halophFGD

Basic Information

Locus ID: Ag8G01105

Species & Taxonomic ID: Apium graveolens & 4045

Genome Assembly: GCA_009905375.1

Description: C-5 cytosine-specific DNA methylase

Maps and Mapping Data

Chromosome	Start	End	Strand	ID
chr8	119735826	119752432	+	Ag8G01105

Protein Data

Protein Properties:

Theoretical pI	Molecular Weight	Instability Index	Aliphatic Index	GRAVY
5.75	109,174.14 Da	45.04	75.46	-0.52

Protein Domain:

Category	ID	Description	Start	End	Evalue/Score	InterPro ID
CDD	cd18635	CD_CMT3_like	514	570	3.39367E-27	-
Pfam	PF00385	Chromo (CHRromatin Organisation MOdifier) domain	529	571	1.3E-10	IPR023780
Pfam	PF01426	BAH domain	250	362	6.1E-9	IPR001025
Pfam	PF00145	C-5 cytosine-specific DNA methylase	579	940	3.8E-36	IPR001525
SUPERFAMILY	SSF54160	Chromo domain-like	504	571	7.56E-12	IPR016197
SUPERFAMILY	SSF53335	S-adenosyl-L-methionine-dependent methyltransferases	407	940	2.98E-77	IPR029063
Gene3D	G3DSA:2.30.30.490	-	186	350	6.7E-42	IPR043151
Gene3D	G3DSA:3.90.120.10	DNA Methylase, subunit A, domain 2	733	906	5.9E-224	-
Gene3D	G3DSA:3.40.50.150	Vaccinia Virus protein VP39	392	492	3.0E-14	-
Gene3D	G3DSA:3.40.50.150	Vaccinia Virus protein VP39	533	957	5.9E-224	-
SMART	SM00439	BAH_4	249	365	2.2E-21	IPR001025
SMART	SM00298	chromo_7	514	573	2.8E-9	IPR000953
TIGRFAM	TIGR00675	dcm: DNA (cytosine-5-)-methyltransferase	582	937	1.4E-30	IPR001525
ProSiteProfiles	PS50013	Chromo and chromo shadow domain profile.	515	571	12.467001	IPR000953
ProSiteProfiles	PS51038	BAH domain profile.	249	365	16.244312	IPR001025
ProSiteProfiles	PS51679	C-5 cytosine-specific DNA methylase (Dnmt) domain profile.	407	947	47.142666	IPR001525
ProSitePatterns	PS00094	C-5 cytosine-specific DNA methylases active site.	585	597	-	IPR018117
ProSitePatterns	PS00598	Chromo domain signature.	538	558	-	IPR023779
PRINTS	PR00105	Cytosine-specific DNA methyltransferase signature	674	687	2.6E-12	IPR001525
PRINTS	PR00105	Cytosine-specific DNA methyltransferase signature	628	642	2.6E-12	IPR001525
PRINTS	PR00105	Cytosine-specific DNA methyltransferase signature	408	424	2.6E-12	IPR001525
MobiDBLite	mobidb-lite	consensus disorder prediction	36	50	-	-
MobiDBLite	mobidb-lite	consensus disorder prediction	1	87	-	-
MobiDBLite	mobidb-lite	consensus disorder prediction	1	17	-	-

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	AT4G19020.1	chromomethylase 2.
RefSeq	XP_017223055.1	PREDICTED: DNA (cytosine-5)-methyltransferase CMT2-like [Daucus carota subsp. sativus]
Swiss-Prot	Q94F87	DNA (cytosine-5)-methyltransferase CMT2 OS=Arabidopsis thaliana OX=3702 GN=CMT2 PE=2 SV=3
TrEMBL	A0A175YKF8	Cytosine-specific methyltransferase OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_028247 PE=3 SV=1

