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

30147.m013814

Common Name

RCOM_1507500

Organism

Ricinus communis

Taxonomic ID

3988

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Euphorbiaceae; Acalyphoideae; Acalypheae; Ricinus

Family

C2H2

Protein Properties

Length: 1736aa MW: 196560 Da PI: 8.126

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
30147.m013814	genome	JCVI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	12.4	0.00048	1620	1645	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 y+C C++sF +k +L +H r+ + 30147.m013814 1620 YQCDieGCTMSFGSKQELAVHKRNiC 1645 99********************9877 PP
2	zf-C2H2	12.7	0.0004	1645	1667	3	23
ET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 3 Cp..dCgksFsrksnLkrHirtH 23 Cp Cgk+F ++ +L++H r+H 30147.m013814 1645 CPvkGCGKTFLSHKYLVQHRRVH 1667 9999*****************99 PP
3	zf-C2H2	11.5	0.00091	1703	1729	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C Cg++F+ s++ rH r+ H 30147.m013814 1703 YVCAeeGCGQTFRFVSDFSRHKRKtgH 1729 89********************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	4.7E-15	29	70	IPR003349	JmjN domain
PROSITE profile	PS51183	14.52	30	71	IPR003349	JmjN domain
Pfam	PF02375	1.9E-14	31	64	IPR003349	JmjN domain
PROSITE profile	PS51184	33.863	196	365	IPR003347	JmjC domain
SMART	SM00558	1.3E-49	196	365	IPR003347	JmjC domain
SuperFamily	SSF51197	4.12E-26	210	384	No hit	No description
Pfam	PF02373	4.7E-37	229	348	IPR003347	JmjC domain
Gene3D	G3DSA:3.30.160.60	1.9E-4	1611	1642	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	8.9	1620	1642	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.57	1643	1672	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	1.58E-6	1643	1679	No hit	No description
SMART	SM00355	0.0033	1643	1667	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	1.4E-5	1644	1671	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1645	1667	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	9.1E-8	1672	1697	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.533	1673	1702	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0038	1673	1697	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1675	1697	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	3.35E-9	1683	1727	No hit	No description
