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

SapurV1A.0486s0080.1.p

Organism

Salix purpurea

Taxonomic ID

77065

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Salicaceae; Saliceae; Salix

Family

C2H2

Protein Properties

Length: 1691aa MW: 190630 Da PI: 8.9982

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
SapurV1A.0486s0080.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	12.7	0.00038	1599	1621	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H r+H SapurV1A.0486s0080.1.p 1599 CPvkGCGKKFFSHKYLVQHRRVH 1621 9999*****************99 PP
2	zf-C2H2	11.6	0.00088	1657	1683	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C Cg++F+ s++ rH r+ H SapurV1A.0486s0080.1.p 1657 YVCAeeGCGQTFRFVSDFSRHKRKtgH 1683 89********************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	4.8E-14	29	68	IPR003349	JmjN domain
PROSITE profile	PS51183	13.495	30	71	IPR003349	JmjN domain
Pfam	PF02375	3.9E-14	31	64	IPR003349	JmjN domain
SuperFamily	SSF51197	6.32E-27	118	177	No hit	No description
SMART	SM00558	1.2E-50	196	365	IPR003347	JmjC domain
PROSITE profile	PS51184	34.251	196	365	IPR003347	JmjC domain
SuperFamily	SSF51197	6.32E-27	214	379	No hit	No description
Pfam	PF02373	9.5E-37	229	348	IPR003347	JmjC domain
SMART	SM00355	13	1574	1596	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	0.0045	1597	1621	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.383	1597	1626	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	2.2E-5	1598	1620	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1599	1621	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	3.02E-9	1613	1655	No hit	No description
Gene3D	G3DSA:3.30.160.60	2.5E-8	1621	1648	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0014	1627	1651	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.741	1627	1656	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1629	1651	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	6.48E-8	1645	1679	No hit	No description
Gene3D	G3DSA:3.30.160.60	3.7E-9	1649	1680	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.85	1657	1683	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	11.24	1657	1688	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1659	1683	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: 1691 aa Download sequence Send to blast
MAAPSGLSLD PPQPPTTTEV CQWLKNLPLA PEYRPTLSEF QDPIAYIFKI EKEASQYGIC 60 KIIPPVLPSA KKTTLSNLNR SLCARNGGSS APTFTTRQQQ IGFCPRKPRP VQKPVWQSGE 120 TYTFQEFETK ARTFEKNYLK KFSKKGALSP LEFETLYWKA TLDKPFSVEY ANDMPGSAFS 180 PRKKEGQGGV AGDGMSVGET EWNMRGVSRA KGSLLRFMKE EIPGVTSPMV YIGMMFSWFA 240 WHVEDHDLHS LNYMHMGAGK TWYGVPREAA VAFEEVVRVH GYGGEINPLV TFSVLGEKTT 300 VMSPEVFISA GVPCCRLVQN AGEFVVTFPR AYHSGFSHGF NCGEAANIAT PEWLMVAKDA 360 AIRRASINYP PMVSHFQLLY DLALEFCTRI PVNISAKPRS SRLKDKQKGE GEMLVKEQFV 420 KNMIQNNDLL HSLGKGSSVV LLPRSSSDIS VCSKLRVGSQ LRDSPTLGLC SQKDVMKSSK 480 SSGSGDILQD KDQEINQVKG FFSVKAKFAS LCERNRFSIL NGNECSERMN IGTGRGSSIH 540 GDKLSDQRLF SCVTCGVLSF DCLAIIQPKE AASRYLMSAD CSFFNDWAIG SGVTRDVFAV 600 AGGIANISEQ NSSRWVEKNT TAGFYDVPVQ SPNYHIQMAD QGVEVASSSA KQLEASALGL 660 LALNYGNSSD SEEDQVEADL SHHDEIKMTN YSLENKYQCQ SSASPTSKQK YCDAATGGLP 720 QSPSSLDEQD DVPLKANDMY PEHGDRGDNL KDKTDDTLKS SFGFPTGNPA SIESNILDGR 780 YTDPMSMPHV SLNCSPIVHD AERTKFNRPI APLEKPDMPF TQRSDKESSC MHVFCLEHAV 840 EIEQQLSQIG GVHILLLCHP EYPRIEREAK LVSEELGIDY LWNDITFRDA AKKDEEWIQS 900 ALDSEVAIPG NGDWAVKLGI NLFYSANLSR SPFYSKQMPY NSVIYNAFGL ASSVSSPPKF 960 KVYGRRSGKP KKVVAGKWCG KVWMSNQVHP FLAIRDHMDQ DHEQEQERSF HALATPDEKL 1020 EKKPQTSNRT ETARKSGKKR KITAGSRSIK KVKCLEAEEP DSEDSMGDNC HGQHVRVHNS 1080 KNNEDAEREI SYDLVPDSHQ QHGRCRRKWA KSVESDDAVS DDPLAEHVRQ QYRRMRRSKQ 1140 DKPIKRENTA SYASVENKFQ KQLKRVHRSD RAKFFKRQSV ASDDSLDGNS DQWHERATRR 1200 TQAKYAESED AISDDSPEES SRWLHGRVPK SKQLKYIDEE GAISDDSLES GSHQHNRRVS 1260 RGTRVQLIKR NDMVSDDSLD ESSYQRLPRF SRSKLAKLIE RENAVSDDSL DGNIHQQHGR 1320 ILKSKQAKFV EGEDAISDDS LEDNTDWQRK RIPRSKMAKF VESEDAASDD LQEEDTHQHR 1380 RRIPKSKRAN FIEREVAISD DLWGNNAHRH SRKTPRSKQA RFIEREDLVS DDLLEDDSDQ 1440 QEKRILRSKQ KKSATFCQMK RGIPRKPKCI APKMMKKETL QSMKQERRIK QETPQLRIGK 1500 SELNARQFDL RAEEGLEGGP STRLRKRPSK PPKQSGTKLK EKQQNSRKKL KDASAAKAPV 1560 GRKNVKIKDE EAEYQCDIDG CTMGFGSKQE LAMHKRNICP VKGCGKKFFS HKYLVQHRRV 1620 HIDDRPLKCP WKGCKMTFKW AWARTEHIRV HTGARPYVCA EEGCGQTFRF VSDFSRHKRK 1680 TGHSAKKGRG *

