PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Dalbergieae; Arachis

Family

C2H2

Protein Properties

Length: 1577aa MW: 178094 Da PI: 8.3035

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Aradu.HLK79	genome	NCGR_PGC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	12.1	0.0006	1462	1487	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 ++C C++sF +k +L++H r+ + Aradu.HLK79 1462 FQCDidGCTMSFGSKQELMHHKRNiC 1487 89********************9877 PP
2	zf-C2H2	12.7	0.00038	1487	1509	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H r+H Aradu.HLK79 1487 CPvkGCGKKFFSHKYLVQHRRVH 1509 9999*****************99 PP
3	zf-C2H2	11.7	0.00077	1545	1571	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C Cg++F+ s++ rH r+ H Aradu.HLK79 1545 YVCAepGCGQTFRFVSDFSRHKRKtgH 1571 899999****************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	1.1E-15	17	58	IPR003349	JmjN domain
PROSITE profile	PS51183	14.354	18	59	IPR003349	JmjN domain
Pfam	PF02375	3.4E-14	19	52	IPR003349	JmjN domain
SuperFamily	SSF51197	7.14E-26	103	134	No hit	No description
SuperFamily	SSF51197	7.14E-26	189	358	No hit	No description
SMART	SM00558	8.3E-52	192	361	IPR003347	JmjC domain
PROSITE profile	PS51184	33.411	192	361	IPR003347	JmjC domain
Pfam	PF02373	7.6E-36	225	344	IPR003347	JmjC domain
Gene3D	G3DSA:3.30.160.60	5.3E-4	1454	1484	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	9.1	1462	1484	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.508	1485	1514	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0045	1485	1509	IPR015880	Zinc finger, C2H2-like
SuperFamily	SSF57667	6.66E-6	1485	1521	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.2E-5	1487	1513	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1487	1509	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	3.7E-8	1514	1539	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0014	1515	1539	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.741	1515	1544	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1517	1539	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	2.89E-9	1525	1569	No hit	No description
Gene3D	G3DSA:3.30.160.60	2.4E-9	1540	1568	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	11.261	1545	1576	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.62	1545	1571	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1547	1571	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: 1577 aa Download sequence Send to blast
MAEANGDVFQ WLKSMPLAPE YRPTLTEFQD PIAYIFKIEK EASKYGICKI IPPFPPPPRK 60 VAIANFTRSL TKPDEPNSKP TFTTRQQQIG FCPRRPRPVQ RPVWQSGENY TFQEFEAKAK 120 AFEKSYLKKH HLHHQGHRKG GGGGGGSGGL GPLEVETLFW KATVDKPFSV EYANDMPGSA 180 FSRKCREECA AALAESAWNM REISRANGSL LRFMKEEIPG VTSPMVYLAM LFSWFAWHVE 240 DHDLHSLNYL HMGSGKTWYG VPRDAAVAFE DVVRVHGYGS EINPLVTFST LGEKNTVMSP 300 EVLINAGVPC CRLVQNAGEF VVTFPRAYHT GFSHGFNCGE AANIATPEWL RVAKDAAIRR 360 ASVNHSPMVS HFQLLYDLAL ALCSRFVFCY YGFLLLAVTG IPELFVQDVS QNNDLLQELS 420 KGSEIILLPR SSFDISLCSK LRSGSKQRKV NSRFSLGACN SEEMNSSKGF VSDDLAFSMN 480 RGIKQEGSLS IKDKITSLCE RSMISSYDVN GNICSSSSKQ LQGDNERESG EGDGSPDKRL 540 FSCVTCGILC FPCVAIVQPR ESAARYLMSA DCSFFNDWVV GSGVSSKKFI AHEEAAFPEP 600 RWTEKKTQGL YQDPVQSAQY QLQTAERNYE ESLGKSNTAL ALLASTYGNS SDSEEEHGDS 660 DIVVDGHESP MINATLGGSP SNFQDGCTIP LTGPDSRNDF SHQSFDHSLE KQDCDTSSGF 720 ALKNMRAMYT NDTEKTLLGK AMVPNDDKNA SVMPQGDQDS SRMHVFCLEH AVEAEQQLRP 780 IGGAHIMLLC HPDFPKIEAE AKLVAEDLGI DYLWKKIEYR HSSKEDEERI QVALDSEEAI 840 PGNGDWCVKL GINLFYSSTL SRSPLYSKQM PYNSVIYYAF GQSSPASSPL EPKVYQRRVN 900 KQKKIVAGKW CGKVWMSSQV HPLLAKRDSE DVEDEKSLHG WGLHDEKIER SGSIPKSETS 960 ARKSGKKRKM TIENGRARKG SFAERDVDLD NPTEDKPNQQ LRRTLRSKQA RDIESEGADL 1020 EGDYSPPYHR KPLSDQTNCT GSDAVSDDSL DDKFIDNDVV SDDTMVYDSD CHQRFEHSSM 1080 QVEDIEDAVS EDSLDDGSLQ LHRKNSKSKH ARYIRKGRCI AEKEEMMSDD QLEPHKKNKQ 1140 QRNPKSRQAK YLAREDAISH GQLEGHCRKY RKTPKGRLAK YVAGEDVSSD EQLENYSRKQ 1200 QTSLPKRQKN KGVLTDDQLE DHFQKQQKSV SRRRQNKGIE RGVKDEMSDD QLEDHVQKQQ 1260 TSVSKRRRNK QIERDDVMSD DEMEDHFQKQ RSSIPRNRQN SNSHLAHKTP KRKQAKCVDD 1320 DDGDDDDVNS DDEVEDDSQQ KQQRTLRSKQ SKPMTLKQMK QARSLQMKNQ TSRSVKRGAQ 1380 TLKKLKASQI RNKQSGKSRE FSLKMEEGEE GGPSTRLRKR APKVEESDGI SKEKQTKKKR 1440 VKNATSAKAA SNAKVKDEEN EFQCDIDGCT MSFGSKQELM HHKRNICPVK GCGKKFFSHK 1500 YLVQHRRVHE DDRPLKCPWK GCKMTFKWAW ARTEHIRVHT GARPYVCAEP GCGQTFRFVS 1560 DFSRHKRKTG HSTKKSR

