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

Cucsa.391680.1

Common Name

Csa_1G050050

Organism

Cucumis sativus

Taxonomic ID

3659

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Cucurbitales; Cucurbitaceae; Benincaseae; Cucumis

Family

C2H2

Protein Properties

Length: 1552aa MW: 173969 Da PI: 8.5383

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Cucsa.391680.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	11.8	0.00076	1518	1544	1	23
EEET..TTTEEESSHHHHHHHHHH..T CS zf-C2H2 1 ykCp..dCgksFsrksnLkrHirt..H 23 y+C Cg++F+ s++ rH r+ H Cucsa.391680.1 1518 YVCAepGCGQTFRFVSDFSRHKRKtgH 1544 899999****************99666 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM00545	5.5E-17	23	64	IPR003349	JmjN domain
PROSITE profile	PS51183	14.284	24	65	IPR003349	JmjN domain
Pfam	PF02375	1.2E-13	25	58	IPR003349	JmjN domain
SMART	SM00558	7.8E-48	196	365	IPR003347	JmjC domain
PROSITE profile	PS51184	32.261	199	365	IPR003347	JmjC domain
SuperFamily	SSF51197	3.3E-25	210	378	No hit	No description
Pfam	PF02373	2.0E-36	229	348	IPR003347	JmjC domain
Gene3D	G3DSA:3.30.160.60	2.5E-4	1427	1457	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	17	1435	1457	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	11.136	1458	1487	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.072	1458	1482	IPR015880	Zinc finger, C2H2-like
Gene3D	G3DSA:3.30.160.60	3.8E-4	1459	1486	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE pattern	PS00028	0	1460	1482	IPR007087	Zinc finger, C2H2
SuperFamily	SSF57667	1.55E-13	1469	1523	No hit	No description
Gene3D	G3DSA:3.30.160.60	3.6E-8	1487	1512	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0014	1488	1512	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	10.741	1488	1517	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	1490	1512	IPR007087	Zinc finger, C2H2
Gene3D	G3DSA:3.30.160.60	2.3E-9	1513	1541	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profile	PS50157	11.032	1518	1549	IPR007087	Zinc finger, C2H2
SMART	SM00355	0.62	1518	1544	IPR015880	Zinc finger, C2H2-like
PROSITE pattern	PS00028	0	1520	1544	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:0040010	Biological Process	positive regulation of growth rate
GO:0045815	Biological Process	positive regulation of gene expression, epigenetic
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
GO:0071558	Molecular Function	histone demethylase activity (H3-K27 specific)

