PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

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

Family

C2H2

Protein Properties

Length: 2706aa MW: 302888 Da PI: 6.5703

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Csa09g050470.1	genome	CSGP	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	11.4	0.001	2588	2613	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 ykC C++sFs+ +L H r+ + Csa09g050470.1 2588 YKCDmeGCTMSFSTEKQLALHKRNiC 2613 99********************9877 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	7.4E-17	19	60	IPR003349	JmjN domain
PROSITE profile	PS51183	13.813	20	61	IPR003349	JmjN domain
Pfam	PF02375	1.2E-13	21	54	IPR003349	JmjN domain
SMART	SM00558	2.6E-50	200	420	IPR003347	JmjC domain
PROSITE profile	PS51184	35.203	203	420	IPR003347	JmjC domain
SuperFamily	SSF51197	2.14E-11	215	287	No hit	No description
Pfam	PF02373	1.9E-15	233	284	IPR003347	JmjC domain
Pfam	PF02373	2.0E-29	300	402	IPR003347	JmjC domain
SuperFamily	SSF51197	4.39E-17	302	438	No hit	No description
SMART	SM00355	8.5	1332	1354	IPR015880	Zinc finger, C2H2-like
SMART	SM00558	5.0E-47	1437	1625	IPR003347	JmjC domain
PROSITE profile	PS51184	32.499	1440	1625	IPR003347	JmjC domain
SuperFamily	SSF51197	4.94E-25	1453	1642	No hit	No description
Pfam	PF02373	9.5E-34	1470	1608	IPR003347	JmjC domain
SMART	SM00355	8.9	2588	2610	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	11.884	2611	2640	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.11	2611	2635	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	5.5E-4	2612	2634	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	2613	2635	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	3.38E-10	2627	2669	No hit	No description
Gene3D	G3DSA:3.30.160.60	6.1E-11	2635	2662	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0026	2641	2665	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.99	2641	2670	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	2643	2665	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	2.7E-7	2659	2693	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.9E-8	2663	2694	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.159	2671	2702	IPR007087	Zinc finger, C2H2
SMART	SM00355	1.1	2671	2697	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	2673	2697	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: 2706 aa Download sequence Send to blast
