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

Thhalv10010066m

Common Name

EUTSA_v10010066mg

Organism

Eutrema salsugineum

Taxonomic ID

72664

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Eutremeae; Eutrema

Family

C2H2

Protein Properties

Length: 1379aa MW: 154581 Da PI: 7.6615

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Thhalv10010066m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	11.4	0.00096	1261	1286	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 y+C C++sF++ +L H r+ + Thhalv10010066m 1261 YQCDmeGCTMSFTSEKQLALHKRNiC 1286 99********************9877 PP
2	zf-C2H2	13.1	0.00028	1286	1308	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H r+H Thhalv10010066m 1286 CPvkGCGKNFFSHKYLVQHRRVH 1308 9999*****************99 PP
3	zf-C2H2	11	0.0013	1344	1370	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C Cg++F+ s++ rH r+ H Thhalv10010066m 1344 YVCAepSCGQTFRFVSDFSRHKRKtgH 1370 899999****************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	1.6E-16	19	60	IPR003349	JmjN domain
PROSITE profile	PS51183	14.077	20	61	IPR003349	JmjN domain
Pfam	PF02375	5.7E-14	21	54	IPR003349	JmjN domain
SMART	SM00558	3.5E-52	201	370	IPR003347	JmjC domain
PROSITE profile	PS51184	34.061	204	370	IPR003347	JmjC domain
SuperFamily	SSF51197	3.84E-27	219	388	No hit	No description
Pfam	PF02373	2.8E-37	234	353	IPR003347	JmjC domain
Gene3D	G3DSA:3.30.160.60	2.5E-4	1260	1283	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	8.5	1261	1283	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	0.016	1284	1308	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.965	1284	1313	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	4.0E-6	1285	1307	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1286	1308	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	6.55E-10	1300	1342	No hit	No description
Gene3D	G3DSA:3.30.160.60	4.5E-10	1308	1335	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0015	1314	1338	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.928	1314	1343	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1316	1338	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	8.38E-8	1332	1366	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.2E-8	1336	1367	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	5.5	1344	1370	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	11.281	1344	1375	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1346	1370	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:0040010	Biological Process	positive regulation of growth rate
GO:0045815	Biological Process	positive regulation of gene expression, epigenetic
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
GO:0071558	Molecular Function	histone demethylase activity (H3-K27 specific)

Sequence ? help Back to Top
Protein Sequence Length: 1379 aa Download sequence Send to blast
MAVSEQSPDV FPWLKSLPVA PEFRPTLAEF QDPIAYIFKI EEEASKYGIC KILPPVPPSS 60 KKTAINNLNR SLAARAAARV RDGADDGAWD YDGAPTFATR QQQIGFCPRK QRPVQRPVWQ 120 SGEHYSFGEF EFKAKNFEKN YLRKCGKRSQ LSALEIETLY WRATVDKPFS VEYANDMPGS 180 AFIPLSLAAA RRRESGGDGG TVGETAWNMR AMARAEGSLL KFMKEEIPGV TSPMVYIAMM 240 FSWFAWHVED HDLHSLNYLH MGAGKTWYGV PKDAAVAFEE VVRVHGYGGE LNPLVTFSTL 300 GEKTTVMSPE VFVRAGIPCC RLVQNPGEFV VTFPGAYHSG FSHGFNFGEA SNIATPQWLR 360 MAKDAAIRRA AINYPPMVSH LQLLYDFALA LGSRVPTSIN TKPRSSRLKD KKRSEGEKLT 420 KELFVQNIIH NNELLCSLGK GSPVALLPQS SSDVSVCSDL RIGSHLRTNQ EKPIQLKSED 480 LSSDSIMPGL NNGFKDAVSV KEKFTSLCER NRNHLASREN ETQGTSTDAE RKKNDRAVGL 540 SDQRLFSCVT CGILSFDCVA IVQPKEAAAR YLMSADCSFF NDWTVASGPA NLGQVAGSLH 600 PQSTGKHDVD YFYNVPVQTT DHSMKTGDQR TSSSSLTKEN KDDGALGLLA SAYGDSSDSE 660 EEDHKGSDIP ISEGITRQYD QEGACVSEAT SFDTDRNEEA RDGPSSDINS QRLTSGKGKE 720 IDVLHATSSC STLSCTSLQE IALPFIPRSD DDSSRLHVFC LEHAAEVEQQ LRPIGGIRIM 780 LLCHPEYPRI EAEAKIVSEE LGVNHEWNDT EFRNVSRVDE ETIQAALDNV EAKAGNSDWS 840 VKLGINLSYS AILSRSPLYS KQMPYNSVIY NAFGRGSPAT SSPTKPQVSG KRSSRQRKYV 900 VGKWCGKVWM SHQVHPFLLQ QDLEGDESER SCHLRGVLED DVIGKRLSPC NASRDATTMF 960 GRKYCRKRKM RAKALPRKKL TSFKREDVVS DDTSEDHSYK QQWRASGNEE ESYFETGNSV 1020 SGDSSNQMSD EQQEFVRHQG DKDFESDDEV SDRSLGEEYA VRECAASESS MENGSQLYRE 1080 NQSMYDHDDD DIYRHPRGLP RSKRTKFFRN PVSYDSEENG LYQQRGRVST SNAQISRMGG 1140 AYDSADNSLE EQEFCSAGKR QTRSTAKRKV KTEIVQSLRD TKRRALRQSG PRKKNQEVDI 1200 YMEGPSTRLR VRNLNPSIGS SETKPKKTGK KRNSNSFSRV ASEEELEEDE EENEQEECAP 1260 YQCDMEGCTM SFTSEKQLAL HKRNICPVKG CGKNFFSHKY LVQHRRVHSD DRPLKCPWKG 1320 CKMTFKWAWS RTEHIRVHTG ARPYVCAEPS CGQTFRFVSD FSRHKRKTGH SVKKTKKR*