Sequence ? help Back to Top
Protein Sequence Length: 1552 aa Download sequence Send to blast
MAGTAMAAEP TQEVLSWLKT LPLAPEYHPT LAEFQDPISY IFKIEKEASK FGICKIVPPV 60 PPSPKKTVIV NFNKSLAARA APCSDSTNSK SPPTFTTRQQ QIGFCPRKTR PVQKSVWQSG 120 EYYTFQQFEA KAKNFEKSYL KKCTKKGGLS PLEIETLYWR ATLDKPFSVE YANDMPGSAF 180 VPVSAKMFRE AGEGTTLGET AWNMRGVSRA KGSLLKFMKE EIPGVTSPMV YVAMMFSWFA 240 WHVEDHDLHS LNYLHMGAGK TWYGVPRDAA VAFEEVVRVQ GYGGEINPLV TFAVLGEKTT 300 VMSPEVLVSA GVPCCRLVQN AGEFVVTFPR AYHTGFSHGF NCGEAANIAT PEWLNVAKDA 360 AIRRASINYP PMVSHYQLLY DLALSSRAPL CTGAEPRSSR LKDKRRSEGD TVIKELFVQN 420 IVENNSLLDN LGGGASVVLL PPGSLESIYS RLRVGSHLRS KPRFPTGVCS SKEETKSPQS 480 FDYDNLALEN SPVINRVKGF YSANGPYSTL SERSTDNVCA SSLRPLNANN ERGGNVQSNG 540 LSDQRLFSCV TCGILSFACV AIIQPREQAA RYLMSADCSF FNDWVVGSGI ASEGISTRDR 600 HPVSSQQISN SGKRDKCVSD GLYDVPVQAV NRQLPLAGES YEANLNTEKR NETSALGMLA 660 LTYGHSSDSE EDNAEADAAL NVDDAKLMIC SSEDQYQFEN SGLTSGEYSK NTAILNHDPS 720 SFGINSADHM QFQVNDYEEF RRADSKDSFN CSSESEMDGI GSTKKNGLTR YQDSHVNGRS 780 SLDADTEKPV FDKSTETVET ENMPFAPDID EDFSRLHVFC LEHAKEVEQQ LRPIGGVHIL 840 LLCHPDYPKM EAEAKLVAQE LSMSHLWTDT IFRDATQDEE KRIQLALDSE EAIPGNGDWA 900 VKLGINLFYS ANLSHSPLYS KQMPYNSVIY NAFGRSTSAN SSGKPKVYQR RTGKLKRVVA 960 GKWCGKVWMS NQVHPLLEKR DPQEEDVDIF PSWTMSDEKV DRKSANIQKN ETVKVNRKSA 1020 GKRKMTYGRE TIKKAKLVES EDMVSDASVE DCIHQHHSIL RNKQSKFVEC NDPMSDDSVE 1080 DDSSRKHGVP VSKGAPYFGT DDTGSDDSLG DRHTLHRGFS GFKLPRWGEI EPSVSDDSLE 1140 HYSSQHRGKN IKSRTGKYIE RQDALSDECL ESGSLKQYRR IPKSKQTKVL KKNAILHDIR 1200 DDSFLWHHQK PSRIKKAKFI ETEDAVSEHS LENSSHQHRS MPQIKPAKHT AWEDAFSDDP 1260 DEDDNSLLQH RNVRSNMQFR EITSDDQLDD GANQYSRRVL RRKPVKTETI SQMKQEILRP 1320 VKRGASQTLK EEFAQSLKRG GRHTLKLETP QPKIHHATNR RGKRNEKLTD LESEDEQPGG 1380 PSTRLRKRTP KPTKLSEAKV KDKKPVAKKK MKTGSSLKTP AGHRDSKARD EESEYLCDIE 1440 GCNMSFGTKQ ELALHKRNIC PVKGCVKKFF SHKYLVQHRR VHMDDRPLKC PWKGCKMTFK 1500 WAWARTEHIR VHTGARPYVC AEPGCGQTFR FVSDFSRHKR KTGHSTKKGR G*

