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

Solyc03g111590.2.1

Common Name

LOC101257458

Organism

Solanum lycopersicum

Taxonomic ID

4081

Taxonomic Lineage

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

Family

C2H2

Protein Properties

Length: 1253aa MW: 139814 Da PI: 9.1879

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Solyc03g111590.2.1	genome	ITAG	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	11.3	0.0011	1136	1161	1	23
EEET..TTTEEESSHHHHHHHHHH.T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt.H 23 y C C++sFs+k +L+ H ++ + Solyc03g111590.2.1 1136 YHCDleGCSMSFSSKQELTLHKKNvC 1161 889999***************99866 PP
2	zf-C2H2	11	0.0014	1160	1183	2	23
EET..TTTEEESSHHHHHHHHHHT CS zf-C2H2 2 kCp..dCgksFsrksnLkrHirtH 23 +Cp C+k F ++ +L++H r+H Solyc03g111590.2.1 1160 VCPveGCKKKFFSHKYLVQHRRVH 1183 69999*****************99 PP
3	zf-C2H2	11.1	0.0013	1219	1245	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y C+ Cg++F+ s++ rH r+ H Solyc03g111590.2.1 1219 YACSeiGCGQTFRFVSDFSRHKRKtgH 1245 889999****************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	3.6E-16	19	60	IPR003349	JmjN domain
PROSITE profile	PS51183	14.991	20	61	IPR003349	JmjN domain
Pfam	PF02375	2.1E-15	21	54	IPR003349	JmjN domain
SMART	SM00558	5.8E-49	184	353	IPR003347	JmjC domain
PROSITE profile	PS51184	32.372	187	353	IPR003347	JmjC domain
SuperFamily	SSF51197	8.79E-25	199	351	No hit	No description
Pfam	PF02373	1.9E-36	217	336	IPR003347	JmjC domain
SMART	SM00355	8.6	1136	1158	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	11.572	1159	1188	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.012	1159	1183	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	4.3E-5	1159	1187	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1161	1183	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	1.39E-9	1175	1217	No hit	No description
Gene3D	G3DSA:3.30.160.60	3.0E-8	1188	1213	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	10.741	1189	1218	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.0014	1189	1213	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1191	1213	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	3.56E-7	1207	1241	No hit	No description
Gene3D	G3DSA:3.30.160.60	2.7E-8	1214	1241	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	11.074	1219	1250	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.48	1219	1245	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1221	1245	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: 1253 aa Download sequence Send to blast
MAEASGNIEV FSWLKTLPVA PEYHPTLEEF QDPIAYIFKI EKEASKYGIC KIVPPVPAPP 60 KKTALANLNR SLSARAGSNG PTFTTRQQQI GFCPRKHRPV KKPVWQSGET YTVQQFQVKA 120 KAFEKNYLRK NSKRALTPLE VETLYWKATV DKPFSVEYAN DMPGSAFAPK KASLAAGGIG 180 EVSTLADTEW NMRGVSRSKG SLLKFMKEEI PGVTSPMVYL AMMFSWFAWH VEDHDLHSLN 240 YLHMGSGKTW YGVPRDAAVA FEEVIRVQGY AGETNPLVTF ATLGEKTTVM SPEVLLSAGI 300 PCCRLVQNAG EFVVTFPRAY HSGFSHGFNC GEASNIATPE WLRVAKDAAI RRASINCPPM 360 VSHFQLLYDL ALSLCSRVPK NIRIEPRSSR LKDKKKSEGD MLVKELFVED LNANNYLLHI 420 LGEGSPVVLL PQNSPGISIC SNLVAGSQSK VNSRLFPSSS NSDHEVKSKK DSAYDDRKLG 480 RKQGMKQYAG ISLEKGKYSS WHTGNSLPDS GRKDDAQSSP ETEKVNLDAA RGMTYKCDTL 540 SEQGLFSCAT CGILCYTCVA IIRPTEAAAR HLMSSDYSDF NGWTGSVSGI TATGRDPNAA 600 ESDSSSGRFV KRAPALIDDP VESSDRIQKL NNGSVEELSR TNTRKETSSL GLLALAYANS 660 SDSDEDEIEV DIPVEACESR HTESEDEVFL RVIDPYGNHR QKRAVSQGRN CQKFDNSVQL 720 ENESYPSGES NTLFGRSSHQ PRSHQVPAKC ISNIREIAQN NAVAPFDNAR MQFTSTSDED 780 SFRIHVFCLQ HAVQVEEQLR RIGGAHISLL CHPDYPKLEA QAKQVAEELG SDHFWREISF 840 REASKEDEEM IQSALEIEEA IHGNGDWTVK LDINLFYSAN LSRSPLYSKQ MPYNFIIYNA 900 FGRDSPDNTP EKSEYTGRGL GKQRRAIVAG KWCGKVWMSS QVHPLLAERT IDEEQEQNKS 960 ISALIKIEVK SERPRERTPT SKTVATTCKT GKKRSSTAAS RNASNAQLII ADDHDDSLLS 1020 SILQQHRRKT NLRSKRIKYE TPEPQKDVDK KKIFGSLIDD DPDGGPSTRL RKRIPKPSNE 1080 SPAKSVKAKP APTKQHESKK GPKVKLPFAN SIAKKEPVTK GPRSNIGKRM REEGEYHCDL 1140 EGCSMSFSSK QELTLHKKNV CPVEGCKKKF FSHKYLVQHR RVHMDDRPLK CPWKGCKMTF 1200 KWAWARTEHI RVHTGARPYA CSEIGCGQTF RFVSDFSRHK RKTGHISKKG RS*