Sequence ? help Back to Top

Protein Sequence Length: 1577 aa Download sequence Send to blast

MAEANGDVFQ WLKSMPLAPE YRPTLTEFQD PIAYIFKIEK EASKYGICKI IPPFPPPPRK  60
VAIANFTRSL TKPDEPNSKP TFTTRQQQIG FCPRRPRPVQ RPVWQSGENY TFQEFEAKAK  120
AFEKSYLKKH HLHHQGHRKG GGGGGGSGGL GPLEVETLFW KATVDKPFSV EYANDMPGSA  180
FSRKCREECA AALAESAWNM REISRANGSL LRFMKEEIPG VTSPMVYLAM LFSWFAWHVE  240
DHDLHSLNYL HMGSGKTWYG VPRDAAVAFE DVVRVHGYGS EINPLVTFST LGEKNTVMSP  300
EVLINAGVPC CRLVQNAGEF VVTFPRAYHT GFSHGFNCGE AANIATPEWL RVAKDAAIRR  360
ASVNHSPMVS HFQLLYDLAL ALCSRFVFCY YGFLLLAVTG IPELFVQDVS QNNDLLQELS  420
KGSEIILLPR SSFDISLCSK LRSGSKQRKV NSRFSLGACN SEEMNSSKGF VSDDLAFSMN  480
RGIKQEGSLS IKDKITSLCE RSMISSYDVN GNICSSSSKQ LQGDNERESG EGDGSPDKRL  540
FSCVTCGILC FPCVAIVQPR ESAARYLMSA DCSFFNDWVV GSGVSSKKFI AHEEAAFPEP  600
RWTEKKTQGL YQDPVQSAQY QLQTAERNYE ESLGKSNTAL ALLASTYGNS SDSEEEHGDS  660
DIVVDGHESP MINATLGGSP SNFQDGCTIP LTGPDSRNDF SHQSFDHSLE KQDCDTSSGF  720
ALKNMRAMYT NDTEKTLLGK AMVPNDDKNA SVMPQGDQDS SRMHVFCLEH AVEAEQQLRP  780
IGGAHIMLLC HPDFPKIEAE AKLVAEDLGI DYLWKKIEYR HSSKEDEERI QVALDSEEAI  840
PGNGDWCVKL GINLFYSSTL SRSPLYSKQM PYNSVIYYAF GQSSPASSPL EPKVYQRRVN  900
KQKKIVAGKW CGKVWMSSQV HPLLAKRDSE DVEDEKSLHG WGLHDEKIER SGSIPKSETS  960
ARKSGKKRKM TIENGRARKG SFAERDVDLD NPTEDKPNQQ LRRTLRSKQA RDIESEGADL  1020
EGDYSPPYHR KPLSDQTNCT GSDAVSDDSL DDKFIDNDVV SDDTMVYDSD CHQRFEHSSM  1080
QVEDIEDAVS EDSLDDGSLQ LHRKNSKSKH ARYIRKGRCI AEKEEMMSDD QLEPHKKNKQ  1140
QRNPKSRQAK YLAREDAISH GQLEGHCRKY RKTPKGRLAK YVAGEDVSSD EQLENYSRKQ  1200
QTSLPKRQKN KGVLTDDQLE DHFQKQQKSV SRRRQNKGIE RGVKDEMSDD QLEDHVQKQQ  1260
TSVSKRRRNK QIERDDVMSD DEMEDHFQKQ RSSIPRNRQN SNSHLAHKTP KRKQAKCVDD  1320
DDGDDDDVNS DDEVEDDSQQ KQQRTLRSKQ SKPMTLKQMK QARSLQMKNQ TSRSVKRGAQ  1380
TLKKLKASQI RNKQSGKSRE FSLKMEEGEE GGPSTRLRKR APKVEESDGI SKEKQTKKKR  1440
VKNATSAKAA SNAKVKDEEN EFQCDIDGCT MSFGSKQELM HHKRNICPVK GCGKKFFSHK  1500
YLVQHRRVHE DDRPLKCPWK GCKMTFKWAW ARTEHIRVHT GARPYVCAEP GCGQTFRFVS  1560
DFSRHKRKTG HSTKKSR

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	4e-75	7	382	4	353	Transcription factor jumonji (Jmj) family protein
6ip4_A	4e-75	7	382	4	353	Arabidopsis JMJ13
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	1417	1439	RKRAPKVEESDGISKEKQTKKKR

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	Aradu.HLK79

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_025688566.1	0.0	lysine-specific demethylase REF6 isoform X2
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A445AAM7	0.0	A0A445AAM7_ARAHY; Uncharacterized protein
STRING	XP_007137965.1	0.0	(Phaseolus vulgaris)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF5648	32	50

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]