MAVSEQSQDV FPWLKSLPVA PEFRPTLAEF QDPIAYIFKI EEEASKYGIC KILPPLPPPS 60 KKASISNLNR SLAARAAGKV RDGGFGACDY DGGPTFATRQ QQIGFCPRKQ RPVQRPVWQS 120 GEEYSFGEFE FKAKTFEKNY LKKCGKKSQL SPLEMETLYW RATVDKPFSV EYANDMPGSA 180 FIPLSLAAAR RRESGGDAGT VGETAWNMRA MARAEGSLLK FMKEDIPGVT SPMVYIAMMF 240 SWFAWHVEDH DLHSLNYLHM GASKTWYGVP KEAAPAFEEV VRVHGYGGEL NPLGEYLVKD 300 HDLHSLNYLH MGASKTWYGV PKEAAPAFEE VVRVHGYGGE LNPLVTFSTL GEKTTVMSPE 360 VFVKAGIPCC RLVQNPGEFV VTFPGAYHSG FSHGFNFGEA SNIATPQWLT MAKDAAIRRA 420 AINYPPMVSH LQLLYDFALA LGSRVPTSIN AKPRSSRLKD KKRSEGERLT KKLFVENIIR 480 NNELLSSLGK GSPVALLPQS SSDISVCSDL RIGSDLTTNQ DNPIQLKSED FSSDSVMVGL 540 NNGLKDTVSV KEKFTSLCER NRNHLASREN ETQGTLPEAE RREKGGAVRL SDQRLFSCVT 600 CGVLSFDCVA IIQPKEAAAR YIMSADSSFF NDRTAVSESS NLGQAARSHH PQSMEKHDVD 660 YFSNVSVQTG HQRTSTTSQT NAQKDNGSLG LLVSAYGDSS DSEEEDNRGL DASTSEGERK 720 KYDQESAFKG SSFDTDENEV ARDGRTSDFN SHSLNGKQNN LSKGDNSSLL DITLPFVPRS 780 DDDPCRLHVF CLEHAAEVEQ QLRAIGGIHI MLLCHPGNSK TPRFHFYWSC DIALSIMQIL 840 ESVSSFERII IAEYRRIEAE AKIVAEELAI NHEWHDTEFR NVTREDEETI QAALDNVEAK 900 GGNSDWTVKL AINLSYSAIL SHSPLYSKQM PYNSVIYNVF GRSSPAISSL SKPEVSGKRF 960 SRQRKYVVGK WCGKVWMSHQ VHPFLLEEDL EGEEERSCHL RTAMDEDVTG KRLFPCTVSR 1020 DAATMFGRKY CRKRKVRAKA VPRKKLTSFK REDGVSDDTS EDHSYKQQWR ASGNEEESYF 1080 ETGHTASGDS SNQMSDQRKE IVRHKGYNVF ESDDEVADRS LGEEYSVREC AVSESSMDNG 1140 FQPYREKQSM YDRDDDDDDD MYKHPREIPR SKRTKVFRNP VSYDSEENGV YQQRGRVSRS 1200 SKQANRMGGE YDSAENSFEE LDFSSTGKRQ TRSTAKRKAK TKSVQSPRDA KGRTLQEFAS 1260 GMKTEELDSF MEGPSTRLRV RKPKPSRGSS ESKPKKIGKK RSSNASFARV ASEEDVQEDE 1320 EAENEEEECT GYQCDMEGCT MSFTSEKQLA LHKRNICPVR GCDFFGFPTT XXXXXXXXXX 1380 XXXXXXXXXX EIETLYWRAS VDKPFSVEYA NDMPGSAFIP LSLAAARRRE YGGDGGTVGE 1440 TAWNMRAMAR AEGSLLKFMN EEIPGVTSPM VYIAMMFSWF AWHVEDHDLH SLNYLHMGAG 1500 KTWYGVPKDA AVAFEEVVRV HGYGGELNPL GLCESGSLVS IHCLIVDILV TSYTLGEKTT 1560 VMSPEVFVKA GIPCCRLVQN PGEFVVTFPR AYHSGFSHGF NCGEASNIAT PEWLRMANDA 1620 AIRRAAINYP PMVSHLQLLY DYALTLGSRV PASINTNPRS SRLKDKKRSE GERLTKKLFV 1680 EIIIRNNELL SSLGKGSPVA LLPQSSSDIS VCSDLRIGSD LRTNQEKPTL LKDEDLSCDS 1740 IMVSFNDGLK DTVSVKEKFT SLCERNRNHL ASRENETQET LSDAERREKG GAVRLSDQRL 1800 FSCVTCGVLS FDCVAIVQPK EAAARYIMSA DSSFFNDWTA VSESANLGQD ASAPVVKLSQ 1860 STEMHDADYF YSVPVQTTDH SMKTSGQTTS AASLTKPHKE DCALGLLASA YGDSSDSDEE 1920 DDIIVSEEKN YDQSGSCAYE TQSFVTNGNE EARDGRSSYL NSQRLVCGKE KGVIEGSHAT 1980 STCSTLSSPV EIALPFVPRS DDDSCRQRLV CGKEKGVIEG SHATSTCSTL SSPVEIALPF 2040 VPRSDDDSCR LHVFCLEHAA EVEQRLRSIG GIHMMLLCHP EYPRIESEAK IVAEELAINH 2100 NWNDTEFRNV AREDEETIQA ALDYVEAKGG NSDWTVKLGI NLSYSAILSR SPLNVAREDE 2160 ETIQAALDYV EAKGGNSDWT VKLGINLSYS AILSRSPLYS KQMPYNSVIY NAFGRSSPAT 2220 SSPSKPEVSG IRSSRQRKYV VGKWCGKVWM SHQVHPFLLE QDLEGEESKR SCHLRAAMDE 2280 DFTGKRLFPS RGATTMFGRT YSRKRNIRAK AVPRKKLTSF KREDGDSDDT SEDHSYKQQW 2340 RASGNEEETY FGTGITASGD SSNQMSDQQI KGIRRHRGLK EFESDDEVSN RSLGEEYTVR 2400 EHAISESSTE KSFQLYQQSI DRNAYEDSVY GHDDGNVYRH LRGIPKSKRT KVFRNPVSYD 2460 SEDNDVHQQK GNRQVSRRIG GEYDSAEDSV EEQDFCITGK RQTTSTAKRK VKNEIVQSPR 2520 ETNEEFNPCM EGPSTRLRVR IPKPSRGTLE TKPKKIGKRR NSNASFSRVA SEEDVDEDVE 2580 EEEECAAYKC DMEGCTMSFS TEKQLALHKR NICPIKGCGK NLFSHKYLVQ HQRVHSDDRP 2640 LKCPWKGCKM TFKWSWSRTE HVRVHTGARP YICAEPGCDQ TFRFVSDFSR HKRKTGHSVK 2700 KTKKR*

