halophFGD

Basic Information

Locus ID: Ag2G00954

Species & Taxonomic ID: Apium graveolens & 4045

Genome Assembly: GCA_009905375.1

Description: Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family

Maps and Mapping Data

Chromosome	Start	End	Strand	ID
chr2	45010120	45028219	+	Ag2G00954

Protein Data

Protein Properties:

Theoretical pI	Molecular Weight	Instability Index	Aliphatic Index	GRAVY
5.94	82,888.07 Da	33.24	80.83	-0.33

Protein Domain:

Category	ID	Description	Start	End	Evalue/Score	InterPro ID
CDD	cd02440	AdoMet_MTases	505	560	1.04854E-6	-
CDD	cd00590	RRM_SF	85	149	2.2511E-9	-
Pfam	PF00076	RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)	87	148	4.7E-6	IPR000504
Pfam	PF00642	Zinc finger C-x8-C-x5-C-x3-H type (and similar)	3	28	5.7E-8	IPR000571
Pfam	PF05958	tRNA (Uracil-5-)-methyltransferase	644	691	1.4E-6	IPR010280
Pfam	PF13847	Methyltransferase domain	503	600	1.9E-9	IPR025714
SUPERFAMILY	SSF54928	RNA-binding domain, RBD	87	162	8.55E-10	IPR035979
SUPERFAMILY	SSF90229	CCCH zinc finger	2	33	1.73E-5	IPR036855
SUPERFAMILY	SSF53335	S-adenosyl-L-methionine-dependent methyltransferases	206	756	2.97E-45	IPR029063
Gene3D	G3DSA:3.40.50.150	Vaccinia Virus protein VP39	437	755	2.0E-64	-
Gene3D	G3DSA:3.30.70.330	-	83	155	1.4E-9	IPR012677
Gene3D	G3DSA:4.10.1000.10	-	1	34	1.8E-7	-
SMART	SM00360	rrm1_1	83	150	4.0E-5	IPR000504
SMART	SM00356	c3hfinal6	2	28	6.6E-4	IPR000571
ProSiteProfiles	PS50103	Zinc finger C3H1-type profile.	1	29	14.126466	IPR000571
ProSiteProfiles	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	87	154	8.808147	IPR000504
ProSiteProfiles	PS51687	SAM-dependent methyltransferase RNA m(5)U-type domain profile.	204	756	46.863789	IPR010280
ProSitePatterns	PS01230	RNA methyltransferase trmA family signature 1.	651	683	-	IPR030390
MobiDBLite	mobidb-lite	consensus disorder prediction	27	60	-	-
MobiDBLite	mobidb-lite	consensus disorder prediction	156	174	-	-
MobiDBLite	mobidb-lite	consensus disorder prediction	155	174	-	-
Coils	Coil	Coil	214	234	-	-

Gene Ontology

Biological Process:

GO:0006396 (RNA processing)

Molecular Function:

GO:0003676 (nucleic acid binding) GO:0008173 (RNA methyltransferase activity) GO:0046872 (metal ion binding)

KEGG Pathway

KO Term:

K15332 (tRNA (uracil-5-)-methyltransferase [EC:2.1.1.-])

Best hit

Source	Best Hit ID	Description
TAIR	AT2G28450.1	zinc finger (CCCH-type) family protein.
RefSeq	XP_017253286.1	PREDICTED: zinc finger CCCH domain-containing protein 24 [Daucus carota subsp. sativus]
Swiss-Prot	Q8L7S3	Zinc finger CCCH domain-containing protein 24 OS=Arabidopsis thaliana OX=3702 GN=At2g28450 PE=1 SV=1
TrEMBL	A0A164Z9P0	C3H1-type domain-containing protein OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_018815 PE=3 SV=1

