halophFGD

Basic Information

Locus ID: Ag6G02571

Species & Taxonomic ID: Apium graveolens & 4045

Genome Assembly: GCA_009905375.1

Description: methyltransferase involved in the maturation of rRNA and in the biogenesis of ribosomal subunits

Maps and Mapping Data

Chromosome	Start	End	Strand	ID
chr6	265249488	265256426	+	Ag6G02571

Protein Data

Protein Properties:

Theoretical pI	Molecular Weight	Instability Index	Aliphatic Index	GRAVY
8.66	93,047.14 Da	44.27	69.99	-0.86

Protein Domain:

Category	ID	Description	Start	End	Evalue/Score	InterPro ID
Pfam	PF11861	Domain of unknown function (DUF3381)	235	388	1.4E-43	IPR024576
Pfam	PF01728	FtsJ-like methyltransferase	22	200	3.4E-50	IPR002877
Pfam	PF07780	Spb1 C-terminal domain	600	795	2.3E-58	IPR012920
SUPERFAMILY	SSF53335	S-adenosyl-L-methionine-dependent methyltransferases	6	213	2.11E-31	IPR029063
Gene3D	G3DSA:3.40.50.150	Vaccinia Virus protein VP39	19	208	2.9E-59	-
Hamap	MF_03163	AdoMet-dependent rRNA methyltransferase <gene_name> [SPB1].	1	797	19.922939	IPR028589
Hamap	MF_01547	Ribosomal RNA large subunit methyltransferase E [rlmE].	6	202	28.360897	IPR015507
MobiDBLite	mobidb-lite	consensus disorder prediction	454	522	-	-
MobiDBLite	mobidb-lite	consensus disorder prediction	555	569	-	-
MobiDBLite	mobidb-lite	consensus disorder prediction	775	793	-	-
MobiDBLite	mobidb-lite	consensus disorder prediction	586	600	-	-
MobiDBLite	mobidb-lite	consensus disorder prediction	429	446	-	-
MobiDBLite	mobidb-lite	consensus disorder prediction	421	628	-	-
MobiDBLite	mobidb-lite	consensus disorder prediction	774	828	-	-

Gene Ontology

Biological Process:

GO:0001510 (RNA methylation) GO:0006364 (rRNA processing) GO:0031167 (rRNA methylation) GO:0032259 (methylation)

Molecular Function:

GO:0008168 (methyltransferase activity) GO:0008649 (rRNA methyltransferase activity)

Cellular Component:

GO:0005634 (nucleus)

KEGG Pathway

KO Term:

K14857 (AdoMet-dependent rRNA methyltransferase SPB1 [EC:2.1.1.-])

Best hit

Source	Best Hit ID	Description
TAIR	AT4G25730.1	FtsJ-like methyltransferase family protein.
RefSeq	XP_017229343.1	PREDICTED: putative rRNA methyltransferase [Daucus carota subsp. sativus]
Swiss-Prot	O42832	AdoMet-dependent rRNA methyltransferase spb1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=spb1 PE=1 SV=2
TrEMBL	A0A166GFU5	Putative rRNA methyltransferase OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_001567 PE=3 SV=1