Sequence ? help Back to Top

Protein Sequence Length: 2706 aa Download sequence Send to blast

MAVSEQSQDV FPWLKSLPVA PEFRPTLAEF QDPIAYIFKI EEEASKYGIC KILPPLPPPS  60
KKASISNLNR SLAARAAGKV RDGGFGACDY DGGPTFATRQ QQIGFCPRKQ RPVQRPVWQS  120
GEEYSFGEFE FKAKTFEKNY LKKCGKKSQL SPLEMETLYW RATVDKPFSV EYANDMPGSA  180
FIPLSLAAAR RRESGGDAGT VGETAWNMRA MARAEGSLLK FMKEDIPGVT SPMVYIAMMF  240
SWFAWHVEDH DLHSLNYLHM GASKTWYGVP KEAAPAFEEV VRVHGYGGEL NPLGEYLVKD  300
HDLHSLNYLH MGASKTWYGV PKEAAPAFEE VVRVHGYGGE LNPLVTFSTL GEKTTVMSPE  360
VFVKAGIPCC RLVQNPGEFV VTFPGAYHSG FSHGFNFGEA SNIATPQWLT MAKDAAIRRA  420
AINYPPMVSH LQLLYDFALA LGSRVPTSIN AKPRSSRLKD KKRSEGERLT KKLFVENIIR  480
NNELLSSLGK GSPVALLPQS SSDISVCSDL RIGSDLTTNQ DNPIQLKSED FSSDSVMVGL  540
NNGLKDTVSV KEKFTSLCER NRNHLASREN ETQGTLPEAE RREKGGAVRL SDQRLFSCVT  600
CGVLSFDCVA IIQPKEAAAR YIMSADSSFF NDRTAVSESS NLGQAARSHH PQSMEKHDVD  660
YFSNVSVQTG HQRTSTTSQT NAQKDNGSLG LLVSAYGDSS DSEEEDNRGL DASTSEGERK  720
KYDQESAFKG SSFDTDENEV ARDGRTSDFN SHSLNGKQNN LSKGDNSSLL DITLPFVPRS  780
DDDPCRLHVF CLEHAAEVEQ QLRAIGGIHI MLLCHPGNSK TPRFHFYWSC DIALSIMQIL  840
ESVSSFERII IAEYRRIEAE AKIVAEELAI NHEWHDTEFR NVTREDEETI QAALDNVEAK  900
GGNSDWTVKL AINLSYSAIL SHSPLYSKQM PYNSVIYNVF GRSSPAISSL SKPEVSGKRF  960
SRQRKYVVGK WCGKVWMSHQ VHPFLLEEDL EGEEERSCHL RTAMDEDVTG KRLFPCTVSR  1020
DAATMFGRKY CRKRKVRAKA VPRKKLTSFK REDGVSDDTS EDHSYKQQWR ASGNEEESYF  1080
ETGHTASGDS SNQMSDQRKE IVRHKGYNVF ESDDEVADRS LGEEYSVREC AVSESSMDNG  1140
FQPYREKQSM YDRDDDDDDD MYKHPREIPR SKRTKVFRNP VSYDSEENGV YQQRGRVSRS  1200
SKQANRMGGE YDSAENSFEE LDFSSTGKRQ TRSTAKRKAK TKSVQSPRDA KGRTLQEFAS  1260
GMKTEELDSF MEGPSTRLRV RKPKPSRGSS ESKPKKIGKK RSSNASFARV ASEEDVQEDE  1320
EAENEEEECT GYQCDMEGCT MSFTSEKQLA LHKRNICPVR GCDFFGFPTT XXXXXXXXXX  1380
XXXXXXXXXX EIETLYWRAS VDKPFSVEYA NDMPGSAFIP LSLAAARRRE YGGDGGTVGE  1440
TAWNMRAMAR AEGSLLKFMN EEIPGVTSPM VYIAMMFSWF AWHVEDHDLH SLNYLHMGAG  1500
KTWYGVPKDA AVAFEEVVRV HGYGGELNPL GLCESGSLVS IHCLIVDILV TSYTLGEKTT  1560
VMSPEVFVKA GIPCCRLVQN PGEFVVTFPR AYHSGFSHGF NCGEASNIAT PEWLRMANDA  1620
AIRRAAINYP PMVSHLQLLY DYALTLGSRV PASINTNPRS SRLKDKKRSE GERLTKKLFV  1680
EIIIRNNELL SSLGKGSPVA LLPQSSSDIS VCSDLRIGSD LRTNQEKPTL LKDEDLSCDS  1740