Expression

BioProject	Accession	TPM	Cultivar	Tissue	Development Stage	Sample Name	Description
PRJNA723697	SRX10692252	15.195205	Shengqin NO.2	seed	S1-1	S1-1	initial formation stage (S1)
PRJNA723697	SRX10692254	9.686318	Shengqin NO.2	seed	S1-3	S1-3	initial formation stage (S1)
PRJNA723697	SRX10692255	9.809519	Shengqin NO.2	seed	S3-1	S3-1	middle development stage (S3)
PRJNA723697	SRX10692256	11.35498	Shengqin NO.2	seed	S3-2	S3-2	middle development stage (S3)
PRJNA723697	SRX10692257	11.117371	Shengqin NO.2	seed	S3-3	S3-3	middle development stage (S3)
PRJNA723697	SRX10692258	14.126143	Shengqin NO.2	seed	S5-1	S5-1	maturation stage (S5)
PRJNA723697	SRX10692259	10.709824	Shengqin NO.2	seed	S5-2	S5-2	maturation stage (S5)
PRJNA723697	SRX10692260	11.163784	Shengqin NO.2	seed	S5-3	S5-3	maturation stage (S5)
PRJNA884666	SRX17729272	14.854681	celery	anther		W99A-r1	male sterile lineÂ
PRJNA884666	SRX17729273	18.370266	celery	anther		W99A-r2	male sterile lineÂ
PRJNA884666	SRX17729274	15.697473	celery	anther		W99A-r3	male sterile lineÂ
PRJNA884666	SRX17729275	15.979065	celery	anther		W99B-r1	maintainer line
PRJNA884666	SRX17729276	18.227415	celery	anther		W99B-r2	maintainer line
PRJNA884666	SRX17729277	13.005997	celery	anther		W99B-r3	maintainer line
PRJNA884180	SRX17743889	5.489823	var. secalinum Yablochny	collenchyma		Col_S1_rep1-1
PRJNA884180	SRX17748056	8.899463	var. secalinum Yablochny	collenchyma		Col_S1_rep3	biological replicate 3
PRJNA884180	SRX17748057	10.465044	var. secalinum Yablochny	collenchyma		Col_S1_rep4	biological replicate 4
PRJNA884180	SRX17748678	10.118112	var. secalinum Yablochny	parenchyma		Par_S1_rep1	Biological replicate 1
PRJNA884180	SRX17748679	9.395589	var. secalinum Yablochny	parenchyma		Par_S1_rep2	Biological replicate 2
PRJNA884180	SRX17748680	9.764957	var. secalinum Yablochny	parenchyma		Par_S1_rep3	Biological replicate 3
PRJNA884180	SRX17748681	8.518513	var. secalinum Yablochny	parenchyma		Par_S1_rep4	Biological replicate 4
PRJNA884180	SRX17748898	14.511307	var. secalinum Yablochny	vascular bundle		Vas_S1_rep1	Biological replicate 1
PRJNA884180	SRX17748899	16.204288	var. secalinum Yablochny	vascular bundle		Vas_S1_rep2	Biological replicate 2
PRJNA884180	SRX17748900	14.199521	var. secalinum Yablochny	vascular bundle		Vas_S1_rep3	Biological replicate 3
PRJNA884180	SRX17748901	15.172071	var. secalinum Yablochny	vascular bundle		Vas_S1_rep4	Biological replicate 4
PRJNA884180	SRX17749129	10.963364	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep1	Biological replicate 1
PRJNA884180	SRX17749130	10.535532	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep2	Biological replicate 2
PRJNA884180	SRX17749131	11.270715	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep3	Biological replicate 3
PRJNA884180	SRX17749132	12.391102	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep4	Biological replicate 4
PRJNA1124269	SRX24936411	4.821955		leaf		CK1	replicate=biological replicate1
PRJNA1124269	SRX24936412	12.447341		leaf		CK2	replicate=biological replicate2
PRJNA1124269	SRX24936413	7.990744		leaf		CK3	replicate=biological replicate3
PRJNA1124269	SRX24936414	6.895326		leaf		D1	replicate=biological replicate1
PRJNA1124269	SRX24936415	7.334636		leaf		D2	replicate=biological replicate2
PRJNA1124269	SRX24936416	6.900279		leaf		D3	replicate=biological replicate3
PRJNA1124269	SRX24936417	6.655187		leaf		MD1	replicate=biological replicate1
PRJNA1124269	SRX24936418	4.251314		leaf		MD2	replicate=biological replicate2
PRJNA1124269	SRX24936419	6.041545		leaf		MD3	replicate=biological replicate3
PRJNA387092	SRX2833309	17.088968	shanghaihuangxin	leaf	leaves between 0.5 and 1 cm in breadth, folded;	stage 2
PRJNA387092	SRX2833321	8.010873	shanghaihuangxin	leaf	leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion	stage 5
PRJNA387092	SRX2833323	4.175776	shanghaihuangxin	leaf	leaves >3 cm, unfolded, with clearstem extension	stage 7
