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

Zosma194g00140.1

Common Name

ZOSMA_194G00140

Organism

Zostera marina

Taxonomic ID

29655

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Alismatales; Zosteraceae; Zostera

Family

C2H2

Protein Properties

Length: 1099aa MW: 123300 Da PI: 8.9509

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Zosma194g00140.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	11.2	0.0011	1063	1089	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C+ C+k+F+ s++ rH r+ H Zosma194g00140.1 1063 YVCQepSCSKTFRFVSDFSRHKRKtgH 1089 89********************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS51184	37.105	27	196	IPR003347	JmjC domain
SMART	SM00558	3.5E-46	27	196	IPR003347	JmjC domain
SuperFamily	SSF51197	3.71E-27	41	213	No hit	No description
Pfam	PF02373	5.9E-37	60	179	IPR003347	JmjC domain
SMART	SM00355	110	980	1002	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	20	1003	1027	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	9.473	1003	1032	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1005	1027	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	9.42E-13	1018	1074	No hit	No description
Gene3D	G3DSA:3.30.160.60	5.4E-10	1031	1057	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	12.591	1033	1062	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0035	1033	1057	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1035	1057	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	1.0E-9	1058	1086	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.575	1063	1094	IPR007087	Zinc finger, C2H2
SMART	SM00355	2.3	1063	1089	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1065	1089	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: 1099 aa Download sequence Send to blast
MPGSGFSPLG EDNSMAERLM EADDWENVGD TPWNMRVVPR TRGSLLKFMK DDIPGVTTPM 60 VYVGMMFSWF AWHVEDHELH SLNYSHLGAG KVWYGIPRDA RLAFEEVVRV QGYGGEVNPL 120 TTLFILGEKT TILSPEVLVA AGVPCCRLVQ NPGEFVVTFP GAYHSGFSLG FNCGEAANIA 180 TPEWLKVAKE AAIRRASINH PPMISHFQLL YKLALSLCSR MVEKNVNEQR SSRSKGKSKC 240 EGDIIIKEQF VKNVIQTNNL LGSITLDDKL SCVLLSQNKY DASLGPNSSS TGSQIKFQPN 300 FPTECSFPSS EFTERIHSFK CNTSEKRQHK CGGSSDQNLF SCVACGILSF ACVAIVWPTE 360 TAAMNLMTYG CSSLSDQSSD KDNIRNSNPS RYNDLVASGH SMASTINDEK ITYSGECQAQ 420 YPSQIEEIAS EGRLKKDLSS LSLIASAYGD SSDDDHPSPS KIVNKNKNEG HLQNKVSKNM 480 DFSLSKVKQY QRWSGLQLDH SGSFLMNKPD KDSSRIHVFC LEHALEVQRK LRSIGGACLL 540 LVCHSDYPKI EAEVKHMAKE LGVNNAWKNI NFKEPSSQDE QIIQSALEDK GAVPVNSDWS 600 VMMGFNLWFS ANISKSFLYS KQMPYNVVIY KVFGRDSSGT SPGKLRKMTR NGKQKKKVVV 660 SGKWCGKVWM SNQVHPYLAY VNENNDGKED DFVKNLRLGQ GTCRRKILTD FANHADAEKV 720 PIPRGSHLEI NMGSRSAIRR KKPSIRKNIK KPNYSQPENC DTIIDHDDSQ SVLADFAKHV 780 ETDKVRPSTS SHLEIETENI SVIRKNKPSK RKNSKKTKYN QLVNHDAIIN DDDDFERVLA 840 DFVNHVGVKK VRTSASRHLG VGTEMASKSS IKRKKTPKKK NTKKPKCSQP ENCDAIINDD 900 DDLVDSWRIL SSRSVKKLPS SPPNCTNDDE MVTAVGLDLE MDGVGSDGCS MAPPKRKSGR 960 HGTTEMKEDK NEETMVKQQY LCDMKGCSMS FNFEHELAMH KNNQCPVIGC GKKLFCHRYA 1020 VQHHRIHLDS RPLKCPWEGC GMTFKWKWPQ TEHYRVHTGE RPYVCQEPSC SKTFRFVSDF 1080 SRHKRKTGHV SVKRKRKI*

Sequence ? help Back to Top

Protein Sequence Length: 1099 aa Download sequence Send to blast

MPGSGFSPLG EDNSMAERLM EADDWENVGD TPWNMRVVPR TRGSLLKFMK DDIPGVTTPM  60
VYVGMMFSWF AWHVEDHELH SLNYSHLGAG KVWYGIPRDA RLAFEEVVRV QGYGGEVNPL  120
TTLFILGEKT TILSPEVLVA AGVPCCRLVQ NPGEFVVTFP GAYHSGFSLG FNCGEAANIA  180
TPEWLKVAKE AAIRRASINH PPMISHFQLL YKLALSLCSR MVEKNVNEQR SSRSKGKSKC  240
EGDIIIKEQF VKNVIQTNNL LGSITLDDKL SCVLLSQNKY DASLGPNSSS TGSQIKFQPN  300
FPTECSFPSS EFTERIHSFK CNTSEKRQHK CGGSSDQNLF SCVACGILSF ACVAIVWPTE  360
TAAMNLMTYG CSSLSDQSSD KDNIRNSNPS RYNDLVASGH SMASTINDEK ITYSGECQAQ  420
YPSQIEEIAS EGRLKKDLSS LSLIASAYGD SSDDDHPSPS KIVNKNKNEG HLQNKVSKNM  480
DFSLSKVKQY QRWSGLQLDH SGSFLMNKPD KDSSRIHVFC LEHALEVQRK LRSIGGACLL  540
LVCHSDYPKI EAEVKHMAKE LGVNNAWKNI NFKEPSSQDE QIIQSALEDK GAVPVNSDWS  600
VMMGFNLWFS ANISKSFLYS KQMPYNVVIY KVFGRDSSGT SPGKLRKMTR NGKQKKKVVV  660
SGKWCGKVWM SNQVHPYLAY VNENNDGKED DFVKNLRLGQ GTCRRKILTD FANHADAEKV  720
PIPRGSHLEI NMGSRSAIRR KKPSIRKNIK KPNYSQPENC DTIIDHDDSQ SVLADFAKHV  780
ETDKVRPSTS SHLEIETENI SVIRKNKPSK RKNSKKTKYN QLVNHDAIIN DDDDFERVLA  840
DFVNHVGVKK VRTSASRHLG VGTEMASKSS IKRKKTPKKK NTKKPKCSQP ENCDAIINDD  900
DDLVDSWRIL SSRSVKKLPS SPPNCTNDDE MVTAVGLDLE MDGVGSDGCS MAPPKRKSGR  960
HGTTEMKEDK NEETMVKQQY LCDMKGCSMS FNFEHELAMH KNNQCPVIGC GKKLFCHRYA  1020
VQHHRIHLDS RPLKCPWEGC GMTFKWKWPQ TEHYRVHTGE RPYVCQEPSC SKTFRFVSDF  1080
SRHKRKTGHV SVKRKRKI*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	7e-52	28	251	160	380	Transcription factor jumonji (Jmj) family protein
6ip4_A	7e-52	28	251	160	380	Arabidopsis JMJ13
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	871	885	KRKKTPKKKNTKKPK

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}.

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_020106930.1	0.0	lysine-specific demethylase REF6
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A0K9PP59	0.0	A0A0K9PP59_ZOSMR; Uncharacterized protein
STRING	GSMUA_Achr10P03980_001	0.0	(Musa acuminata)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP6718	30	35

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	Zosma194g00140.1

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]