halophFGD

Basic Information

Locus ID: Ag11G05071

Species & Taxonomic ID: Apium graveolens & 4045

Genome Assembly: GCA_009905375.1

Description: DNA (cytosine-5)-methyltransferase

Maps and Mapping Data

Chromosome	Start	End	Strand	ID
chr11	206316112	206330784	-	Ag11G05071

Protein Data

Protein Properties:

Theoretical pI	Molecular Weight	Instability Index	Aliphatic Index	GRAVY
6.44	83,966.49 Da	38.09	86.42	-0.31

Protein Domain:

Category	ID	Description	Start	End	Evalue/Score	InterPro ID
CDD	cd18635	CD_CMT3_like	301	357	1.27528E-30	-
Pfam	PF00145	C-5 cytosine-specific DNA methylase	366	741	7.8E-33	IPR001525
Pfam	PF00385	Chromo (CHRromatin Organisation MOdifier) domain	302	356	3.0E-12	IPR023780
Pfam	PF01426	BAH domain	43	159	5.4E-13	IPR001025
SUPERFAMILY	SSF53335	S-adenosyl-L-methionine-dependent methyltransferases	191	741	1.27E-67	IPR029063
SUPERFAMILY	SSF54160	Chromo domain-like	296	357	7.88E-13	IPR016197
Gene3D	G3DSA:3.90.120.10	DNA Methylase, subunit A, domain 2	530	626	4.3E-23	-
Gene3D	G3DSA:2.30.30.490	-	5	146	2.5E-39	IPR043151
Gene3D	G3DSA:3.40.50.150	Vaccinia Virus protein VP39	716	742	2.4E-22	-
Gene3D	G3DSA:3.40.50.150	Vaccinia Virus protein VP39	147	529	2.5E-153	-
Gene3D	G3DSA:3.90.120.10	DNA Methylase, subunit A, domain 2	693	715	2.4E-22	-
SMART	SM00439	BAH_4	42	161	2.6E-16	IPR001025
SMART	SM00298	chromo_7	301	360	1.6E-8	IPR000953
ProSiteProfiles	PS50013	Chromo and chromo shadow domain profile.	302	355	12.991901	IPR000953
ProSiteProfiles	PS51038	BAH domain profile.	42	161	18.381496	IPR001025
ProSiteProfiles	PS51679	C-5 cytosine-specific DNA methylase (Dnmt) domain profile.	191	742	41.261166	IPR001525
ProSitePatterns	PS00598	Chromo domain signature.	325	345	-	IPR023779
PRINTS	PR00105	Cytosine-specific DNA methyltransferase signature	415	429	2.3E-12	IPR001525
PRINTS	PR00105	Cytosine-specific DNA methyltransferase signature	461	474	2.3E-12	IPR001525
PRINTS	PR00105	Cytosine-specific DNA methyltransferase signature	192	208	2.3E-12	IPR001525
MobiDBLite	mobidb-lite	consensus disorder prediction	274	298	-	-

Gene Ontology

Molecular Function:

GO:0003682 (chromatin binding) GO:0008168 (methyltransferase activity)

KEGG Pathway

KO Term:

K00558 (DNA (cytosine-5)-methyltransferase 1 [EC:2.1.1.37])

Pathway:

ko00270 (Cysteine and methionine metabolism) map00270 (Cysteine and methionine metabolism) ko01100 (Metabolic pathways) map01100 (Metabolic pathways)

Module:

M00035 (Methionine degradation)

Reaction:

R04858 (S-Adenosyl-L-methionine + DNA cytosine <=> S-Adenosyl-L-homocysteine + 5-Methylcytosine in DNA)

Best hit

Source	Best Hit ID	Description
TAIR	AT1G69770.1	chromomethylase 3. Encodes a chromomethylase involved in methylating cytosine residues at non-CG sites. Involved in preferentially methylating transposon-related sequences, reducing their mobility. CMT3 interacts with an Arabidopsis homologue of HP1 (heterochromatin protein 1), which in turn interacts with methylated histones. Involved in gene silencing.
RefSeq	XP_017236074.1	PREDICTED: DNA (cytosine-5)-methyltransferase 1-like [Daucus carota subsp. sativus]
Swiss-Prot	Q9AXT8	DNA (cytosine-5)-methyltransferase 1 OS=Zea mays OX=4577 GN=MET2A PE=1 SV=1
TrEMBL	A0A161WZM8	DNA (cytosine-5-)-methyltransferase OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_005032 PE=3 SV=1

