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

GSBRNA2T00068139001

Common Name

GSBRNA2T00068139001

Organism

Brassica napus

Taxonomic ID

3708

Taxonomic Lineage

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

Family

C2H2

Protein Properties

Length: 1326aa MW: 148033 Da PI: 7.2028

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00068139001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	11.2	0.0011	1208	1233	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 y+C C++sFs+ +L H r+ + GSBRNA2T00068139001 1208 YQCDmeGCTMSFSSEKQLSLHKRNiC 1233 99********************9877 PP
2	zf-C2H2	16.5	2.4e-05	1233	1255	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk+F ++ +L++H+r+H GSBRNA2T00068139001 1233 CPvkGCGKTFFSHKYLVQHQRVH 1255 9999*****************99 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	4.1E-17	19	60	IPR003349	JmjN domain
PROSITE profile	PS51183	14.284	20	61	IPR003349	JmjN domain
Pfam	PF02375	1.6E-15	21	54	IPR003349	JmjN domain
SMART	SM00558	3.0E-53	200	369	IPR003347	JmjC domain
PROSITE profile	PS51184	33.783	203	369	IPR003347	JmjC domain
SuperFamily	SSF51197	1.02E-27	215	386	No hit	No description
Pfam	PF02373	1.7E-37	233	352	IPR003347	JmjC domain
Gene3D	G3DSA:3.30.160.60	9.7E-4	1207	1230	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	9.4	1208	1230	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	0.0015	1231	1255	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	13.339	1231	1260	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	6.9E-7	1232	1259	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1233	1255	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	1.3E-10	1247	1289	No hit	No description
Gene3D	G3DSA:3.30.160.60	9.0E-10	1260	1284	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	11.801	1261	1290	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0015	1261	1285	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1263	1285	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	2.47E-8	1279	1313	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.2E-9	1285	1314	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	2.2	1291	1317	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.388	1291	1322	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1293	1317	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: 1326 aa Download sequence Send to blast
MAVSEQSQDV FPWLKSLPVA PEFRPTLAEF QDPMAYICKI EEEASRYGIC KIVPPVPPSS 60 KKTAINNLNR SLAARARARA RDGNGGKSDY DGGPTFTTRQ QQIGFCPRRQ RPVQRPVWQS 120 GERYTFDEFE FKAKNFEKSY LKKCGKKGSV SPLEVETLYW RASVDKPFSV EYANDMPGSA 180 FVPLSLAAAR RRESGGDCGT VGETAWNMRA MARAEGSLLK FMKEEIPGVT SPMVYIAMMF 240 SWFAWHVEDH DLHSLNYLHM GAAKTWYGVP KDAAMAFEEV VRVHGYGEEL NPLVTFSTLG 300 EKTTVMSPEV FVRAGIPCCR LVQNPGDFVI TFPGAYHSGF SHGFNFGEAS NIATPQWLRM 360 AKDAAIRRAS INYPPMVSHL QLLYDYALAL GSRVPDSIHN KPRSSRLKDK KKSEGEKLTN 420 ELFVQNVIHN NELLHSLGKG SPIALLPQSS SDVSVCSDVR IGSHLGANQG QTTLLIKSED 480 LKKFTSLCER NRDHLASKED ETQGTSTDGE KRKNNGAVGL SDQRLFSCVT CGVLSFDCVA 540 IIQPKEAAAR YLMSADCSFL NDWTVASGSA NLGQDVVMPP SENTGKQDVG DLYNAPVQTP 600 YHSTTKTVDQ RTSSSSLTKE NGALGLLASA YGDSSDSEEE DHKGLDNPVS DEVEASSFVT 660 DGNDEAGNGL SSALNSQGLT CEKGKEVDVS HANLSKGGNT SSVEITLPFI PRSDDDFSRL 720 HVFCLEHAAE VEQRLHPIGG INIMLLCHPD YPRIEAEGKV VAKELGVNHE WNDTEFKNVT 780 HEETIQAALA NVEAKAGNSD WAVKLGINLS HSAILSRSPL YSKQMPYNSV IYNVFGRTSP 840 ATPQLSGIRS SRQRKYVAGK WCGKVWMSHQ VHPFLLEEDL EGEETERSHL RAALDEDVTV 900 HGNDSRDATT MFGRKYSRKR KARGKAAPRK KLTSFKREAG VSDDTTSEDH SYKQQWRAYG 960 DEEESYFETG NEVSGDSSNQ MSDQQQLKGV ESDDDEVSER SLGQEYAVRR EYASSESSME 1020 NGFQVYREDQ PMYGDDDMYR HPRGIPRNKR TKVFRDLVSY DSEDQQRERV FTSDAQTSRM 1080 GDEYDSEENS LEEQDFCSSG KRQTRSIAKR KVKTKIVQSL GDTGGHTLLQ SGSRKKMKEL 1140 DSYMEGPSTR LRVRTPKPSR GSSATKPKKT GKKGRNVSFS EVASEEEVEE NEEESEEAST 1200 RIRECLPYQC DMEGCTMSFS SEKQLSLHKR NICPVKGCGK TFFSHKYLVQ HQRVHSDDRP 1260 LKCPWKGCKM TFKWAWSRTE HIRVHTGERP YICAEPGCSQ TFRFVSDFSR HKRKTGHSAK 1320 KIKKK*

