PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

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

Family

C2H2

Protein Properties

Length: 1686aa MW: 191195 Da PI: 9.0985

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Potri.012G092400.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	11	0.0013	1569	1594	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 y+C C +sF +k +L H r+ + Potri.012G092400.1 1569 YQCDidGCRMSFVSKQELALHKRNiC 1594 99********************9877 PP
2	zf-C2H2	12.7	0.00038	1594	1616	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk F ++ +L++H r+H Potri.012G092400.1 1594 CPvkGCGKKFFSHKYLVQHRRVH 1616 9999*****************99 PP
3	zf-C2H2	11.6	0.00088	1652	1678	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C Cg++F+ s++ rH r+ H Potri.012G092400.1 1652 YVCAeeGCGQTFRFVSDFSRHKRKtgH 1678 89********************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	1.1E-13	29	68	IPR003349	JmjN domain
PROSITE profile	PS51183	13.55	30	71	IPR003349	JmjN domain
Pfam	PF02375	4.4E-14	31	64	IPR003349	JmjN domain
SuperFamily	SSF51197	3.3E-28	117	177	No hit	No description
SMART	SM00558	3.6E-52	196	365	IPR003347	JmjC domain
PROSITE profile	PS51184	35.234	196	365	IPR003347	JmjC domain
SuperFamily	SSF51197	3.3E-28	214	383	No hit	No description
Pfam	PF02373	1.3E-36	229	348	IPR003347	JmjC domain
SMART	SM00355	8.9	1569	1591	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	0.0045	1592	1616	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.383	1592	1621	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	2.3E-5	1593	1620	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1594	1616	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	2.5E-9	1608	1650	No hit	No description
Gene3D	G3DSA:3.30.160.60	4.0E-8	1621	1646	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.741	1622	1651	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0014	1622	1646	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1624	1646	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	6.38E-8	1640	1674	No hit	No description
Gene3D	G3DSA:3.30.160.60	2.9E-9	1647	1674	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.679	1652	1683	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.85	1652	1678	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1654	1678	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: 1686 aa Download sequence Send to blast
MAAPSGLSPE PPQPPTSTEV CQWLKNLPLA PEYRPTQAEF QDPIAYIFKI EKEASQYGIC 60 KIIPPVLPSA KKTTLSNLNR SLSARNGDSS APTFTTRQQQ IGFCPRKPRP VQKPVWQSGE 120 TYTFQEFETK AKSFEKNYLK KFSKKGGLSP LEIENLYWKA TLDKPFAVEY ANDMPGSAFS 180 PRKKEGQGGV VGEGMYVGET EWNMRSVSRA KGSLLRFMKE EIPGVTSPMV YIGMIFSWFA 240 WHVEDHDLHS LNYMHMGAGK TWYGVPREAA VAFEEVVRVH GYGGENNPLV TFAVLGEKTT 300 VMSPEVFISA GVPCCRLVQN AGEFVVTFPR AYHSGFSHGF NCGEAANIAT PEWLTVAKDA 360 AIRRASINYP PMVSHFQLLY DLALEFCTRI PVNISAKPRS SRLKDKQKGE GETLVKEQFV 420 KNMMQNNDLL HILGKGSSVV LLPRSSSDIS VCSNLRVGSQ LRDNPTLGLS SQKDFMKSSK 480 SSGSDDILMD ENQEINQVKG FFSVKAKFAS LCERNRFSTI NGNECTQSMN MSTERGSPIH 540 GDKLSDQRLF SCVTCGILSF DCLAIIQPKE AASRYLMSAD CSFFNDWVVG SGVTRDVFTV 600 AGGIANIPEQ NSSMRWVRKN TVAGLYDVPV QSLNYQIQMA DQSVEVASSS AKQMESSALG 660 LLALNYGNSS DSEDDQVEAG LSCHDETNFT NCSLESKYQG QSSACPSYKQ KYYDAETGGH 720 PLSPSKHDQR GDVPFKAIDM YPEHGDRPDN FKDRSDDTLG CSFGFPANNP ACIESNGLDG 780 RYRDPVSIPH MSLNCSPIVH DTEKTKFNRP TVPIENPDMP FTQRSDRDSS CLHVFCLEHA 840 VEIEQQLRQI GGVHIFLLCH PEYPRIEAEA KSVSEELGID HLWNDITFRD AAKEDEERIQ 900 SALDTEEAIP GNGDWAVKLG INLFYSANLS RSPLYSKQMP YNSVIYNAFG RASPVSSPPK 960 FKVYGRRSGK PKKVVAGKWC GKVWMSNQVH PFLVKRDFVY QNQEQEQERS FHALATPDEK 1020 LEKKPQTIHR NETSRKSGRK RKIIAGSRTV KKVKCLEAEE ADSEDSVGDN SHRQHMRIHN 1080 RKNTEDIERE ISYDLVEDSN QQHGSYRRKW AKSVESDDAV SDDPLAEHVR QQYRRMRRSK 1140 QAKSIKRENT VSYASVENKF RKQLRRVHRS DQAKCSERRC VASDDSLDDN SDQWHGRAPR 1200 STLAKYTERE DANSDDSPEE SSRWQHGRVS RSKLLRYVKK ESAISDDSLE NGFKQHNKRI 1260 SRGKRAQVIK RDDVVSDDSL DESAFQQLPR FSRIKLAKLI EREDAFSDGS LEENIHQQHG 1320 RILRSKQSKF VEREDAISDD SLEDSTHWQH RRIPRSKMAK FVESEDAASD DLQEDDGHQH 1380 HRRIPKRKKA NSIESEDVVS DDLWQNNIHR HLRKTPRGKQ PNIVEREEAV SDDLLENSSD 1440 QQDRIILRSK QKKSSMKQGI PRQLKQSAPK MIKKETPQLM KQERQIKPET PQLRFGKSDM 1500 NARQFDSHAE EERGGPRMRL RKRLSKAPKQ SLTRLKEKQN IKKKVKDATA VKAPAGRKNV 1560 KMKDEEAEYQ CDIDGCRMSF VSKQELALHK RNICPVKGCG KKFFSHKYLV QHRRVHIDDR 1620 PLKCPWKGCK MTFKWAWART EHIRVHTGAR PYVCAEEGCG QTFRFVSDFS RHKRKTGHLA 1680 KKGRG*