Expression

BioProject	Accession	TPM	Cultivar	Tissue	Development Stage	Sample Name	Description
PRJNA723697	SRX10692252	1.178451	Shengqin NO.2	seed	S1-1	S1-1	initial formation stage (S1)
PRJNA723697	SRX10692254	0.787682	Shengqin NO.2	seed	S1-3	S1-3	initial formation stage (S1)
PRJNA723697	SRX10692255	0.260607	Shengqin NO.2	seed	S3-1	S3-1	middle development stage (S3)
PRJNA723697	SRX10692256	0.33657	Shengqin NO.2	seed	S3-2	S3-2	middle development stage (S3)
PRJNA723697	SRX10692257	0.445289	Shengqin NO.2	seed	S3-3	S3-3	middle development stage (S3)
PRJNA723697	SRX10692258	0.600726	Shengqin NO.2	seed	S5-1	S5-1	maturation stage (S5)
PRJNA723697	SRX10692259	0.523031	Shengqin NO.2	seed	S5-2	S5-2	maturation stage (S5)
PRJNA723697	SRX10692260	0.8218	Shengqin NO.2	seed	S5-3	S5-3	maturation stage (S5)
PRJNA884666	SRX17729272	23.37405	celery	anther		W99A-r1	male sterile lineÂ
PRJNA884666	SRX17729273	24.367985	celery	anther		W99A-r2	male sterile lineÂ
PRJNA884666	SRX17729274	25.053892	celery	anther		W99A-r3	male sterile lineÂ
PRJNA884666	SRX17729275	26.85696	celery	anther		W99B-r1	maintainer line
PRJNA884666	SRX17729276	18.941362	celery	anther		W99B-r2	maintainer line
PRJNA884666	SRX17729277	14.793642	celery	anther		W99B-r3	maintainer line
PRJNA884180	SRX17743889	0.771128	var. secalinum Yablochny	collenchyma		Col_S1_rep1-1
PRJNA884180	SRX17748056	1.040565	var. secalinum Yablochny	collenchyma		Col_S1_rep3	biological replicate 3
PRJNA884180	SRX17748057	1.662318	var. secalinum Yablochny	collenchyma		Col_S1_rep4	biological replicate 4
PRJNA884180	SRX17748678	1.365772	var. secalinum Yablochny	parenchyma		Par_S1_rep1	Biological replicate 1
PRJNA884180	SRX17748679	0.766987	var. secalinum Yablochny	parenchyma		Par_S1_rep2	Biological replicate 2
PRJNA884180	SRX17748680	1.778215	var. secalinum Yablochny	parenchyma		Par_S1_rep3	Biological replicate 3
PRJNA884180	SRX17748681	0.896671	var. secalinum Yablochny	parenchyma		Par_S1_rep4	Biological replicate 4
PRJNA884180	SRX17748898	2.245273	var. secalinum Yablochny	vascular bundle		Vas_S1_rep1	Biological replicate 1
PRJNA884180	SRX17748899	3.176313	var. secalinum Yablochny	vascular bundle		Vas_S1_rep2	Biological replicate 2
PRJNA884180	SRX17748900	3.838412	var. secalinum Yablochny	vascular bundle		Vas_S1_rep3	Biological replicate 3
PRJNA884180	SRX17748901	2.921674	var. secalinum Yablochny	vascular bundle		Vas_S1_rep4	Biological replicate 4
PRJNA884180	SRX17749129	2.447652	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep1	Biological replicate 1
PRJNA884180	SRX17749130	1.980603	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep2	Biological replicate 2
PRJNA884180	SRX17749131	1.573428	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep3	Biological replicate 3
PRJNA884180	SRX17749132	2.839221	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep4	Biological replicate 4
PRJNA1124269	SRX24936411	1.385799		leaf		CK1	replicate=biological replicate1
PRJNA1124269	SRX24936412	2.823349		leaf		CK2	replicate=biological replicate2
PRJNA1124269	SRX24936413	1.781897		leaf		CK3	replicate=biological replicate3
PRJNA1124269	SRX24936414	0.704865		leaf		D1	replicate=biological replicate1
PRJNA1124269	SRX24936415	5.153325		leaf		D2	replicate=biological replicate2
PRJNA1124269	SRX24936416	0.890261		leaf		D3	replicate=biological replicate3
PRJNA1124269	SRX24936417	1.218217		leaf		MD1	replicate=biological replicate1
PRJNA1124269	SRX24936418	0.969228		leaf		MD2	replicate=biological replicate2
PRJNA1124269	SRX24936419	0.746582		leaf		MD3	replicate=biological replicate3
PRJNA387092	SRX2833309	3.699122	shanghaihuangxin	leaf	leaves between 0.5 and 1 cm in breadth, folded;	stage 2
PRJNA387092	SRX2833321	0.789954	shanghaihuangxin	leaf	leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion	stage 5
PRJNA387092	SRX2833323	0.981672	shanghaihuangxin	leaf	leaves >3 cm, unfolded, with clearstem extension	stage 7
PRJNA543957	SRX5879598	1.654537	Zhangzhou lvqing	stem		Se3	100 ppm Na2SeO4
PRJNA543957	SRX5879599	1.196943	Zhangzhou lvqing	stem		Se2	100 ppm Na2SeO4
PRJNA543957	SRX5879600	1.150556	Zhangzhou lvqing	stem		Mock2	mock
PRJNA543957	SRX5879601	1.065528	Zhangzhou lvqing	stem		Mock1	mock
PRJNA543957	SRX5879602	2.423657	Zhangzhou lvqing	stem		Se1	100 ppm Na2SeO4
PRJNA543957	SRX5879603	1.735136	Zhangzhou lvqing	stem		Mock3	mock
PRJNA609149	SRX7815917	8.237508	Jinnan Shiqin	flower bud	early flower bud	early flower bud
PRJNA609149	SRX7815918	8.653205	Jinnan Shiqin	flower bud	middle flower bud	middle flower bud
PRJNA609149	SRX7815919	6.581034	Jinnan Shiqin	flower bud	early flowering period	early flowering period