Sequence ? help Back to Top

Protein Sequence Length: 1552 aa Download sequence Send to blast

MAGTAMAAEP TQEVLSWLKT LPLAPEYHPT LAEFQDPISY IFKIEKEASK FGICKIVPPV  60
PPSPKKTVIV NFNKSLAARA APCSDSTNSK SPPTFTTRQQ QIGFCPRKTR PVQKSVWQSG  120
EYYTFQQFEA KAKNFEKSYL KKCTKKGGLS PLEIETLYWR ATLDKPFSVE YANDMPGSAF  180
VPVSAKMFRE AGEGTTLGET AWNMRGVSRA KGSLLKFMKE EIPGVTSPMV YVAMMFSWFA  240
WHVEDHDLHS LNYLHMGAGK TWYGVPRDAA VAFEEVVRVQ GYGGEINPLV TFAVLGEKTT  300
VMSPEVLVSA GVPCCRLVQN AGEFVVTFPR AYHTGFSHGF NCGEAANIAT PEWLNVAKDA  360
AIRRASINYP PMVSHYQLLY DLALSSRAPL CTGAEPRSSR LKDKRRSEGD TVIKELFVQN  420
IVENNSLLDN LGGGASVVLL PPGSLESIYS RLRVGSHLRS KPRFPTGVCS SKEETKSPQS  480
FDYDNLALEN SPVINRVKGF YSANGPYSTL SERSTDNVCA SSLRPLNANN ERGGNVQSNG  540
LSDQRLFSCV TCGILSFACV AIIQPREQAA RYLMSADCSF FNDWVVGSGI ASEGISTRDR  600
HPVSSQQISN SGKRDKCVSD GLYDVPVQAV NRQLPLAGES YEANLNTEKR NETSALGMLA  660
LTYGHSSDSE EDNAEADAAL NVDDAKLMIC SSEDQYQFEN SGLTSGEYSK NTAILNHDPS  720
SFGINSADHM QFQVNDYEEF RRADSKDSFN CSSESEMDGI GSTKKNGLTR YQDSHVNGRS  780
SLDADTEKPV FDKSTETVET ENMPFAPDID EDFSRLHVFC LEHAKEVEQQ LRPIGGVHIL  840
LLCHPDYPKM EAEAKLVAQE LSMSHLWTDT IFRDATQDEE KRIQLALDSE EAIPGNGDWA  900
VKLGINLFYS ANLSHSPLYS KQMPYNSVIY NAFGRSTSAN SSGKPKVYQR RTGKLKRVVA  960
GKWCGKVWMS NQVHPLLEKR DPQEEDVDIF PSWTMSDEKV DRKSANIQKN ETVKVNRKSA  1020
GKRKMTYGRE TIKKAKLVES EDMVSDASVE DCIHQHHSIL RNKQSKFVEC NDPMSDDSVE  1080
DDSSRKHGVP VSKGAPYFGT DDTGSDDSLG DRHTLHRGFS GFKLPRWGEI EPSVSDDSLE  1140
HYSSQHRGKN IKSRTGKYIE RQDALSDECL ESGSLKQYRR IPKSKQTKVL KKNAILHDIR  1200
DDSFLWHHQK PSRIKKAKFI ETEDAVSEHS LENSSHQHRS MPQIKPAKHT AWEDAFSDDP  1260
DEDDNSLLQH RNVRSNMQFR EITSDDQLDD GANQYSRRVL RRKPVKTETI SQMKQEILRP  1320
VKRGASQTLK EEFAQSLKRG GRHTLKLETP QPKIHHATNR RGKRNEKLTD LESEDEQPGG  1380
PSTRLRKRTP KPTKLSEAKV KDKKPVAKKK MKTGSSLKTP AGHRDSKARD EESEYLCDIE  1440
GCNMSFGTKQ ELALHKRNIC PVKGCVKKFF SHKYLVQHRR VHMDDRPLKC PWKGCKMTFK  1500
WAWARTEHIR VHTGARPYVC AEPGCGQTFR FVSDFSRHKR KTGHSTKKGR G*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6ip0_A	1e-76	15	379	6	346	Transcription factor jumonji (Jmj) family protein
6ip4_A	1e-76	15	379	6	346	Arabidopsis JMJ13
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	1385	1411	RKRTPKPTKLSEAKVKDKKPVAKKKMK

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

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	LN681932	0.0	LN681932.1 Cucumis melo genomic scaffold, anchoredscaffold00001.
GenBank	LN713266	0.0	LN713266.1 Cucumis melo genomic chromosome, chr_12.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_011651913.1	0.0	PREDICTED: lysine-specific demethylase JMJ705
Swissprot	Q9STM3	0.0	REF6_ARATH; Lysine-specific demethylase REF6
TrEMBL	A0A0A0LWI2	0.0	A0A0A0LWI2_CUCSA; Uncharacterized protein
STRING	XP_004157814.1	0.0	(Cucumis sativus)

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	Cucsa.391680.1

Publications ? help Back to Top
Ren Y, et al. An integrated genetic and cytogenetic map of the cucumber genome. PLoS ONE, 2009. 4(6): p. e5795 [PMID:19495411] Guo S, et al. Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types. BMC Genomics, 2010. 11: p. 384 [PMID:20565788] Li Z, et al. RNA-Seq improves annotation of protein-coding genes in the cucumber genome. BMC Genomics, 2011. 12: p. 540 [PMID:22047402] 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]