Expression

BioProject	Accession	TPM	Cultivar	Tissue	Development Stage	Sample Name	Description
PRJNA723697	SRX10692252	18.867029	Shengqin NO.2	seed	S1-1	S1-1	initial formation stage (S1)
PRJNA723697	SRX10692254	12.777779	Shengqin NO.2	seed	S1-3	S1-3	initial formation stage (S1)
PRJNA723697	SRX10692255	8.794571	Shengqin NO.2	seed	S3-1	S3-1	middle development stage (S3)
PRJNA723697	SRX10692256	11.281262	Shengqin NO.2	seed	S3-2	S3-2	middle development stage (S3)
PRJNA723697	SRX10692257	11.658164	Shengqin NO.2	seed	S3-3	S3-3	middle development stage (S3)
PRJNA723697	SRX10692258	9.727586	Shengqin NO.2	seed	S5-1	S5-1	maturation stage (S5)
PRJNA723697	SRX10692259	11.274405	Shengqin NO.2	seed	S5-2	S5-2	maturation stage (S5)
PRJNA723697	SRX10692260	8.943054	Shengqin NO.2	seed	S5-3	S5-3	maturation stage (S5)
PRJNA884666	SRX17729272	30.792641	celery	anther		W99A-r1	male sterile lineÂ
PRJNA884666	SRX17729273	31.697983	celery	anther		W99A-r2	male sterile lineÂ
PRJNA884666	SRX17729274	36.912704	celery	anther		W99A-r3	male sterile lineÂ
PRJNA884666	SRX17729275	36.299679	celery	anther		W99B-r1	maintainer line
PRJNA884666	SRX17729276	34.988453	celery	anther		W99B-r2	maintainer line
PRJNA884666	SRX17729277	28.0408	celery	anther		W99B-r3	maintainer line
PRJNA884180	SRX17743889	6.458722	var. secalinum Yablochny	collenchyma		Col_S1_rep1-1
PRJNA884180	SRX17748056	10.150012	var. secalinum Yablochny	collenchyma		Col_S1_rep3	biological replicate 3
PRJNA884180	SRX17748057	13.45977	var. secalinum Yablochny	collenchyma		Col_S1_rep4	biological replicate 4
PRJNA884180	SRX17748678	13.490593	var. secalinum Yablochny	parenchyma		Par_S1_rep1	Biological replicate 1
PRJNA884180	SRX17748679	10.914349	var. secalinum Yablochny	parenchyma		Par_S1_rep2	Biological replicate 2
PRJNA884180	SRX17748680	18.794333	var. secalinum Yablochny	parenchyma		Par_S1_rep3	Biological replicate 3
PRJNA884180	SRX17748681	16.084635	var. secalinum Yablochny	parenchyma		Par_S1_rep4	Biological replicate 4
PRJNA884180	SRX17748898	16.017395	var. secalinum Yablochny	vascular bundle		Vas_S1_rep1	Biological replicate 1
PRJNA884180	SRX17748899	21.772171	var. secalinum Yablochny	vascular bundle		Vas_S1_rep2	Biological replicate 2
PRJNA884180	SRX17748900	20.122469	var. secalinum Yablochny	vascular bundle		Vas_S1_rep3	Biological replicate 3
PRJNA884180	SRX17748901	20.327303	var. secalinum Yablochny	vascular bundle		Vas_S1_rep4	Biological replicate 4
PRJNA884180	SRX17749129	18.857649	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep1	Biological replicate 1
PRJNA884180	SRX17749130	16.407192	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep2	Biological replicate 2
PRJNA884180	SRX17749131	14.520179	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep3	Biological replicate 3
PRJNA884180	SRX17749132	19.77265	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep4	Biological replicate 4
PRJNA1124269	SRX24936411	2.588838		leaf		CK1	replicate=biological replicate1