IMVSFNDGLK DTVSVKEKFT SLCERNRNHL ASRENETQET LSDAERREKG GAVRLSDQRL  1800
FSCVTCGVLS FDCVAIVQPK EAAARYIMSA DSSFFNDWTA VSESANLGQD ASAPVVKLSQ  1860
STEMHDADYF YSVPVQTTDH SMKTSGQTTS AASLTKPHKE DCALGLLASA YGDSSDSDEE  1920
DDIIVSEEKN YDQSGSCAYE TQSFVTNGNE EARDGRSSYL NSQRLVCGKE KGVIEGSHAT  1980
STCSTLSSPV EIALPFVPRS DDDSCRQRLV CGKEKGVIEG SHATSTCSTL SSPVEIALPF  2040
VPRSDDDSCR LHVFCLEHAA EVEQRLRSIG GIHMMLLCHP EYPRIESEAK IVAEELAINH  2100
NWNDTEFRNV AREDEETIQA ALDYVEAKGG NSDWTVKLGI NLSYSAILSR SPLNVAREDE  2160
ETIQAALDYV EAKGGNSDWT VKLGINLSYS AILSRSPLYS KQMPYNSVIY NAFGRSSPAT  2220
SSPSKPEVSG IRSSRQRKYV VGKWCGKVWM SHQVHPFLLE QDLEGEESKR SCHLRAAMDE  2280
DFTGKRLFPS RGATTMFGRT YSRKRNIRAK AVPRKKLTSF KREDGDSDDT SEDHSYKQQW  2340
RASGNEEETY FGTGITASGD SSNQMSDQQI KGIRRHRGLK EFESDDEVSN RSLGEEYTVR  2400
EHAISESSTE KSFQLYQQSI DRNAYEDSVY GHDDGNVYRH LRGIPKSKRT KVFRNPVSYD  2460
SEDNDVHQQK GNRQVSRRIG GEYDSAEDSV EEQDFCITGK RQTTSTAKRK VKNEIVQSPR  2520
ETNEEFNPCM EGPSTRLRVR IPKPSRGTLE TKPKKIGKRR NSNASFSRVA SEEDVDEDVE  2580
EEEECAAYKC DMEGCTMSFS TEKQLALHKR NICPIKGCGK NLFSHKYLVQ HQRVHSDDRP  2640
LKCPWKGCKM TFKWSWSRTE HVRVHTGARP YICAEPGCDQ TFRFVSDFSR HKRKTGHSVK  2700
KTKKR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6a57_A	8e-76	1329	2705	20	140	Lysine-specific demethylase REF6
6a58_A	8e-76	1329	2705	20	140	Lysine-specific demethylase REF6
6a59_A	8e-76	1329	2705	20	140	Lysine-specific demethylase REF6
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	1032	1044	KRKVRAKAVPRKK

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Csa09g050470.1

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	AY664499	0.0	AY664499.1 Arabidopsis thaliana relative of early flowering 6 (REF6) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010426332.1	0.0	PREDICTED: lysine-specific demethylase REF6-like isoform X2
Refseq	XP_010426335.2	0.0	PREDICTED: lysine-specific demethylase REF6-like isoform X1
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	R0FN14	0.0	R0FN14_9BRAS; Uncharacterized protein
STRING	XP_010426332.1	0.0	(Camelina sativa)

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
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]