTSTSDEDS FRIHVFCLQH AVQIEEQLRQ 780 VGGVHISLLC HPDYPKLEAQ AKKMAEELGR DHFWREISFR EATKEDEEMI QSALEVEEAI 840 HGNGDWTVKL DINLFYSANL SRSPLYSKQM PCNFIIYNAF GRSSPDEKSE YTGTGRGSGK 900 QKRAVVAGKW CGKVWMSSQV HPLLAERRDT DEEQQQNNNI ISTRVKPEVK SERPCEMTPT 960 GKTVARTGKK RKSRVENKRN SKLLIADDSS VSDVPQQQRK TNLRSKRIKY ETPEPKEEDV 1020 DKKKRIGSPI NDDPDGGPST RLRKRMLKPS KESLVKSRPA PIKQQNESKK AEKGSKVKIP 1080 SANSNSKKDP VMKANTSKKM KDKEGEYHCD LEGCSMSFST KQELSLHKKN VCPVEGCKKK 1140 FFSHKYLVQH RRVHMDDRPL KCPWKGCKMT FKWAWARTEH IRVHTGARPY VCTESGCGQT 1200 FRFVSDFSRH KRKTGHISKK GRG

Sequence ? help Back to Top

Protein Sequence Length: 1223 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 SHVAKDAAIR RASINCPPMV SHFQLLYDLA LSLCSRVPKN  360
TRIEPRSSRL KDKKKSEGDM LVKELFVEDL NCNNYLLHIL GEGSPVVLLP QHYSGISIGS  420
NSVAGSQLKV NSRFPSISSP DHEVKSKTDS ASDALMLGRK QRMKQLASVS LEKGKHSSWH  480
AGNRLPESGR DEAESSPETE RGNLDPARGL TYRCDTLSEH GLFSCVTCGI LCYTCVAIIQ  540
PTEAAAHHLM SSDYRNFNDW TGNVGGVTAT SRDDAAESDS SSGWLVKRAP GGLIDVSIES  600
SDRIRKLNNE RVGVLSSTKA RKETSSLSLL ALNYANSSDS DEDEVEANIP VEACESRHMD  660
FEDEVSLRVI DPYANHRQRR AVSDGRNCQS LDNSIHLESE NPPPGESNTL PDRSRHQLRS  720
HQVGANCIPF SHRGEIANSD RVAPFDNGPM QFTSTSDEDS FRIHVFCLQH AVQIEEQLRQ  780
VGGVHISLLC HPDYPKLEAQ AKKMAEELGR DHFWREISFR EATKEDEEMI QSALEVEEAI  840
HGNGDWTVKL DINLFYSANL SRSPLYSKQM PCNFIIYNAF GRSSPDEKSE YTGTGRGSGK  900
QKRAVVAGKW CGKVWMSSQV HPLLAERRDT DEEQQQNNNI ISTRVKPEVK SERPCEMTPT  960
GKTVARTGKK RKSRVENKRN SKLLIADDSS VSDVPQQQRK TNLRSKRIKY ETPEPKEEDV  1020
DKKKRIGSPI NDDPDGGPST RLRKRMLKPS KESLVKSRPA PIKQQNESKK AEKGSKVKIP  1080
SANSNSKKDP VMKANTSKKM KDKEGEYHCD LEGCSMSFST KQELSLHKKN VCPVEGCKKK  1140
FFSHKYLVQH RRVHMDDRPL KCPWKGCKMT FKWAWARTEH IRVHTGARPY VCTESGCGQT  1200
FRFVSDFSRH KRKTGHISKK GRG

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6a57_A	1e-62	1107	1220	23	136	Lysine-specific demethylase REF6
6a58_A	1e-62	1107	1220	23	136	Lysine-specific demethylase REF6
6a59_A	1e-62	1107	1220	23	136	Lysine-specific demethylase REF6
6ip0_A	3e-60	13	353	8	353	Transcription factor jumonji (Jmj) family protein
6ip4_A	3e-60	13	353	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_016468900.1	0.0	PREDICTED: lysine-specific demethylase REF6-like isoform X2
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A1S3ZWS7	0.0	A0A1S3ZWS7_TOBAC; lysine-specific demethylase REF6-like isoform X2
STRING	XP_009791083.1	0.0	(Nicotiana sylvestris)

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]