PRJNA1124269	SRX24936412	6.077398		leaf		CK2	replicate=biological replicate2
PRJNA1124269	SRX24936413	5.297919		leaf		CK3	replicate=biological replicate3
PRJNA1124269	SRX24936414	5.890325		leaf		D1	replicate=biological replicate1
PRJNA1124269	SRX24936415	6.577795		leaf		D2	replicate=biological replicate2
PRJNA1124269	SRX24936416	6.508251		leaf		D3	replicate=biological replicate3
PRJNA1124269	SRX24936417	4.713574		leaf		MD1	replicate=biological replicate1
PRJNA1124269	SRX24936418	2.606202		leaf		MD2	replicate=biological replicate2
PRJNA1124269	SRX24936419	3.020743		leaf		MD3	replicate=biological replicate3
PRJNA387092	SRX2833309	13.601161	shanghaihuangxin	leaf	leaves between 0.5 and 1 cm in breadth, folded;	stage 2
PRJNA387092	SRX2833321	8.958341	shanghaihuangxin	leaf	leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion	stage 5
PRJNA387092	SRX2833323	4.632648	shanghaihuangxin	leaf	leaves >3 cm, unfolded, with clearstem extension	stage 7
PRJNA543957	SRX5879598	26.079597	Zhangzhou lvqing	stem		Se3	100 ppm Na2SeO4
PRJNA543957	SRX5879599	11.778059	Zhangzhou lvqing	stem		Se2	100 ppm Na2SeO4
PRJNA543957	SRX5879600	36.892109	Zhangzhou lvqing	stem		Mock2	mock
PRJNA543957	SRX5879601	21.180916	Zhangzhou lvqing	stem		Mock1	mock
PRJNA543957	SRX5879602	33.663109	Zhangzhou lvqing	stem		Se1	100 ppm Na2SeO4
PRJNA543957	SRX5879603	20.656054	Zhangzhou lvqing	stem		Mock3	mock
PRJNA609149	SRX7815917	21.91382	Jinnan Shiqin	flower bud	early flower bud	early flower bud
PRJNA609149	SRX7815918	16.714348	Jinnan Shiqin	flower bud	middle flower bud	middle flower bud
PRJNA609149	SRX7815919	15.268154	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	2	jg26204, jg40568
Aizoaceae	Mesembryanthemum crystallinum	1	gene_7747
Amaranthaceae	Atriplex hortensis	1	Ah028898
Amaranthaceae	Salicornia bigelovii	2	Sbi_jg19526, Sbi_jg44087
Amaranthaceae	Salicornia europaea	1	Seu_jg17885
Amaranthaceae	Suaeda aralocaspica	1	GOSA_00014542
Amaranthaceae	Suaeda glauca	4	Sgl41813, Sgl46611, Sgl51098, Sgl56406
Amaranthaceae	Chenopodium album	8	gene:ENSEOMG00000017896, gene:ENSEOMG00000019354 ... gene:ENSEOMG00000020393, gene:ENSEOMG00000020689, gene:ENSEOMG00000041451, gene:ENSEOMG00000041981, gene:ENSEOMG00000049398, gene:ENSEOMG00000051033
Amaranthaceae	Chenopodium quinoa	3	CQ.Regalona.r1.2AG0010210, CQ.Regalona.r1.2BG0010940 ... CQ.Regalona.r1.7BG0024250
Anacardiaceae	Pistacia vera	2	pistato.v30114880, pistato.v30121440
Apiaceae	Apium graveolens	1	Ag6G02571
Arecaceae	Cocos nucifera	1	COCNU_06G007140
Arecaceae	Phoenix dactylifera	1	gene-LOC103720214
Asparagaceae	Asparagus officinalis	1	AsparagusV1_05.1083.V1.1
Asteraceae	Flaveria trinervia	1	Ftri8G08930
Brassicaceae	Arabidopsis thaliana	1	AT4G25730.1
Brassicaceae	Eutrema salsugineum	1	Thhalv10024417m.g.v1.0
Brassicaceae	Schrenkiella parvula	1	Sp7g23760.v2.2
Brassicaceae	Brassica nigra	2	BniB02g082090.2N, BniB05g055680.2N
