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

Gh_A10G0045

Organism

Gossypium hirsutum

Taxonomic ID

3635

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium

Family

LSD

Protein Properties

Length: 1208aa MW: 136122 Da PI: 6.1378

Description

LSD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Gh_A10G0045	genome	NAU-NBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-LSD1	35.5	1.6e-11	11	35	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 C+gCr L YPrGA++V+CalC+t+ Gh_A10G0045 11 CSGCRSNLLYPRGATNVCCALCNTI 35 ***********************97 PP
2	zf-LSD1	35.7	1.5e-11	50	73	1	24
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdt 24 CggCrtlL+Y rG +sVRC++C+t Gh_A10G0045 50 CGGCRTLLMYARGGTSVRCSCCHT 73 ***********************8 PP
3	zf-LSD1	45.7	1.1e-14	88	112	1	25
zf-LSD1 1 CggCrtlLsYPrGApsVRCalCdtV 25 Cg+Crt+L+YP+GApsV+Ca+C+ V Gh_A10G0045 88 CGHCRTTLMYPYGAPSVKCAICQYV 112 **********************987 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
TIGRFAMs	TIGR01053	1.3E-11	8	38	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	1.8E-9	11	35	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	6.9E-14	47	76	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	2.7E-9	50	73	IPR005735	Zinc finger, LSD1-type
TIGRFAMs	TIGR01053	4.7E-12	85	115	IPR005735	Zinc finger, LSD1-type
Pfam	PF06943	2.7E-13	88	112	IPR005735	Zinc finger, LSD1-type
SMART	SM00545	1.0E-21	202	243	IPR003349	JmjN domain
PROSITE profile	PS51183	17.985	203	244	IPR003349	JmjN domain
Pfam	PF02375	2.7E-15	204	237	IPR003349	JmjN domain
SuperFamily	SSF51197	1.02E-37	317	345	No hit	No description
PROSITE profile	PS51184	39.96	410	576	IPR003347	JmjC domain
SMART	SM00558	7.4E-69	410	576	IPR003347	JmjC domain
SuperFamily	SSF51197	1.02E-37	411	597	No hit	No description
Pfam	PF02373	2.7E-45	443	559	IPR003347	JmjC domain
Pfam	PF02928	8.8E-11	666	717	IPR004198	Zinc finger, C5HC2-type
PROSITE profile	PS51542	24.732	962	1020	IPR003888	FY-rich, N-terminal
Pfam	PF05964	4.3E-8	973	1017	IPR003888	FY-rich, N-terminal
SMART	SM00541	3.7E-13	976	1020	IPR003888	FY-rich, N-terminal
PROSITE profile	PS51543	25.077	1022	1112	IPR003889	FY-rich, C-terminal
Pfam	PF05965	6.3E-23	1024	1111	IPR003889	FY-rich, C-terminal
SMART	SM00542	3.6E-25	1026	1121	IPR003889	FY-rich, C-terminal

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0005634	Cellular Component	nucleus

Sequence ? help Back to Top
Protein Sequence Length: 1208 aa Download sequence Send to blast
MIADMQSQIV CSGCRSNLLY PRGATNVCCA LCNTITQVPL PGMDMGQLIC GGCRTLLMYA 60 RGGTSVRCSC CHTLNLAPAP NQIAHINCGH CRTTLMYPYG APSVKCAICQ YVTNVGTGNA 120 RAPFCFNRPN QIASAGTMPS TSTSQTVVVE NPMSVDESGK LDHSSQLSMK RDNNIESLGS 180 PRHRRVSARW DPDEPCRPNI DDAPVFYPTI EEFEDTLAYI EKIRAEAQSF GICRIVPPPS 240 WTPPCPLKEK DIWEHAKFST RIQQVDLLQN REPMRKKNRS RKRKRRRHSR MGATRRQANS 300 SSESVVTSET DEKFGFNSGS DFTLEEFQRY ADEFKEMYFQ RDCSEDLESS MIECRQWEPS 360 WEDIEGEYWR IVEQPKDEVE VYYGADLETG TFGSGFPKLS SVLTGNDADK YATSGWNLNN 420 FPRLQGSVLS FEGCDISGVL VPWLYVGMCF SSFCWHVEDH HLYSLNYMHF GDPKIWYGVP 480 GNQATSLEAA MRKHLPDLFE EQPDLLNELV TQLSPSVLKA EGVPVYRAVQ HSGEFVLTFP 540 RAYHAGFNCG FNCAEAVNVA PVDWLEHGQL AVELYSEQHR KTSLSHDKLL LGSARQAIQA 600 LRELHVLGRE TPGNSRWKRV CGKDGMLTKA FRMRKQMEEE RVNCLPPDMP VRKMEKDFDL 660 ESERECFSCF YDLHLSACSC KCSPERFACL KHVKSFCSCQ DEDKFVLLRY TVDELQMLIE 720 ALEGGLDAVK LWASKDLGLV SGIDCDAYLS KWVQDSEVLK FEPAQPRESF SCSSRVEEKM 780 DINTPYLYGH FSSEVSPSER QPATKLKASH VTLDSHNNVV NVGVLVMENR TNSEQDACID 840 LNLDIISDYP ATARKSICDS DSSTNHSVTD VETFLREKSC GFDEVREPVL KRLKSDCSSS 900 VSREYSEKYQ HSISTGHDGF EGKKLFGVEL QFPHINAGQS NTLLKAETLN CSDVIASMAH 960 QGHPLLNRAV EPLNFGSVIF GKLWCNSQAI FPKGFRSRVK YFSVLDPTKI SSYISEVLDI 1020 GLLGPLFKVT LEGCPTTTFS NVLPNKCWEM VLQQLNQEIL RRKNLGESGL LPLQSLQSIN 1080 GLEMFGFLSP PIIQAIEALD PNHQCSEYWN HKTACVNNEV KKYALGLSCS VGESKAKIFG 1140 VDLTKQDHED PNQHSVDEEI QVVLRGLFKK ASPEELKIMR RILCSDSRSP ERRMAYETLM 1200 EEIRKTCQ