Sequence ? help Back to Top

Protein Sequence Length: 1691 aa Download sequence Send to blast

MAAPSGLSLD PPQPPTTTEV CQWLKNLPLA PEYRPTLSEF QDPIAYIFKI EKEASQYGIC  60
KIIPPVLPSA KKTTLSNLNR SLCARNGGSS APTFTTRQQQ IGFCPRKPRP VQKPVWQSGE  120
TYTFQEFETK ARTFEKNYLK KFSKKGALSP LEFETLYWKA TLDKPFSVEY ANDMPGSAFS  180
PRKKEGQGGV AGDGMSVGET EWNMRGVSRA KGSLLRFMKE EIPGVTSPMV YIGMMFSWFA  240
WHVEDHDLHS LNYMHMGAGK TWYGVPREAA VAFEEVVRVH GYGGEINPLV TFSVLGEKTT  300
VMSPEVFISA GVPCCRLVQN AGEFVVTFPR AYHSGFSHGF NCGEAANIAT PEWLMVAKDA  360
AIRRASINYP PMVSHFQLLY DLALEFCTRI PVNISAKPRS SRLKDKQKGE GEMLVKEQFV  420
KNMIQNNDLL HSLGKGSSVV LLPRSSSDIS VCSKLRVGSQ LRDSPTLGLC SQKDVMKSSK  480
SSGSGDILQD KDQEINQVKG FFSVKAKFAS LCERNRFSIL NGNECSERMN IGTGRGSSIH  540
GDKLSDQRLF SCVTCGVLSF DCLAIIQPKE AASRYLMSAD CSFFNDWAIG SGVTRDVFAV  600
AGGIANISEQ NSSRWVEKNT TAGFYDVPVQ SPNYHIQMAD QGVEVASSSA KQLEASALGL  660
LALNYGNSSD SEEDQVEADL SHHDEIKMTN YSLENKYQCQ SSASPTSKQK YCDAATGGLP  720
QSPSSLDEQD DVPLKANDMY PEHGDRGDNL KDKTDDTLKS SFGFPTGNPA SIESNILDGR  780
YTDPMSMPHV SLNCSPIVHD AERTKFNRPI APLEKPDMPF TQRSDKESSC MHVFCLEHAV  840
EIEQQLSQIG GVHILLLCHP EYPRIEREAK LVSEELGIDY LWNDITFRDA AKKDEEWIQS  900
ALDSEVAIPG NGDWAVKLGI NLFYSANLSR SPFYSKQMPY NSVIYNAFGL ASSVSSPPKF  960
KVYGRRSGKP KKVVAGKWCG KVWMSNQVHP FLAIRDHMDQ DHEQEQERSF HALATPDEKL  1020
EKKPQTSNRT ETARKSGKKR KITAGSRSIK KVKCLEAEEP DSEDSMGDNC HGQHVRVHNS  1080
KNNEDAEREI SYDLVPDSHQ QHGRCRRKWA KSVESDDAVS DDPLAEHVRQ QYRRMRRSKQ  1140
DKPIKRENTA SYASVENKFQ KQLKRVHRSD RAKFFKRQSV ASDDSLDGNS DQWHERATRR  1200
TQAKYAESED AISDDSPEES SRWLHGRVPK SKQLKYIDEE GAISDDSLES GSHQHNRRVS  1260
RGTRVQLIKR NDMVSDDSLD ESSYQRLPRF SRSKLAKLIE RENAVSDDSL DGNIHQQHGR  1320
ILKSKQAKFV EGEDAISDDS LEDNTDWQRK RIPRSKMAKF VESEDAASDD LQEEDTHQHR  1380
RRIPKSKRAN FIEREVAISD DLWGNNAHRH SRKTPRSKQA RFIEREDLVS DDLLEDDSDQ  1440
QEKRILRSKQ KKSATFCQMK RGIPRKPKCI APKMMKKETL QSMKQERRIK QETPQLRIGK  1500
SELNARQFDL RAEEGLEGGP STRLRKRPSK PPKQSGTKLK EKQQNSRKKL KDASAAKAPV  1560
GRKNVKIKDE EAEYQCDIDG CTMGFGSKQE LAMHKRNICP VKGCGKKFFS HKYLVQHRRV  1620
HIDDRPLKCP WKGCKMTFKW AWARTEHIRV HTGARPYVCA EEGCGQTFRF VSDFSRHKRK  1680
TGHSAKKGRG *

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	3e-79	18	493	3	457	Transcription factor jumonji (Jmj) family protein
6ip4_A	3e-79	18	493	3	457	Arabidopsis JMJ13
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	1524	1550	RKRPSKPPKQSGTKLKEKQQNSRKKLK
2	1537	1548	KLKEKQQNSRKK

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	SapurV1A.0486s0080.1.p

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_011024100.1	0.0	PREDICTED: lysine-specific demethylase JMJ705 isoform X1
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A2K1XK92	0.0	A0A2K1XK92_POPTR; Uncharacterized protein
STRING	POPTR_0015s10040.1	0.0	(Populus trichocarpa)

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

Link Out ? help Back to Top
Phytozome	SapurV1A.0486s0080.1.p

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]