PRJNA543957	SRX5879598	9.564233	Zhangzhou lvqing	stem		Se3	100 ppm Na2SeO4
PRJNA543957	SRX5879599	14.279271	Zhangzhou lvqing	stem		Se2	100 ppm Na2SeO4
PRJNA543957	SRX5879600	36.58802	Zhangzhou lvqing	stem		Mock2	mock
PRJNA543957	SRX5879601	26.570745	Zhangzhou lvqing	stem		Mock1	mock
PRJNA543957	SRX5879602	10.26925	Zhangzhou lvqing	stem		Se1	100 ppm Na2SeO4
PRJNA543957	SRX5879603	24.604521	Zhangzhou lvqing	stem		Mock3	mock
PRJNA609149	SRX7815917	18.098192	Jinnan Shiqin	flower bud	early flower bud	early flower bud
PRJNA609149	SRX7815918	17.561541	Jinnan Shiqin	flower bud	middle flower bud	middle flower bud
PRJNA609149	SRX7815919	18.949953	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	1	jg35872
Aizoaceae	Mesembryanthemum crystallinum	1	gene_20859
Amaranthaceae	Atriplex hortensis	1	Ah037774
Amaranthaceae	Beta vulgaris	1	BVRB_9g208060
Amaranthaceae	Salicornia bigelovii	2	Sbi_jg41873, Sbi_jg48254
Amaranthaceae	Salicornia europaea	1	Seu_jg27595
Amaranthaceae	Suaeda aralocaspica	1	GOSA_00019765
Amaranthaceae	Suaeda glauca	4	Sgl22058, Sgl27336, Sgl78570, Sgl81054
Amaranthaceae	Chenopodium album	4	gene:ENSEOMG00000016164, gene:ENSEOMG00000016348 ... gene:ENSEOMG00000036117, gene:ENSEOMG00000051914
Amaranthaceae	Chenopodium quinoa	2	CQ.Regalona.r1.9AG0004940, CQ.Regalona.r1.9BG0017370
Anacardiaceae	Pistacia vera	1	pistato.v30058730
Apiaceae	Apium graveolens	4	Ag2G00954, AgUnG00514, AgUnG01597, AgUnG01598
Arecaceae	Cocos nucifera	1	COCNU_07G000100
Arecaceae	Phoenix dactylifera	1	gene-LOC103708402
Asparagaceae	Asparagus officinalis	1	AsparagusV1_04.21.V1.1
Asteraceae	Flaveria trinervia	1	Ftri16G31703
Brassicaceae	Arabidopsis thaliana	1	AT2G28450.1
Brassicaceae	Eutrema salsugineum	1	Thhalv10016347m.g.v1.0
Brassicaceae	Schrenkiella parvula	1	Sp4g11270.v2.2
Brassicaceae	Brassica nigra	1	BniB06g017450.2N
Casuarinaceae	Casuarina equisetifolia	1	Ceq08G1718
Casuarinaceae	Casuarina glauca	1	Cgl08G1758
Cymodoceaceae	Cymodocea nodosa	1	gene.Cymno15g04020
Hydrocharitaceae	Thalassia testudinum	1	gene.Thate03g06300
Nitrariaceae	Nitraria sibirica	1	evm.TU.LG09.923
Plantaginaceae	Plantago ovata	1	Pov_00014650
Plumbaginaceae	Limonium bicolor	1	Lb6G32392
Poaceae	Echinochloa crus-galli	3	AH09.31, BH09.106, CH09.76
Poaceae	Eleusine coracana subsp. coracana	2	gene-QOZ80_4AG0328510, gene-QOZ80_4BG0360510
Poaceae	Hordeum vulgare	1	HORVU.MOREX.r3.2HG0100410.2
Poaceae	Lolium multiflorum	2	gene-QYE76_038082, gene-QYE76_038083
Poaceae	Oryza coarctata	1	Oco08G000150
Poaceae	Oryza sativa	1	LOC_Os04g01480.1
Poaceae	Paspalum vaginatum	1	gene-BS78_06G004200
Poaceae	Puccinellia tenuiflora	2	Pt_Chr0305932, Pt_Chr0306000
Poaceae	Sporobolus alterniflorus	4	Chr23G019170, Chr25G016790, Chr26G000780, Chr30G014600
Poaceae	Thinopyrum elongatum	1	Tel2E01G096800
Poaceae	Triticum dicoccoides	1	gene_TRIDC2BG004730
Poaceae	Triticum aestivum	3	TraesCS2A02G039200.1, TraesCS2B02G051800.1 ... TraesCS2D02G037700.2
Poaceae	Zea mays	2	Zm00001eb089580_P001, Zm00001eb418880_P001
Poaceae	Zoysia japonica	1	nbis-gene-46845
Poaceae	Zoysia macrostachya	1	Zma_g19214
Portulacaceae	Portulaca oleracea	2	evm.TU.LG02.2197, evm.TU.LG23.431
Posidoniaceae	Posidonia oceanica	1	gene.Posoc06g00040
Rhizophoraceae	Bruguiera sexangula	1	evm.TU.Scaffold_13_RagTag.713
Rhizophoraceae	Carallia pectinifolia	1	nbisL1-mrna-30333
Rhizophoraceae	Ceriops tagal	1	nbisL1-mrna-19756
Rhizophoraceae	Ceriops zippeliana	1	nbisL1-mrna-16094
Rhizophoraceae	Kandelia candel	1	evm.TU.utg000015l.413
Rhizophoraceae	Kandelia obovata	1	Maker00015772
Rhizophoraceae	Rhizophora apiculata	1	nbisL1-mrna-4332
Rhizophoraceae	Rhizophora mangle	1	nbisL1-mrna-15083
Salicaceae	Populus euphratica	1	populus_peu35491
Solanaceae	Lycium barbarum	1	gene-LOC132600428
Solanaceae	Solanum chilense	1	SOLCI004152300
Solanaceae	Solanum pennellii	1	gene-LOC107004810
Tamaricaceae	Reaumuria soongarica	1	gene_14615
Tamaricaceae	Tamarix chinensis	1	TC01G2749
Zosteraceae	Zostera marina	1	Zosma01g38900.v3.1