Sequence ? help Back to Top

Protein Sequence Length: 1253 aa Download sequence Send to blast

MAEASGNIEV FSWLKTLPVA PEYHPTLEEF QDPIAYIFKI EKEASKYGIC KIVPPVPAPP  60
KKTALANLNR SLSARAGSNG PTFTTRQQQI GFCPRKHRPV KKPVWQSGET YTVQQFQVKA  120
KAFEKNYLRK NSKRALTPLE VETLYWKATV DKPFSVEYAN DMPGSAFAPK KASLAAGGIG  180
EVSTLADTEW NMRGVSRSKG SLLKFMKEEI PGVTSPMVYL AMMFSWFAWH VEDHDLHSLN  240
YLHMGSGKTW YGVPRDAAVA FEEVIRVQGY AGETNPLVTF ATLGEKTTVM SPEVLLSAGI  300
PCCRLVQNAG EFVVTFPRAY HSGFSHGFNC GEASNIATPE WLRVAKDAAI RRASINCPPM  360
VSHFQLLYDL ALSLCSRVPK NIRIEPRSSR LKDKKKSEGD MLVKELFVED LNANNYLLHI  420
LGEGSPVVLL PQNSPGISIC SNLVAGSQSK VNSRLFPSSS NSDHEVKSKK DSAYDDRKLG  480
RKQGMKQYAG ISLEKGKYSS WHTGNSLPDS GRKDDAQSSP ETEKVNLDAA RGMTYKCDTL  540
SEQGLFSCAT CGILCYTCVA IIRPTEAAAR HLMSSDYSDF NGWTGSVSGI TATGRDPNAA  600
ESDSSSGRFV KRAPALIDDP VESSDRIQKL NNGSVEELSR TNTRKETSSL GLLALAYANS  660
SDSDEDEIEV DIPVEACESR HTESEDEVFL RVIDPYGNHR QKRAVSQGRN CQKFDNSVQL  720
ENESYPSGES NTLFGRSSHQ PRSHQVPAKC ISNIREIAQN NAVAPFDNAR MQFTSTSDED  780
SFRIHVFCLQ HAVQVEEQLR RIGGAHISLL CHPDYPKLEA QAKQVAEELG SDHFWREISF  840
REASKEDEEM IQSALEIEEA IHGNGDWTVK LDINLFYSAN LSRSPLYSKQ MPYNFIIYNA  900
FGRDSPDNTP EKSEYTGRGL GKQRRAIVAG KWCGKVWMSS QVHPLLAERT IDEEQEQNKS  960
ISALIKIEVK SERPRERTPT SKTVATTCKT GKKRSSTAAS RNASNAQLII ADDHDDSLLS  1020
SILQQHRRKT NLRSKRIKYE TPEPQKDVDK KKIFGSLIDD DPDGGPSTRL RKRIPKPSNE  1080
SPAKSVKAKP APTKQHESKK GPKVKLPFAN SIAKKEPVTK GPRSNIGKRM REEGEYHCDL  1140
EGCSMSFSSK QELTLHKKNV CPVEGCKKKF FSHKYLVQHR RVHMDDRPLK CPWKGCKMTF  1200
KWAWARTEHI RVHTGARPYA CSEIGCGQTF RFVSDFSRHK RKTGHISKKG RS*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	3e-73	13	386	8	366	Transcription factor jumonji (Jmj) family protein
6ip4_A	3e-73	13	386	8	366	Arabidopsis JMJ13
Search in ModeBase

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}.

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	Solyc03g111590.2.1

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC238563	0.0	Solanum lycopersicum chromosome 3 clone C03HBa0049N20, complete sequence

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_004236313.1	0.0	lysine-specific demethylase REF6
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A3Q7FPK7	0.0	A0A3Q7FPK7_SOLLC; Uncharacterized protein
STRING	Solyc03g111590.2.1	0.0	(Solanum lycopersicum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA4988	23	31
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	Solyc03g111590.2.1
Entrez Gene	101257458

Publications ? help Back to Top
Wang Y,van der Hoeven RS,Nielsen R,Mueller LA,Tanksley SD Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments. Theor. Appl. Genet., 2005. 112(1): p. 72-84 [PMID:16208505] 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]