Sequence ? help Back to Top

Protein Sequence Length: 1686 aa Download sequence Send to blast

MAAPSGLSPE PPQPPTSTEV CQWLKNLPLA PEYRPTQAEF QDPIAYIFKI EKEASQYGIC  60
KIIPPVLPSA KKTTLSNLNR SLSARNGDSS APTFTTRQQQ IGFCPRKPRP VQKPVWQSGE  120
TYTFQEFETK AKSFEKNYLK KFSKKGGLSP LEIENLYWKA TLDKPFAVEY ANDMPGSAFS  180
PRKKEGQGGV VGEGMYVGET EWNMRSVSRA KGSLLRFMKE EIPGVTSPMV YIGMIFSWFA  240
WHVEDHDLHS LNYMHMGAGK TWYGVPREAA VAFEEVVRVH GYGGENNPLV TFAVLGEKTT  300
VMSPEVFISA GVPCCRLVQN AGEFVVTFPR AYHSGFSHGF NCGEAANIAT PEWLTVAKDA  360
AIRRASINYP PMVSHFQLLY DLALEFCTRI PVNISAKPRS SRLKDKQKGE GETLVKEQFV  420
KNMMQNNDLL HILGKGSSVV LLPRSSSDIS VCSNLRVGSQ LRDNPTLGLS SQKDFMKSSK  480
SSGSDDILMD ENQEINQVKG FFSVKAKFAS LCERNRFSTI NGNECTQSMN MSTERGSPIH  540
GDKLSDQRLF SCVTCGILSF DCLAIIQPKE AASRYLMSAD CSFFNDWVVG SGVTRDVFTV  600
AGGIANIPEQ NSSMRWVRKN TVAGLYDVPV QSLNYQIQMA DQSVEVASSS AKQMESSALG  660
LLALNYGNSS DSEDDQVEAG LSCHDETNFT NCSLESKYQG QSSACPSYKQ KYYDAETGGH  720
PLSPSKHDQR GDVPFKAIDM YPEHGDRPDN FKDRSDDTLG CSFGFPANNP ACIESNGLDG  780
RYRDPVSIPH MSLNCSPIVH DTEKTKFNRP TVPIENPDMP FTQRSDRDSS CLHVFCLEHA  840
VEIEQQLRQI GGVHIFLLCH PEYPRIEAEA KSVSEELGID HLWNDITFRD AAKEDEERIQ  900
SALDTEEAIP GNGDWAVKLG INLFYSANLS RSPLYSKQMP YNSVIYNAFG RASPVSSPPK  960
FKVYGRRSGK PKKVVAGKWC GKVWMSNQVH PFLVKRDFVY QNQEQEQERS FHALATPDEK  1020
LEKKPQTIHR NETSRKSGRK RKIIAGSRTV KKVKCLEAEE ADSEDSVGDN SHRQHMRIHN  1080
RKNTEDIERE ISYDLVEDSN QQHGSYRRKW AKSVESDDAV SDDPLAEHVR QQYRRMRRSK  1140
QAKSIKRENT VSYASVENKF RKQLRRVHRS DQAKCSERRC VASDDSLDDN SDQWHGRAPR  1200
STLAKYTERE DANSDDSPEE SSRWQHGRVS RSKLLRYVKK ESAISDDSLE NGFKQHNKRI  1260
SRGKRAQVIK RDDVVSDDSL DESAFQQLPR FSRIKLAKLI EREDAFSDGS LEENIHQQHG  1320
RILRSKQSKF VEREDAISDD SLEDSTHWQH RRIPRSKMAK FVESEDAASD DLQEDDGHQH  1380
HRRIPKRKKA NSIESEDVVS DDLWQNNIHR HLRKTPRGKQ PNIVEREEAV SDDLLENSSD  1440
QQDRIILRSK QKKSSMKQGI PRQLKQSAPK MIKKETPQLM KQERQIKPET PQLRFGKSDM  1500
NARQFDSHAE EERGGPRMRL RKRLSKAPKQ SLTRLKEKQN IKKKVKDATA VKAPAGRKNV  1560
KMKDEEAEYQ CDIDGCRMSF VSKQELALHK RNICPVKGCG KKFFSHKYLV QHRRVHIDDR  1620
PLKCPWKGCK MTFKWAWART EHIRVHTGAR PYVCAEEGCG QTFRFVSDFS RHKRKTGHLA  1680
KKGRG*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	4e-79	18	379	3	346	Transcription factor jumonji (Jmj) family protein
6ip4_A	4e-79	18	379	3	346	Arabidopsis JMJ13
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	1381	1387	RRIPKRK

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Pth.12495	0.0	bud\| catkin

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Potri.012G092400.1

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_024438277.1	0.0	lysine-specific demethylase REF6
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A2K1YB81	0.0	A0A2K1YB81_POPTR; Uncharacterized protein
STRING	POPTR_0012s09390.1	0.0	(Populus trichocarpa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF5648	32	50
Representative plant	OGRP4401	12	17

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	Potri.012G092400.1
Entrez Gene	7484447

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]