Casuarinaceae	Casuarina equisetifolia	1	Ceq09G0160
Casuarinaceae	Casuarina glauca	1	Cgl09G0194
Cymodoceaceae	Cymodocea nodosa	1	gene.Cymno15g05350
Dunaliellaceae	Dunaliella salina	2	Dusal.0355s00010.v1.0, Dusal.0355s00011.v1.0
Hydrocharitaceae	Thalassia testudinum	2	gene.Thate06g10450, gene.Thate08g10880
Malvaceae	Hibiscus hamabo Siebold & Zucc.	1	nbisL1-mrna-9629
Nitrariaceae	Nitraria sibirica	1	evm.TU.LG08.153
Plantaginaceae	Plantago ovata	1	Pov_00005791
Plumbaginaceae	Limonium bicolor	3	Lb3G16704, Lb3G16705, Lb3G17267
Poaceae	Echinochloa crus-galli	3	AH05.1364, BH05.1536, CH05.1738
Poaceae	Eleusine coracana subsp. coracana	2	gene-QOZ80_5AG0362790, gene-QOZ80_5BG0410950
Poaceae	Hordeum vulgare	3	HORVU.MOREX.r3.1HG0079400.1.CDS1 ... HORVU.MOREX.r3.1HG0089590.1, HORVU.MOREX.r3.2HG0201730.1
Poaceae	Lolium multiflorum	9	gene-QYE76_007213, gene-QYE76_007214, gene-QYE76_007217 ... gene-QYE76_007225, gene-QYE76_015335, gene-QYE76_015441, gene-QYE76_015770, gene-QYE76_062010, gene-QYE76_071904
Poaceae	Oryza coarctata	2	Oco09G017000, Oco10G016910
Poaceae	Oryza sativa	3	LOC_Os05g49230.1, LOC_Os09g27270.1, LOC_Os10g42404.1
Poaceae	Paspalum vaginatum	1	gene-BS78_09G238900
Poaceae	Puccinellia tenuiflora	3	Pt_Chr0502978, Pt_Chr0505637, Pt_Chr0700738
Poaceae	Sporobolus alterniflorus	4	Chr01G015760, Chr12G020970, Chr18G016750, Chr22G001030
Poaceae	Thinopyrum elongatum	6	Tel1E01G597500, Tel1E01G597800, Tel1E01G597900 ... Tel1E01G598300, Tel1E01G676000, Tel5E01G561100
Poaceae	Triticum dicoccoides	7	gene_TRIDC1AG053970, gene_TRIDC1AG059670 ... gene_TRIDC1BG061800, gene_TRIDC1BG068120, gene_TRIDC5BG075940, gene_TRIDC7AG060140, gene_TRIDC7BG052990
Poaceae	Triticum aestivum	8	TraesCS1A02G404700.1, TraesCS1B02G434500.1 ... TraesCS1D02G373100.1.cds1, TraesCS1D02G373400.1, TraesCS1D02G412700.1, TraesCS7A02G430800.3, TraesCS7B02G331000.1, TraesCS7D02G422700.3
Poaceae	Zea mays	2	Zm00001eb296160_P001, Zm00001eb343980_P001
Poaceae	Zoysia japonica	1	nbis-gene-13631
Poaceae	Zoysia macrostachya	1	Zma_g27400
Portulacaceae	Portulaca oleracea	2	evm.TU.LG04.2508, evm.TU.LG08.176
Posidoniaceae	Posidonia oceanica	2	gene.Posoc03g13900, gene.Posoc07g09810
Rhizophoraceae	Bruguiera sexangula	1	evm.TU.Scaffold_1_RagTag.2259
Rhizophoraceae	Ceriops tagal	1	nbisL1-mrna-14085
Rhizophoraceae	Ceriops zippeliana	1	nbisL1-mrna-3293
Rhizophoraceae	Kandelia candel	1	evm.TU.utg000016l.105
Rhizophoraceae	Kandelia obovata	1	Maker00016388
Rhizophoraceae	Rhizophora apiculata	1	nbisL1-mrna-4664
Rhizophoraceae	Rhizophora mangle	1	nbisL1-mrna-22404
Salicaceae	Populus euphratica	1	populus_peu36497
Solanaceae	Lycium barbarum	1	gene-LOC132626953
Solanaceae	Solanum chilense	1	SOLCI003696800
Solanaceae	Solanum pennellii	3	gene-LOC107002312, gene-LOC107002354, gene-LOC107004744
Tamaricaceae	Reaumuria soongarica	1	gene_7833
Tamaricaceae	Tamarix chinensis	1	TC10G0458
Zosteraceae	Zostera marina	2	Zosma04g24150.v3.1, Zosma04g24180.v3.1