Gene3D	G3DSA:3.30.160.60	3.2E-9	1698	1726	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	11.032	1703	1734	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.85	1703	1729	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1705	1729	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: 1736 aa Download sequence Send to blast
MAAPSGLVTE PTASQQPQEV FQWLKNLPLA PEYHPTLAEF QDPIAYIFKI EKEASKYGIC 60 KIVPPVLAAP KKAAIANLNR SLAARSSSSK SAPTFTTRQQ QIGFCPRKPR PVQKPVWQSG 120 ENYTFQEFEA KAKSFEKSYF KKCPKKTAFS PLEVETLYWK ATVDKPFSVE YANDMPGSAF 180 SVKKMSGGKE IIEGVTVGET EWNMRGVSRA KGSLLRFMKE EIPGVTSPMV YVAMMFSWFA 240 WHVEDHDLHS LNYLHLGAGK TWYGVPKEAA VAFEEVVRDH GYGGEINPLV TFSVLGEKTT 300 VMSPEVFVTA GVPCCRLVQN AGEFVVTFPR AYHSGFSHGF NCGEAANIAT PEWLRVAKDA 360 AIRRASINYP PMVSHFQLLY DLALELCTRM PVSISAKPRS SRLKDKQKGE GETLVKEQFV 420 QNVIHNNELL HILGKGSSVV LLPRSSSDIS VCSDLQRNYG IDQSKGTISV KEKFASLCER 480 NRFSSLNGNE NKHTTNTRTE NKGTTHGDKL SDQRLFSCVT CGILSFDCIA VVQPTETAAR 540 YLMSADCSFF NDWIVGSGAT NNRLTTTNGD PNTCQLDQPT GWVENSVVDH LYDVPVQSVN 600 YQPQKIDKSK VNSNATMQGE SSALGLLALN YGNSSDSEED QDEPDVSDHA IDMPTCSSEN 660 KYKYQNCALP SFKQECHHDE TVSHTLSLVT LDCGDKVSLQ TDDCHKEHGD RAGNFKDGTP 720 DCFLDFGTDN MEPNGSECRF GDAVSISHIN SNCSPAVHDT EKMKFRRVVP RGNGDMPFAQ 780 RSDEDSSRMH VFCLEHAVEV EQQFRSIGGV HILLLCHPEY PRLEAEAKLV SEELGIDHLW 840 NDIAFRDATK NDEENIQSAL DSEEAIPGNG DWAVKLGINL FYSASLSHSS LYSKQMPYNS 900 VIYKAFGRVS PASSPTKLNV YGRRSGKQKK VVAGRWCGKV WMSNQVHNFL LKNASEDRDQ 960 EEEQDGSFHG WKMLDEKVER KLQNFYKTET ALAAAKSVRK RKLTTVTRPI KKVKSPETEA 1020 AASDDLEEDV SHKQHTKVYS RKQTKHIERE VSYDSLDNSH QQHGKTHRIK QAKSVERDDA 1080 VSDDSLGGNT HQQQHRRIPR SKQVKYIDSE NDVSDTLIGS NSQKQHSRIP KPRSKQVKYI 1140 RRKSEISDDS LEGDINEWHG RGPRSTQAGF YGREVAVSDD SLEESSHRPL GTVRRSKQAA 1200 YFESEDALSD DSVENSSLQQ NRRVSRGSLA KYFEREDEVS DDMLEENTFQ QCTGSHRSRK 1260 KKFVDREGEV SDNLLDESTQ LQHRRIFRSK QGRFVEREDE VSDDSLEDNS QQQRRIPTSK 1320 RAKFVESEDA VSDELEDDTH LKHWRIPRSK KAKIMEREAC SDDLQENDAQ WQPRKTPRGK 1380 PVKFIEREDV SDDLEEATHW QQRKTSRHKP VTSFEREDVS DDLQEENTRW QPRKTTRGKQ 1440 TKFFEKEDVS DDLQEDDTRW HPSKTPKSKQ AKYAELEDAV SDDLLEDNST KQHRRILRNK 1500 QKSGTLGKVN RESIQHVKQG TARAKKKENS KSIKKEKEVK QENPGFRNSK SGRLFESHVE 1560 EEVEGGPSTR LRKRPSKASK ESETKLKEKL QSNKKKVRGS ASAVKRASGQ KNNKDEDAEY 1620 QCDIEGCTMS FGSKQELAVH KRNICPVKGC GKTFLSHKYL VQHRRVHLDD RPLKCPWKGC 1680 KVTFKWAWAR TEHIRVHTGA RPYVCAEEGC GQTFRFVSDF SRHKRKTGHS VKKSRN