Sequence ? help Back to Top

Protein Sequence Length: 1326 aa Download sequence Send to blast

MAVSEQSQDV FPWLKSLPVA PEFRPTLAEF QDPMAYICKI EEEASRYGIC KIVPPVPPSS  60
KKTAINNLNR SLAARARARA RDGNGGKSDY DGGPTFTTRQ QQIGFCPRRQ RPVQRPVWQS  120
GERYTFDEFE FKAKNFEKSY LKKCGKKGSV SPLEVETLYW RASVDKPFSV EYANDMPGSA  180
FVPLSLAAAR RRESGGDCGT VGETAWNMRA MARAEGSLLK FMKEEIPGVT SPMVYIAMMF  240
SWFAWHVEDH DLHSLNYLHM GAAKTWYGVP KDAAMAFEEV VRVHGYGEEL NPLVTFSTLG  300
EKTTVMSPEV FVRAGIPCCR LVQNPGDFVI TFPGAYHSGF SHGFNFGEAS NIATPQWLRM  360
AKDAAIRRAS INYPPMVSHL QLLYDYALAL GSRVPDSIHN KPRSSRLKDK KKSEGEKLTN  420
ELFVQNVIHN NELLHSLGKG SPIALLPQSS SDVSVCSDVR IGSHLGANQG QTTLLIKSED  480
LKKFTSLCER NRDHLASKED ETQGTSTDGE KRKNNGAVGL SDQRLFSCVT CGVLSFDCVA  540
IIQPKEAAAR YLMSADCSFL NDWTVASGSA NLGQDVVMPP SENTGKQDVG DLYNAPVQTP  600
YHSTTKTVDQ RTSSSSLTKE NGALGLLASA YGDSSDSEEE DHKGLDNPVS DEVEASSFVT  660
DGNDEAGNGL SSALNSQGLT CEKGKEVDVS HANLSKGGNT SSVEITLPFI PRSDDDFSRL  720
HVFCLEHAAE VEQRLHPIGG INIMLLCHPD YPRIEAEGKV VAKELGVNHE WNDTEFKNVT  780
HEETIQAALA NVEAKAGNSD WAVKLGINLS HSAILSRSPL YSKQMPYNSV IYNVFGRTSP  840
ATPQLSGIRS SRQRKYVAGK WCGKVWMSHQ VHPFLLEEDL EGEETERSHL RAALDEDVTV  900
HGNDSRDATT MFGRKYSRKR KARGKAAPRK KLTSFKREAG VSDDTTSEDH SYKQQWRAYG  960
DEEESYFETG NEVSGDSSNQ MSDQQQLKGV ESDDDEVSER SLGQEYAVRR EYASSESSME  1020
NGFQVYREDQ PMYGDDDMYR HPRGIPRNKR TKVFRDLVSY DSEDQQRERV FTSDAQTSRM  1080
GDEYDSEENS LEEQDFCSSG KRQTRSIAKR KVKTKIVQSL GDTGGHTLLQ SGSRKKMKEL  1140
DSYMEGPSTR LRVRTPKPSR GSSATKPKKT GKKGRNVSFS EVASEEEVEE NEEESEEAST  1200
RIRECLPYQC DMEGCTMSFS SEKQLSLHKR NICPVKGCGK TFFSHKYLVQ HQRVHSDDRP  1260
LKCPWKGCKM TFKWAWSRTE HIRVHTGERP YICAEPGCSQ TFRFVSDFSR HKRKTGHSAK  1320
KIKKK*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6a57_A	3e-73	1205	1325	20	140	Lysine-specific demethylase REF6
6a58_A	3e-73	1205	1325	20	140	Lysine-specific demethylase REF6
6a59_A	3e-73	1205	1325	20	140	Lysine-specific demethylase REF6
6ip0_A	1e-70	9	392	4	355	Transcription factor jumonji (Jmj) family protein
6ip4_A	1e-70	9	392	4	355	Arabidopsis JMJ13
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	918	930	KRKARGKAAPRKK

Expression -- Description ? help Back to Top
Source	Description
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}.

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	GSBRNA2T00068139001

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_013724852.1	0.0	lysine-specific demethylase REF6
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A078HQG9	0.0	A0A078HQG9_BRANA; BnaCnng09530D protein
STRING	Bo8g076910.1	0.0	(Brassica oleracea)

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

Publications ? help Back to Top
Chalhoub B, et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 2014. 345(6199): p. 950-3 [PMID:25146293] 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]