Network

🔍 Co-expression Network

🔍 Protein-Protein Interaction Network

Orthology

Family	Species	Count	Orthologous Genes
Acanthaceae	Avicennia marina	3	jg13794, jg23605, jg36130
Aizoaceae	Mesembryanthemum crystallinum	4	gene_12059, gene_2168, gene_23938, gene_3430
Amaranthaceae	Atriplex hortensis	3	Ah004889, Ah018388, Ah027458
Amaranthaceae	Beta vulgaris	4	BVRB_3g050080, BVRB_4g071490, BVRB_5g107290, BVRB_7g164870
Amaranthaceae	Salicornia bigelovii	8	Sbi_jg13016, Sbi_jg14869, Sbi_jg18035, Sbi_jg23779 ... Sbi_jg52856, Sbi_jg55645, Sbi_jg62665, Sbi_jg7611
Amaranthaceae	Salicornia europaea	4	Seu_jg12410, Seu_jg1264, Seu_jg26200, Seu_jg9012
Amaranthaceae	Suaeda aralocaspica	4	GOSA_00010231, GOSA_00010921, GOSA_00014366, GOSA_00017942
Amaranthaceae	Suaeda glauca	8	Sgl01110, Sgl06195, Sgl23814, Sgl28979, Sgl33949, Sgl39332 ... Sgl51217, Sgl56517
Amaranthaceae	Chenopodium album	10	gene:ENSEOMG00000000267, gene:ENSEOMG00000001655 ... gene:ENSEOMG00000005549, gene:ENSEOMG00000021096, gene:ENSEOMG00000024208, gene:ENSEOMG00000025935, gene:ENSEOMG00000029648, gene:ENSEOMG00000031445, gene:ENSEOMG00000040689, gene:ENSEOMG00000046216
Amaranthaceae	Chenopodium quinoa	7	CQ.Regalona.r1.3AG0007160, CQ.Regalona.r1.3BG0007170 ... CQ.Regalona.r1.4AG0000540, CQ.Regalona.r1.4BG0000630, CQ.Regalona.r1.5AG0001530, CQ.Regalona.r1.6AG0024980, CQ.Regalona.r1.6BG0026480
Anacardiaceae	Pistacia vera	5	pistato.v30030200, pistato.v30054360, pistato.v30172360 ... pistato.v30172370, pistato.v30197810
Apiaceae	Apium graveolens	4	Ag11G04623, Ag11G05049, Ag11G05071, Ag8G01105
Arecaceae	Cocos nucifera	3	COCNU_04G007180, COCNU_04G007220, COCNU_05G008940
Arecaceae	Phoenix dactylifera	2	gene-LOC103707986, gene-LOC103712941
Asparagaceae	Asparagus officinalis	6	AsparagusV1_01.1635.V1.1, AsparagusV1_01.2680.V1.1 ... AsparagusV1_01.2681.V1.1, AsparagusV1_03.2173.V1.1, AsparagusV1_05.968.V1.1, AsparagusV1_08.89.V1.1
Asteraceae	Flaveria trinervia	3	Ftri13G13364, Ftri2G01683, Ftri7G08977
Brassicaceae	Arabidopsis thaliana	3	AT1G69770.1, AT1G80740.1, AT4G19020.1
Brassicaceae	Eutrema salsugineum	3	Thhalv10006850m.g.v1.0, Thhalv10018159m.g.v1.0 ... Thhalv10024250m.g.v1.0
