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

CA03g25230

Organism

Capsicum annuum

Taxonomic ID

4072

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Capsiceae; Capsicum

Family

C2H2

Protein Properties

Length: 1273aa MW: 141303 Da PI: 9.065

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
CA03g25230	genome	PEP	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	11	0.0014	1180	1203	2	23
EET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 2 kCp..dCgksFsrksnLkrHirtH 23 +Cp C+k F ++ +L++H r+H CA03g25230 1180 VCPveGCKKKFFSHKYLVQHRRVH 1203 69999*****************99 PP
2	zf-C2H2	11.9	0.00071	1239	1265	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C Cg++F+ s++ rH r+ H CA03g25230 1239 YVCAetGCGQTFRFVSDFSRHKRKtgH 1265 89********************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	1.0E-15	19	60	IPR003349	JmjN domain
PROSITE profile	PS51183	14.395	20	61	IPR003349	JmjN domain
Pfam	PF02375	2.8E-15	21	54	IPR003349	JmjN domain
SMART	SM00558	9.0E-49	187	356	IPR003347	JmjC domain
PROSITE profile	PS51184	32.57	190	356	IPR003347	JmjC domain
SuperFamily	SSF51197	2.61E-25	202	371	No hit	No description
Pfam	PF02373	1.1E-36	220	339	IPR003347	JmjC domain
SMART	SM00355	7.4	1156	1178	IPR015880	Zinc finger, C2H2-like
SMART	SM00355	0.012	1179	1203	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	4.4E-5	1179	1207	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	11.572	1179	1208	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1181	1203	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	1.4E-9	1195	1237	No hit	No description
Gene3D	G3DSA:3.30.160.60	2.9E-8	1208	1233	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.741	1209	1238	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0014	1209	1233	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1211	1233	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	8.1E-8	1227	1261	No hit	No description
Gene3D	G3DSA:3.30.160.60	1.3E-8	1234	1261	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.85	1239	1265	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.907	1239	1270	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1241	1265	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: 1273 aa Download sequence Send to blast
MAEASGNIEV FPWLKTLPVA PEYYPTLEEF QDPIAYIFKI EKEASKYGIC KIVPPLPAPK 60 QKTALANLNR SLSARPGSNG PTFTTRQQQI GFCPRKHRPV KKPVWQSGET YTVQQFQAKA 120 KAFEKNYLKR NSKRALTALE IETLYWKATV DKPFSVEYAN DMPGSAFAPK KAGSGSVGAG 180 GIGEVATLAD TEWNMRGVSR SKGSLLKFMK EEIPGVTSPM VYLAMMFSWF AWHVEDHDLH 240 SLNYLHMGAG KTWYGVPRDA AVAFEEVISV QGYAGETNPL VTFATLGEKT TVMSPEVLLS 300 AGIPCCRLVQ NAGDFVVTFP RAYHSGFSHG FNCGEASNIA TPEWLRFAKD AAIRRASTNC 360 PPMVSHFQLL YDLALSLCSR VPKNIRIEPR SSRLKDKKKS EGDMLVKELF VEDLNSNNYL 420 LHVLGEGSPV VLLPQTSTGI SICSNLVAGT QSKVNSRLFL GLSSSDHELR SQKDIGYDHF 480 KLGRKQGMKQ VASVSSEKGK YSSLHAGNRL PDSGRKDDAQ SSPETERVNL DTGRGMTHKC 540 DTLSEQGLFS CVTCGILCYT CVAIIRPTEA AAHHLMSSDY HNFNDWTGNV GGVFATGRDP 600 NAGESDSSSG GLVKTAPGDF IDAPVESSDR IQKLNNGSVE GVSRTKARKE TSSLGLLALA 660 YANSSDSDED EVEADIPVEA CESRHTDSDD EVFLQVIDPY ANHRQRRAVS QGRSCQKIDN 720 SSPSGESNTL FGRSSHQLRS NQVTAKCISN KGEIAQNNAV APFDNTHMQF TSASDEDSFR 780 IHVFCLQHAV QVEEKLRQIG GADISLLCHP DYPKLEAQAK KVAEELGSDH FWRDISFREA 840 TKEDEEMIQS ALEIQEAIHG NGDWTVKLDI NLFYSANLSR SPLYSKQMPY NFIIYNAFGR 900 DSPDNTPEKS EYTGRGSGKQ RRAVVAGKWC GKVWMSSQVH PLLAERDIDE EQEQNKNISV 960 QIKTEVKSER PRERTVTGKT VATTCKTGKK RNSTAEDRNA SNTQLIADDH DDSLLCSLLQ 1020 QHRKTNFRSK RIKYETPEPQ KDVDKKKRFG SLIDDDPDGG PSARLNVDKK KRFGSLIDDD 1080 PDGGPSTRLR KRVPKPSKVS AAKLIKAKPA TTKQEESKKG PKVKLPSVNS TAKKEPVMKS 1140 PRSNTGRKMR DKEGEYHCDL EGCSMSFSSK PELTLHKKNV CPVEGCKKKF FSHKYLVQHR 1200 RVHMDDRPLK CPWKGCKMTF KWAWARTEHI RVHTGARPYV CAETGCGQTF RFVSDFSRHK 1260 RKTGHVSKKG RG*