Expression

BioProject	Accession	TPM	Cultivar	Tissue	Development Stage	Sample Name	Description
PRJNA723697	SRX10692252	21.862329	Shengqin NO.2	seed	S1-1	S1-1	initial formation stage (S1)
PRJNA723697	SRX10692254	14.103835	Shengqin NO.2	seed	S1-3	S1-3	initial formation stage (S1)
PRJNA723697	SRX10692255	12.075338	Shengqin NO.2	seed	S3-1	S3-1	middle development stage (S3)
PRJNA723697	SRX10692256	12.030852	Shengqin NO.2	seed	S3-2	S3-2	middle development stage (S3)
PRJNA723697	SRX10692257	12.184972	Shengqin NO.2	seed	S3-3	S3-3	middle development stage (S3)
PRJNA723697	SRX10692258	6.237631	Shengqin NO.2	seed	S5-1	S5-1	maturation stage (S5)
PRJNA723697	SRX10692259	7.326738	Shengqin NO.2	seed	S5-2	S5-2	maturation stage (S5)
PRJNA723697	SRX10692260	2.422464	Shengqin NO.2	seed	S5-3	S5-3	maturation stage (S5)
PRJNA884666	SRX17729272	50.268002	celery	anther		W99A-r1	male sterile lineÂ
PRJNA884666	SRX17729273	48.073429	celery	anther		W99A-r2	male sterile lineÂ
PRJNA884666	SRX17729274	52.632622	celery	anther		W99A-r3	male sterile lineÂ
PRJNA884666	SRX17729275	46.490196	celery	anther		W99B-r1	maintainer line
PRJNA884666	SRX17729276	45.545578	celery	anther		W99B-r2	maintainer line
PRJNA884666	SRX17729277	36.858917	celery	anther		W99B-r3	maintainer line
PRJNA884180	SRX17743889	29.007105	var. secalinum Yablochny	collenchyma		Col_S1_rep1-1
PRJNA884180	SRX17748056	35.989628	var. secalinum Yablochny	collenchyma		Col_S1_rep3	biological replicate 3
PRJNA884180	SRX17748057	29.796093	var. secalinum Yablochny	collenchyma		Col_S1_rep4	biological replicate 4
PRJNA884180	SRX17748678	35.251617	var. secalinum Yablochny	parenchyma		Par_S1_rep1	Biological replicate 1
PRJNA884180	SRX17748679	29.34548	var. secalinum Yablochny	parenchyma		Par_S1_rep2	Biological replicate 2
PRJNA884180	SRX17748680	24.270025	var. secalinum Yablochny	parenchyma		Par_S1_rep3	Biological replicate 3
PRJNA884180	SRX17748681	24.214367	var. secalinum Yablochny	parenchyma		Par_S1_rep4	Biological replicate 4
PRJNA884180	SRX17748898	30.429707	var. secalinum Yablochny	vascular bundle		Vas_S1_rep1	Biological replicate 1
PRJNA884180	SRX17748899	31.567183	var. secalinum Yablochny	vascular bundle		Vas_S1_rep2	Biological replicate 2
PRJNA884180	SRX17748900	32.820133	var. secalinum Yablochny	vascular bundle		Vas_S1_rep3	Biological replicate 3
PRJNA884180	SRX17748901	29.612597	var. secalinum Yablochny	vascular bundle		Vas_S1_rep4	Biological replicate 4
PRJNA884180	SRX17749129	37.869164	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep1	Biological replicate 1
PRJNA884180	SRX17749130	34.39397	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep2	Biological replicate 2
PRJNA884180	SRX17749131	23.122793	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep3	Biological replicate 3
PRJNA884180	SRX17749132	37.600266	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep4	Biological replicate 4
PRJNA1124269	SRX24936411	0.679906		leaf		CK1	replicate=biological replicate1
PRJNA1124269	SRX24936412	1.087893		leaf		CK2	replicate=biological replicate2
PRJNA1124269	SRX24936413	1.498403		leaf		CK3	replicate=biological replicate3
PRJNA1124269	SRX24936414	7.604862		leaf		D1	replicate=biological replicate1
PRJNA1124269	SRX24936415	8.211566		leaf		D2	replicate=biological replicate2
PRJNA1124269	SRX24936416	5.791584		leaf		D3	replicate=biological replicate3
PRJNA1124269	SRX24936417	1.477146		leaf		MD1	replicate=biological replicate1
PRJNA1124269	SRX24936418	0.558602		leaf		MD2	replicate=biological replicate2
PRJNA1124269	SRX24936419	0.628247		leaf		MD3	replicate=biological replicate3
PRJNA387092	SRX2833309	35.565552	shanghaihuangxin	leaf	leaves between 0.5 and 1 cm in breadth, folded;	stage 2
PRJNA387092	SRX2833321	13.566073	shanghaihuangxin	leaf	leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion	stage 5
PRJNA387092	SRX2833323	4.191231	shanghaihuangxin	leaf	leaves >3 cm, unfolded, with clearstem extension	stage 7
PRJNA543957	SRX5879598	5.602845	Zhangzhou lvqing	stem		Se3	100 ppm Na2SeO4
PRJNA543957	SRX5879599	5.81879	Zhangzhou lvqing	stem		Se2	100 ppm Na2SeO4
PRJNA543957	SRX5879600	3.500284	Zhangzhou lvqing	stem		Mock2	mock
PRJNA543957	SRX5879601	4.722517	Zhangzhou lvqing	stem		Mock1	mock
PRJNA543957	SRX5879602	6.174141	Zhangzhou lvqing	stem		Se1	100 ppm Na2SeO4
PRJNA543957	SRX5879603	8.117764	Zhangzhou lvqing	stem		Mock3	mock
PRJNA609149	SRX7815917	32.70713	Jinnan Shiqin	flower bud	early flower bud	early flower bud
PRJNA609149	SRX7815918	26.465105	Jinnan Shiqin	flower bud	middle flower bud	middle flower bud
PRJNA609149	SRX7815919	25.205044	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