Sequence ? help Back to Top

Protein Sequence Length: 1736 aa Download sequence Send to blast

MAAPSGLVTE PTASQQPQEV FQWLKNLPLA PEYHPTLAEF QDPIAYIFKI EKEASKYGIC  60
KIVPPVLAAP KKAAIANLNR SLAARSSSSK SAPTFTTRQQ QIGFCPRKPR PVQKPVWQSG  120
ENYTFQEFEA KAKSFEKSYF KKCPKKTAFS PLEVETLYWK ATVDKPFSVE YANDMPGSAF  180
SVKKMSGGKE IIEGVTVGET EWNMRGVSRA KGSLLRFMKE EIPGVTSPMV YVAMMFSWFA  240
WHVEDHDLHS LNYLHLGAGK TWYGVPKEAA VAFEEVVRDH GYGGEINPLV TFSVLGEKTT  300
VMSPEVFVTA GVPCCRLVQN AGEFVVTFPR AYHSGFSHGF NCGEAANIAT PEWLRVAKDA  360
AIRRASINYP PMVSHFQLLY DLALELCTRM PVSISAKPRS SRLKDKQKGE GETLVKEQFV  420
QNVIHNNELL HILGKGSSVV LLPRSSSDIS VCSDLQRNYG IDQSKGTISV KEKFASLCER  480
NRFSSLNGNE NKHTTNTRTE NKGTTHGDKL SDQRLFSCVT CGILSFDCIA VVQPTETAAR  540
YLMSADCSFF NDWIVGSGAT NNRLTTTNGD PNTCQLDQPT GWVENSVVDH LYDVPVQSVN  600
YQPQKIDKSK VNSNATMQGE SSALGLLALN YGNSSDSEED QDEPDVSDHA IDMPTCSSEN  660
KYKYQNCALP SFKQECHHDE TVSHTLSLVT LDCGDKVSLQ TDDCHKEHGD RAGNFKDGTP  720
DCFLDFGTDN MEPNGSECRF GDAVSISHIN SNCSPAVHDT EKMKFRRVVP RGNGDMPFAQ  780
RSDEDSSRMH VFCLEHAVEV EQQFRSIGGV HILLLCHPEY PRLEAEAKLV SEELGIDHLW  840
NDIAFRDATK NDEENIQSAL DSEEAIPGNG DWAVKLGINL FYSASLSHSS LYSKQMPYNS  900
VIYKAFGRVS PASSPTKLNV YGRRSGKQKK VVAGRWCGKV WMSNQVHNFL LKNASEDRDQ  960
EEEQDGSFHG WKMLDEKVER KLQNFYKTET ALAAAKSVRK RKLTTVTRPI KKVKSPETEA  1020
AASDDLEEDV SHKQHTKVYS RKQTKHIERE VSYDSLDNSH QQHGKTHRIK QAKSVERDDA  1080
VSDDSLGGNT HQQQHRRIPR SKQVKYIDSE NDVSDTLIGS NSQKQHSRIP KPRSKQVKYI  1140
RRKSEISDDS LEGDINEWHG RGPRSTQAGF YGREVAVSDD SLEESSHRPL GTVRRSKQAA  1200
YFESEDALSD DSVENSSLQQ NRRVSRGSLA KYFEREDEVS DDMLEENTFQ QCTGSHRSRK  1260
KKFVDREGEV SDNLLDESTQ LQHRRIFRSK QGRFVEREDE VSDDSLEDNS QQQRRIPTSK  1320
RAKFVESEDA VSDELEDDTH LKHWRIPRSK KAKIMEREAC SDDLQENDAQ WQPRKTPRGK  1380
PVKFIEREDV SDDLEEATHW QQRKTSRHKP VTSFEREDVS DDLQEENTRW QPRKTTRGKQ  1440
TKFFEKEDVS DDLQEDDTRW HPSKTPKSKQ AKYAELEDAV SDDLLEDNST KQHRRILRNK  1500
QKSGTLGKVN RESIQHVKQG TARAKKKENS KSIKKEKEVK QENPGFRNSK SGRLFESHVE  1560
EEVEGGPSTR LRKRPSKASK ESETKLKEKL QSNKKKVRGS ASAVKRASGQ KNNKDEDAEY  1620
QCDIEGCTMS FGSKQELAVH KRNICPVKGC GKTFLSHKYL VQHRRVHLDD RPLKCPWKGC  1680
KVTFKWAWAR TEHIRVHTGA RPYVCAEEGC GQTFRFVSDF SRHKRKTGHS VKKSRN

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	2e-78	21	513	6	457	Transcription factor jumonji (Jmj) family protein
6ip4_A	2e-78	21	513	6	457	Arabidopsis JMJ13
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	995	1001	KSVRKRK

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	30147.m013814

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_015580157.1	0.0	lysine-specific demethylase REF6
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	B9RAP0	0.0	B9RAP0_RICCO; Nucleic acid binding protein, putative
STRING	XP_002511265.1	0.0	(Ricinus communis)

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	30147.m013814

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]