Sequence ? help Back to Top

Protein Sequence Length: 1208 aa Download sequence Send to blast

MIADMQSQIV CSGCRSNLLY PRGATNVCCA LCNTITQVPL PGMDMGQLIC GGCRTLLMYA  60
RGGTSVRCSC CHTLNLAPAP NQIAHINCGH CRTTLMYPYG APSVKCAICQ YVTNVGTGNA  120
RAPFCFNRPN QIASAGTMPS TSTSQTVVVE NPMSVDESGK LDHSSQLSMK RDNNIESLGS  180
PRHRRVSARW DPDEPCRPNI DDAPVFYPTI EEFEDTLAYI EKIRAEAQSF GICRIVPPPS  240
WTPPCPLKEK DIWEHAKFST RIQQVDLLQN REPMRKKNRS RKRKRRRHSR MGATRRQANS  300
SSESVVTSET DEKFGFNSGS DFTLEEFQRY ADEFKEMYFQ RDCSEDLESS MIECRQWEPS  360
WEDIEGEYWR IVEQPKDEVE VYYGADLETG TFGSGFPKLS SVLTGNDADK YATSGWNLNN  420
FPRLQGSVLS FEGCDISGVL VPWLYVGMCF SSFCWHVEDH HLYSLNYMHF GDPKIWYGVP  480
GNQATSLEAA MRKHLPDLFE EQPDLLNELV TQLSPSVLKA EGVPVYRAVQ HSGEFVLTFP  540
RAYHAGFNCG FNCAEAVNVA PVDWLEHGQL AVELYSEQHR KTSLSHDKLL LGSARQAIQA  600
LRELHVLGRE TPGNSRWKRV CGKDGMLTKA FRMRKQMEEE RVNCLPPDMP VRKMEKDFDL  660
ESERECFSCF YDLHLSACSC KCSPERFACL KHVKSFCSCQ DEDKFVLLRY TVDELQMLIE  720
ALEGGLDAVK LWASKDLGLV SGIDCDAYLS KWVQDSEVLK FEPAQPRESF SCSSRVEEKM  780
DINTPYLYGH FSSEVSPSER QPATKLKASH VTLDSHNNVV NVGVLVMENR TNSEQDACID  840
LNLDIISDYP ATARKSICDS DSSTNHSVTD VETFLREKSC GFDEVREPVL KRLKSDCSSS  900
VSREYSEKYQ HSISTGHDGF EGKKLFGVEL QFPHINAGQS NTLLKAETLN CSDVIASMAH  960
QGHPLLNRAV EPLNFGSVIF GKLWCNSQAI FPKGFRSRVK YFSVLDPTKI SSYISEVLDI  1020
GLLGPLFKVT LEGCPTTTFS NVLPNKCWEM VLQQLNQEIL RRKNLGESGL LPLQSLQSIN  1080
GLEMFGFLSP PIIQAIEALD PNHQCSEYWN HKTACVNNEV KKYALGLSCS VGESKAKIFG  1140
VDLTKQDHED PNQHSVDEEI QVVLRGLFKK ASPEELKIMR RILCSDSRSP ERRMAYETLM  1200
EEIRKTCQ

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ykn_A	0.0	185	735	5	555	Probable lysine-specific demethylase JMJ14
5yko_A	0.0	185	735	5	555	Probable lysine-specific demethylase JMJ14
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	280	285	RKRKRR
2	280	286	RKRKRRR
3	281	286	KRKRRR
4	282	286	RKRRR

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Ghi.18870	0.0	boll

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in shoot apex, primary root tip, trichomes of young leaves, leaf vascular tissues, anther filaments and styles. Detected in inflorescences, leaves, stems, roots and siliques. Mostly expressed in floral organs, and, at low levels, in other organs (PubMed:25578968). {ECO:0000269\|PubMed:18713399, ECO:0000269\|PubMed:19946624, ECO:0000269\|PubMed:20202164, ECO:0000269\|PubMed:25578968}.
Uniprot	TISSUE SPECIFICITY: Expressed in vascular tissues of roots, cotyledons, leaves and flowers. Expressed predominantly in phloem companion cells of roots. {ECO:0000269\|PubMed:22536163}.