Sequence ? help Back to Top

Protein Sequence Length: 1273 aa Download sequence Send to blast

MAEASGNIEV FPWLKTLPVA PEYYPTLEEF QDPIAYIFKI EKEASKYGIC KIVPPLPAPK  60
QKTALANLNR SLSARPGSNG PTFTTRQQQI GFCPRKHRPV KKPVWQSGET YTVQQFQAKA  120
KAFEKNYLKR NSKRALTALE IETLYWKATV DKPFSVEYAN DMPGSAFAPK KAGSGSVGAG  180
GIGEVATLAD TEWNMRGVSR SKGSLLKFMK EEIPGVTSPM VYLAMMFSWF AWHVEDHDLH  240
SLNYLHMGAG KTWYGVPRDA AVAFEEVISV QGYAGETNPL VTFATLGEKT TVMSPEVLLS  300
AGIPCCRLVQ NAGDFVVTFP RAYHSGFSHG FNCGEASNIA TPEWLRFAKD AAIRRASTNC  360
PPMVSHFQLL YDLALSLCSR VPKNIRIEPR SSRLKDKKKS EGDMLVKELF VEDLNSNNYL  420
LHVLGEGSPV VLLPQTSTGI SICSNLVAGT QSKVNSRLFL GLSSSDHELR SQKDIGYDHF  480
KLGRKQGMKQ VASVSSEKGK YSSLHAGNRL PDSGRKDDAQ SSPETERVNL DTGRGMTHKC  540
DTLSEQGLFS CVTCGILCYT CVAIIRPTEA AAHHLMSSDY HNFNDWTGNV GGVFATGRDP  600
NAGESDSSSG GLVKTAPGDF IDAPVESSDR IQKLNNGSVE GVSRTKARKE TSSLGLLALA  660
YANSSDSDED EVEADIPVEA CESRHTDSDD EVFLQVIDPY ANHRQRRAVS QGRSCQKIDN  720
SSPSGESNTL FGRSSHQLRS NQVTAKCISN KGEIAQNNAV APFDNTHMQF TSASDEDSFR  780
IHVFCLQHAV QVEEKLRQIG GADISLLCHP DYPKLEAQAK KVAEELGSDH FWRDISFREA  840
TKEDEEMIQS ALEIQEAIHG NGDWTVKLDI NLFYSANLSR SPLYSKQMPY NFIIYNAFGR  900
DSPDNTPEKS EYTGRGSGKQ RRAVVAGKWC GKVWMSSQVH PLLAERDIDE EQEQNKNISV  960
QIKTEVKSER PRERTVTGKT VATTCKTGKK RNSTAEDRNA SNTQLIADDH DDSLLCSLLQ  1020
QHRKTNFRSK RIKYETPEPQ KDVDKKKRFG SLIDDDPDGG PSARLNVDKK KRFGSLIDDD  1080
PDGGPSTRLR KRVPKPSKVS AAKLIKAKPA TTKQEESKKG PKVKLPSVNS TAKKEPVMKS  1140
PRSNTGRKMR DKEGEYHCDL EGCSMSFSSK PELTLHKKNV CPVEGCKKKF FSHKYLVQHR  1200
RVHMDDRPLK CPWKGCKMTF KWAWARTEHI RVHTGARPYV CAETGCGQTF RFVSDFSRHK  1260
RKTGHVSKKG RG*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	4e-73	13	389	8	366	Transcription factor jumonji (Jmj) family protein
6ip4_A	4e-73	13	389	8	366	Arabidopsis JMJ13
Search in ModeBase

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	HG975442	0.0	HG975442.1 Solanum pennellii chromosome ch03, complete genome.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_016563761.1	0.0	PREDICTED: lysine-specific demethylase REF6
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A1U8FXA8	0.0	A0A1U8FXA8_CAPAN; Lysine-specific demethylase REF6
TrEMBL	A0A2G2ZW03	0.0	A0A2G2ZW03_CAPAN; lysine-specific demethylase REF6
STRING	PGSC0003DMT400039224	0.0	(Solanum tuberosum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA4988	23	31

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]