Brassicaceae	Schrenkiella parvula	3	Sp1g10040.v2.2, Sp2g28030.v2.2, Sp7g17750.v2.2
Brassicaceae	Brassica nigra	4	BniB04g028310.2N, BniB05g017360.2N, BniB06g013250.2N ... BniB06g013260.2N
Casuarinaceae	Casuarina equisetifolia	2	Ceq01G0137, Ceq05G2187
Casuarinaceae	Casuarina glauca	2	Cgl01G0122, Cgl05G2282
Cymodoceaceae	Cymodocea nodosa	2	gene.Cymno15g07660, gene.Cymno16g05000
Dunaliellaceae	Dunaliella salina	1	Dusal.0129s00008.v1.0
Hydrocharitaceae	Thalassia testudinum	1	gene.Thate05g07140
Nitrariaceae	Nitraria sibirica	4	evm.TU.LG05.910, evm.TU.LG08.1063, evm.TU.LG08.789 ... evm.TU.LG09.452
Plantaginaceae	Plantago ovata	7	Pov_00000623, Pov_00019906, Pov_00020850, Pov_00022750 ... Pov_00028526, Pov_00033087, Pov_00033105
Plumbaginaceae	Limonium bicolor	4	Lb2G11984, Lb2G14941, Lb2G14947, Lb7G33201
Poaceae	Echinochloa crus-galli	6	AH01.2711, AH05.592, BH01.3040, BH05.642, CH01.3251 ... CH05.744
Poaceae	Eleusine coracana subsp. coracana	4	gene-QOZ80_2AG0119120, gene-QOZ80_2BG0173050 ... gene-QOZ80_5AG0401060, gene-QOZ80_5BG0449640
Poaceae	Hordeum vulgare	3	HORVU.MOREX.r3.4HG0386550.1, HORVU.MOREX.r3.4HG0394000.1 ... HORVU.MOREX.r3.6HG0628050.1
Poaceae	Lolium multiflorum	14	gene-QYE76_028897, gene-QYE76_029117, gene-QYE76_029530 ... gene-QYE76_030995, gene-QYE76_035944, gene-QYE76_035963, gene-QYE76_036534, gene-QYE76_036535, gene-QYE76_036900, gene-QYE76_036923, gene-QYE76_048451, gene-QYE76_057611, gene-QYE76_068908, gene-QYE76_069568
Poaceae	Oryza coarctata	4	Oco09G004880, Oco10G003930, Oco19G000130, Oco20G000170
Poaceae	Oryza sativa	4	LOC_Os03g12570.1, LOC_Os05g13780.1, LOC_Os05g13790.1 ... LOC_Os10g01570.1
Poaceae	Paspalum vaginatum	3	gene-BS78_01G251500, gene-BS78_09G088600, gene-BS78_K225600
Poaceae	Puccinellia tenuiflora	11	Pt_Chr0102392, Pt_Chr0104248, Pt_Chr0104250, Pt_Chr0200522 ... Pt_Chr0200523, Pt_Chr0200524, Pt_Chr0200526, Pt_Chr0200846, Pt_Chr0306853, Pt_Chr0306855, Pt_Chr0405152
Poaceae	Sporobolus alterniflorus	4	Chr03G002470, Chr08G002600, Chr09G006770, Chr13G017990
Poaceae	Thinopyrum elongatum	8	Tel4E01G357200, Tel4E01G403300, Tel6E01G055600 ... Tel6E01G475200, Tel6E01G688100, Tel7E01G004700, Tel7E01G005700, Tel7E01G960000