Sequence ? help Back to Top

Protein Sequence Length: 1379 aa Download sequence Send to blast

MAVSEQSPDV FPWLKSLPVA PEFRPTLAEF QDPIAYIFKI EEEASKYGIC KILPPVPPSS  60
KKTAINNLNR SLAARAAARV RDGADDGAWD YDGAPTFATR QQQIGFCPRK QRPVQRPVWQ  120
SGEHYSFGEF EFKAKNFEKN YLRKCGKRSQ LSALEIETLY WRATVDKPFS VEYANDMPGS  180
AFIPLSLAAA RRRESGGDGG TVGETAWNMR AMARAEGSLL KFMKEEIPGV TSPMVYIAMM  240
FSWFAWHVED HDLHSLNYLH MGAGKTWYGV PKDAAVAFEE VVRVHGYGGE LNPLVTFSTL  300
GEKTTVMSPE VFVRAGIPCC RLVQNPGEFV VTFPGAYHSG FSHGFNFGEA SNIATPQWLR  360
MAKDAAIRRA AINYPPMVSH LQLLYDFALA LGSRVPTSIN TKPRSSRLKD KKRSEGEKLT  420
KELFVQNIIH NNELLCSLGK GSPVALLPQS SSDVSVCSDL RIGSHLRTNQ EKPIQLKSED  480
LSSDSIMPGL NNGFKDAVSV KEKFTSLCER NRNHLASREN ETQGTSTDAE RKKNDRAVGL  540
SDQRLFSCVT CGILSFDCVA IVQPKEAAAR YLMSADCSFF NDWTVASGPA NLGQVAGSLH  600
PQSTGKHDVD YFYNVPVQTT DHSMKTGDQR TSSSSLTKEN KDDGALGLLA SAYGDSSDSE  660
EEDHKGSDIP ISEGITRQYD QEGACVSEAT SFDTDRNEEA RDGPSSDINS QRLTSGKGKE  720
IDVLHATSSC STLSCTSLQE IALPFIPRSD DDSSRLHVFC LEHAAEVEQQ LRPIGGIRIM  780
LLCHPEYPRI EAEAKIVSEE LGVNHEWNDT EFRNVSRVDE ETIQAALDNV EAKAGNSDWS  840
VKLGINLSYS AILSRSPLYS KQMPYNSVIY NAFGRGSPAT SSPTKPQVSG KRSSRQRKYV  900
VGKWCGKVWM SHQVHPFLLQ QDLEGDESER SCHLRGVLED DVIGKRLSPC NASRDATTMF  960
GRKYCRKRKM RAKALPRKKL TSFKREDVVS DDTSEDHSYK QQWRASGNEE ESYFETGNSV  1020
SGDSSNQMSD EQQEFVRHQG DKDFESDDEV SDRSLGEEYA VRECAASESS MENGSQLYRE  1080
NQSMYDHDDD DIYRHPRGLP RSKRTKFFRN PVSYDSEENG LYQQRGRVST SNAQISRMGG  1140
AYDSADNSLE EQEFCSAGKR QTRSTAKRKV KTEIVQSLRD TKRRALRQSG PRKKNQEVDI  1200
YMEGPSTRLR VRNLNPSIGS SETKPKKTGK KRNSNSFSRV ASEEELEEDE EENEQEECAP  1260
YQCDMEGCTM SFTSEKQLAL HKRNICPVKG CGKNFFSHKY LVQHRRVHSD DRPLKCPWKG  1320
CKMTFKWAWS RTEHIRVHTG ARPYVCAEPS CGQTFRFVSD FSRHKRKTGH SVKKTKKR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6a57_A	2e-77	1258	1378	20	140	Lysine-specific demethylase REF6
6a58_A	2e-77	1258	1378	20	140	Lysine-specific demethylase REF6
6a59_A	2e-77	1258	1378	20	140	Lysine-specific demethylase REF6
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	966	978	KRKMRAKALPRKK

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

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Thhalv10010066m

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006404261.1	0.0	lysine-specific demethylase REF6
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	V4LPK0	0.0	V4LPK0_EUTSA; Uncharacterized protein
STRING	XP_006404261.1	0.0	(Eutrema salsugineum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5259	28	43

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

Link Out ? help Back to Top
Phytozome	Thhalv10010066m
Entrez Gene	18020751

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]