Functional Description ? help Back to Top
Source	Description
UniProt	Histone demethylase that demethylates 'Lys-4' (H3K4me) of histone H3 with a specific activity for H3K4me3 and H3K4me2. No activity on H3K9me3/2, H3K27me3/2 and H3K36me3/2. Involved in the control of flowering time by demethylating H3K4me3 at the FLC locus and repressing its expression. The repression of FLC level and reduction in H3K4me3 at the FLC locus results in induction of the flowering activator FT, which is a downstream target of FLC. {ECO:0000269\|PubMed:22536163}.
UniProt	Transcriptional repressor (PubMed:25578968). Histone demethylase that demethylates 'Lys-4' (H3K4me) of histone H3 with a higher activity for H3K4me3 and H3K4me2 than H3K4me1. No activity on H3K9me3/2, H3K36me3/2 and H3K27me3/2. Represses FT and TSF expression to inhibit the floral transition. Binds around the transcription start site of the FT locus. Involved in the DRM2-mediated maintenance of DNA methylation, but not required for the de novo DNA methylation. Required for demethylating histone H3K4me3 at the target of RNA silencing. Together with NAC051/NAC052 and NAC050, regulates gene expression and flowering time, probably by the promotion of RNA-mediated gene silencing (PubMed:25578968). {ECO:0000269\|PubMed:19946624, ECO:0000269\|PubMed:20177424, ECO:0000269\|PubMed:20202164, ECO:0000269\|PubMed:20478993, ECO:0000269\|PubMed:21052090, ECO:0000269\|PubMed:25578968, ECO:0000269\|PubMed:26617990}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_017648805.1	0.0	PREDICTED: lysine-specific demethylase JMJ18-like isoform X1
Swissprot	F4I6G4	0.0	JMJ18_ARATH; Lysine-specific demethylase JMJ18
Swissprot	Q8GUI6	0.0	JMJ14_ARATH; Probable lysine-specific demethylase JMJ14
TrEMBL	A0A2P5XBB4	0.0	A0A2P5XBB4_GOSBA; Uncharacterized protein
STRING	Gorai.011G005400.1	0.0	(Gossypium raimondii)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G20380.7	6e-64	LSD family protein

Publications ? help Back to Top
Lu F,Cui X,Zhang S,Liu C,Cao X JMJ14 is an H3K4 demethylase regulating flowering time in Arabidopsis. Cell Res., 2010. 20(3): p. 387-90 [PMID:20177424] Yang W,Jiang D,Jiang J,He Y A plant-specific histone H3 lysine 4 demethylase represses the floral transition in Arabidopsis. Plant J., 2010. 62(4): p. 663-73 [PMID:20202164] Searle IR,Pontes O,Melnyk CW,Smith LM,Baulcombe DC JMJ14, a JmjC domain protein, is required for RNA silencing and cell-to-cell movement of an RNA silencing signal in Arabidopsis. Genes Dev., 2010. 24(10): p. 986-91 [PMID:20478993] Deleris A, et al. Involvement of a Jumonji-C domain-containing histone demethylase in DRM2-mediated maintenance of DNA methylation. EMBO Rep., 2010. 11(12): p. 950-5 [PMID:21052090] Le Masson I, et al. Mutations in the Arabidopsis H3K4me2/3 demethylase JMJ14 suppress posttranscriptional gene silencing by decreasing transgene transcription. Plant Cell, 2012. 24(9): p. 3603-12 [PMID:23001035] Greenberg MV, et al. Interplay between active chromatin marks and RNA-directed DNA methylation in Arabidopsis thaliana. PLoS Genet., 2013. 9(11): p. e1003946 [PMID:24244201] Zhang S, et al. C-terminal domains of a histone demethylase interact with a pair of transcription factors and mediate specific chromatin association. Cell Discov, 2019. [PMID:26617990] Kabelitz T, et al. A JUMONJI Protein with E3 Ligase and Histone H3 Binding Activities Affects Transposon Silencing in Arabidopsis. Plant Physiol., 2016. 171(1): p. 344-58 [PMID:26979329] Chen YC,Wang HJ,Jauh GY Dual Role of a SAS10/C1D Family Protein in Ribosomal RNA Gene Expression and Processing Is Essential for Reproduction in Arabidopsis thaliana. PLoS Genet., 2016. 12(10): p. e1006408 [PMID:27792779] Butel N,Le Masson I,Bouteiller N,Vaucheret H,Elmayan T sgs1: a neomorphic nac52 allele impairing post-transcriptional gene silencing through SGS3 downregulation. Plant J., 2017. 90(3): p. 505-519 [PMID:28207953] Sanz-Fernández M, et al. Screening Arabidopsis mutants in genes useful for phytoremediation. J. Hazard. Mater., 2017. 335: p. 143-151 [PMID:28441590] Yang Z, et al. Structure of the Arabidopsis JMJ14-H3K4me3 Complex Provides Insight into the Substrate Specificity of KDM5 Subfamily Histone Demethylases. Plant Cell, 2018. 30(1): p. 167-177 [PMID:29233856]