Poaceae	Triticum dicoccoides	10	gene_TRIDC1AG041150, gene_TRIDC4AG009670 ... gene_TRIDC4AG013990, gene_TRIDC4AG070470, gene_TRIDC4BG036340, gene_TRIDC4BG041110, gene_TRIDC6AG001840, gene_TRIDC6AG056600, gene_TRIDC6BG002370, gene_TRIDC6BG066120
Poaceae	Triticum aestivum	14	TraesCS4A02G077400.1, TraesCS4A02G102700.2 ... TraesCS4B02G201800.1, TraesCS4B02G233500.1, TraesCS4D02G202600.2, TraesCS4D02G234700.1, TraesCS6A02G015800.1, TraesCS6A02G380200.1, TraesCS6B02G022800.1, TraesCS6B02G419000.1, TraesCS6D02G018700.1, TraesCS6D02G364900.1, TraesCS7B02G474900.1, TraesCS7D02G537800.1
Poaceae	Zoysia japonica	3	nbis-gene-17933, nbis-gene-17934, nbis-gene-38248
Poaceae	Zoysia macrostachya	2	Zma_g15807, Zma_g27881
Portulacaceae	Portulaca oleracea	8	evm.TU.LG01.353, evm.TU.LG01.643, evm.TU.LG04.129 ... evm.TU.LG04.2961, evm.TU.LG04.402, evm.TU.LG16.645, evm.TU.LG18.1131, evm.TU.LG20.740
Posidoniaceae	Posidonia oceanica	3	gene.Posoc07g10180, gene.Posoc07g15600, gene.Posoc09g01100
Rhizophoraceae	Bruguiera sexangula	3	evm.TU.Scaffold_14_RagTag.753, evm.TU.Scaffold_7_RagTag.1729 ... evm.TU.Scaffold_8_RagTag.57
Rhizophoraceae	Carallia pectinifolia	2	nbisL1-mrna-10299, nbisL1-mrna-17713
Rhizophoraceae	Ceriops tagal	2	nbisL1-mrna-13149, nbisL1-mrna-17591
Rhizophoraceae	Ceriops zippeliana	2	nbisL1-mrna-17094, nbisL1-mrna-17703
Rhizophoraceae	Kandelia candel	2	evm.TU.utg000018l.950, evm.TU.utg000025l.3
Rhizophoraceae	Kandelia obovata	2	Maker00003298, Maker00012350
Rhizophoraceae	Rhizophora apiculata	2	nbisL1-mrna-15850, nbisL1-mrna-3061
Rhizophoraceae	Rhizophora mangle	2	nbisL1-mrna-11516, nbisL1-mrna-9003
Salicaceae	Populus euphratica	3	populus_peu04412, populus_peu34112, populus_peu35235
Solanaceae	Lycium barbarum	4	gene-LOC132604622, gene-LOC132609666, gene-LOC132626037 ... gene-LOC132626038
Solanaceae	Solanum chilense	3	SOLCI000047500, SOLCI003665100, SOLCI004429900
Solanaceae	Solanum pennellii	3	gene-LOC107007094, gene-LOC107008257, gene-LOC107028898
Tamaricaceae	Reaumuria soongarica	4	gene_13979, gene_15769, gene_3936, gene_7516
Tamaricaceae	Tamarix chinensis	2	TC01G4672, TC06G2785
Zosteraceae	Zostera marina	1	Zosma03g15410.v3.1