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

Csa09g050470.2

Organism

Camelina sativa

Taxonomic ID

90675

Taxonomic Lineage

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: 2668aa MW: 298347 Da PI: 6.615

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Csa09g050470.2	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	2550	2575	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 ykC C++sFs+ +L H r+ + Csa09g050470.2 2550 YKCDmeGCTMSFSTEKQLALHKRNiC 2575 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	2.11E-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	1399	1587	IPR003347	JmjC domain
PROSITE profile	PS51184	32.499	1402	1587	IPR003347	JmjC domain
SuperFamily	SSF51197	4.39E-25	1415	1604	No hit	No description
Pfam	PF02373	9.3E-34	1432	1570	IPR003347	JmjC domain
SMART	SM00355	8.9	2550	2572	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	11.884	2573	2602	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.11	2573	2597	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	5.4E-4	2574	2596	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	2575	2597	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	3.44E-10	2589	2631	No hit	No description
Gene3D	G3DSA:3.30.160.60	6.0E-11	2597	2624	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.99	2603	2632	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0026	2603	2627	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	2605	2627	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	2.48E-7	2621	2655	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.8E-8	2625	2656	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.159	2633	2664	IPR007087	Zinc finger, C2H2
SMART	SM00355	1.1	2633	2659	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	2635	2659	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: 2668 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 GCVDKPFSVE YANDMPGSAF 1380 IPLSLAAARR REYGGDGGTV GETAWNMRAM ARAEGSLLKF MNEEIPGVTS PMVYIAMMFS 1440 WFAWHVEDHD LHSLNYLHMG AGKTWYGVPK DAAVAFEEVV RVHGYGGELN PLGLCESGSL 1500 VSIHCLIVDI LVTSYTLGEK TTVMSPEVFV KAGIPCCRLV QNPGEFVVTF PRAYHSGFSH 1560 GFNCGEASNI ATPEWLRMAN DAAIRRAAIN YPPMVSHLQL LYDYALTLGS RVPASINTNP 1620 RSSRLKDKKR SEGERLTKKL FVEIIIRNNE LLSSLGKGSP VALLPQSSSD ISVCSDLRIG 1680 SDLRTNQEKP TLLKDEDLSC DSIMVSFNDG LKDTVSVKEK FTSLCERNRN HLASRENETQ 1740 ETLSDAERRE KGGAVRLSDQ RLFSCVTCGV LSFDCVAIVQ PKEAAARYIM SADSSFFNDW 1800 TAVSESANLG QDASAPVVKL SQSTEMHDAD YFYSVPVQTT DHSMKTSGQT TSAASLTKPH 1860 KEDCALGLLA SAYGDSSDSD EEDDIIVSEE KNYDQSGSCA YETQSFVTNG NEEARDGRSS 1920 YLNSQRLVCG KEKGVIEGSH ATSTCSTLSS PVEIALPFVP RSDDDSCRQR LVCGKEKGVI 1980 EGSHATSTCS TLSSPVEIAL PFVPRSDDDS CRLHVFCLEH AAEVEQRLRS IGGIHMMLLC 2040 HPEYPRIESE AKIVAEELAI NHNWNDTEFR NVAREDEETI QAALDYVEAK GGNSDWTVKL 2100 GINLSYSAIL SRSPLNVARE DEETIQAALD YVEAKGGNSD WTVKLGINLS YSAILSRSPL 2160 YSKQMPYNSV IYNAFGRSSP ATSSPSKPEV SGIRSSRQRK YVVGKWCGKV WMSHQVHPFL 2220 LEQDLEGEES KRSCHLRAAM DEDFTGKRLF PSRGATTMFG RTYSRKRNIR AKAVPRKKLT 2280 SFKREDGDSD DTSEDHSYKQ QWRASGNEEE TYFGTGITAS GDSSNQMSDQ QIKGIRRHRG 2340 LKEFESDDEV SNRSLGEEYT VREHAISESS TEKSFQLYQQ SIDRNAYEDS VYGHDDGNVY 2400 RHLRGIPKSK RTKVFRNPVS YDSEDNDVHQ QKGNRQVSRR IGGEYDSAED SVEEQDFCIT 2460 GKRQTTSTAK RKVKNEIVQS PRETNEEFNP CMEGPSTRLR VRIPKPSRGT LETKPKKIGK 2520 RRNSNASFSR VASEEDVDED VEEEEECAAY KCDMEGCTMS FSTEKQLALH KRNICPIKGC 2580 GKNLFSHKYL VQHQRVHSDD RPLKCPWKGC KMTFKWSWSR TEHVRVHTGA RPYICAEPGC 2640 DQTFRFVSDF SRHKRKTGHS VKKTKKR*

Sequence ? help Back to Top

Protein Sequence Length: 2668 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 GCVDKPFSVE YANDMPGSAF  1380
IPLSLAAARR REYGGDGGTV GETAWNMRAM ARAEGSLLKF MNEEIPGVTS PMVYIAMMFS  1440
WFAWHVEDHD LHSLNYLHMG AGKTWYGVPK DAAVAFEEVV RVHGYGGELN PLGLCESGSL  1500
VSIHCLIVDI LVTSYTLGEK TTVMSPEVFV KAGIPCCRLV QNPGEFVVTF PRAYHSGFSH  1560
GFNCGEASNI ATPEWLRMAN DAAIRRAAIN YPPMVSHLQL LYDYALTLGS RVPASINTNP  1620
RSSRLKDKKR SEGERLTKKL FVEIIIRNNE LLSSLGKGSP VALLPQSSSD ISVCSDLRIG  1680
SDLRTNQEKP TLLKDEDLSC DSIMVSFNDG LKDTVSVKEK FTSLCERNRN HLASRENETQ  1740
ETLSDAERRE KGGAVRLSDQ RLFSCVTCGV LSFDCVAIVQ PKEAAARYIM SADSSFFNDW  1800
TAVSESANLG QDASAPVVKL SQSTEMHDAD YFYSVPVQTT DHSMKTSGQT TSAASLTKPH  1860
KEDCALGLLA SAYGDSSDSD EEDDIIVSEE KNYDQSGSCA YETQSFVTNG NEEARDGRSS  1920
YLNSQRLVCG KEKGVIEGSH ATSTCSTLSS PVEIALPFVP RSDDDSCRQR LVCGKEKGVI  1980
EGSHATSTCS TLSSPVEIAL PFVPRSDDDS CRLHVFCLEH AAEVEQRLRS IGGIHMMLLC  2040
HPEYPRIESE AKIVAEELAI NHNWNDTEFR NVAREDEETI QAALDYVEAK GGNSDWTVKL  2100
GINLSYSAIL SRSPLNVARE DEETIQAALD YVEAKGGNSD WTVKLGINLS YSAILSRSPL  2160
YSKQMPYNSV IYNAFGRSSP ATSSPSKPEV SGIRSSRQRK YVVGKWCGKV WMSHQVHPFL  2220
LEQDLEGEES KRSCHLRAAM DEDFTGKRLF PSRGATTMFG RTYSRKRNIR AKAVPRKKLT  2280
SFKREDGDSD DTSEDHSYKQ QWRASGNEEE TYFGTGITAS GDSSNQMSDQ QIKGIRRHRG  2340
LKEFESDDEV SNRSLGEEYT VREHAISESS TEKSFQLYQQ SIDRNAYEDS VYGHDDGNVY  2400
RHLRGIPKSK RTKVFRNPVS YDSEDNDVHQ QKGNRQVSRR IGGEYDSAED SVEEQDFCIT  2460
GKRQTTSTAK RKVKNEIVQS PRETNEEFNP CMEGPSTRLR VRIPKPSRGT LETKPKKIGK  2520
RRNSNASFSR VASEEDVDED VEEEEECAAY KCDMEGCTMS FSTEKQLALH KRNICPIKGC  2580
GKNLFSHKYL VQHQRVHSDD RPLKCPWKGC KMTFKWSWSR TEHVRVHTGA RPYICAEPGC  2640
DQTFRFVSDF SRHKRKTGHS VKKTKKR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6a57_A	7e-76	1329	2667	20	140	Lysine-specific demethylase REF6
6a58_A	7e-76	1329	2667	20	140	Lysine-specific demethylase REF6
6a59_A	7e-76	1329	2667	20	140	Lysine-specific demethylase REF6
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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	Csa09g050470.2

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)

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]