halophFGD

Basic Information

Locus ID: Ag11G04616

Species & Taxonomic ID: Apium graveolens & 4045

Genome Assembly: GCA_009905375.1

Description: U3 small nucleolar RNA-associated protein

Maps and Mapping Data

Chromosome	Start	End	Strand	ID
chr11	188945587	188950842	-	Ag11G04616

Protein Data

Protein Properties:

Theoretical pI	Molecular Weight	Instability Index	Aliphatic Index	GRAVY
9.56	58,089.51 Da	33.80	85.18	-0.24

Protein Domain:

Category	ID	Description	Start	End	Evalue/Score	InterPro ID
CDD	cd00200	WD40	44	331	5.77424E-44	-
Pfam	PF09384	UTP15 C terminal	379	519	1.2E-32	IPR018983
Pfam	PF00400	WD domain, G-beta repeat	218	246	0.21	IPR001680
Pfam	PF00400	WD domain, G-beta repeat	125	161	0.14	IPR001680
Pfam	PF00400	WD domain, G-beta repeat	168	204	0.0078	IPR001680
SUPERFAMILY	SSF50978	WD40 repeat-like	48	337	6.23E-55	IPR036322
Gene3D	G3DSA:2.130.10.10	-	213	336	2.8E-13	IPR015943
Gene3D	G3DSA:2.130.10.10	-	29	212	1.8E-35	IPR015943
SMART	SM00320	WD40_4	79	118	0.0013	IPR001680
SMART	SM00320	WD40_4	40	76	7.6	IPR001680
SMART	SM00320	WD40_4	209	246	0.0052	IPR001680
SMART	SM00320	WD40_4	164	204	2.1E-6	IPR001680
SMART	SM00320	WD40_4	250	298	0.1	IPR001680
SMART	SM00320	WD40_4	121	161	0.0011	IPR001680
ProSiteProfiles	PS50082	Trp-Asp (WD) repeats profile.	171	213	12.112524	IPR001680
ProSiteProfiles	PS50294	Trp-Asp (WD) repeats circular profile.	128	164	8.518333	-
ProSiteProfiles	PS50082	Trp-Asp (WD) repeats profile.	128	170	10.70896	IPR001680
ProSiteProfiles	PS50294	Trp-Asp (WD) repeats circular profile.	171	206	9.941962	-
PRINTS	PR00320	G protein beta WD-40 repeat signature	191	205	4.1E-5	IPR020472
PRINTS	PR00320	G protein beta WD-40 repeat signature	233	247	4.1E-5	IPR020472
PRINTS	PR00320	G protein beta WD-40 repeat signature	148	162	4.1E-5	IPR020472
MobiDBLite	mobidb-lite	consensus disorder prediction	1	32	-	-

Gene Ontology

Biological Process:

GO:0006364 (rRNA processing)

Molecular Function:

GO:0005515 (protein binding)

Cellular Component:

GO:0005730 (nucleolus)

KEGG Pathway

KO Term:

K14549 (U3 small nucleolar RNA-associated protein 15)

Pathway:

ko03008 (Ribosome biogenesis in eukaryotes) map03008 (Ribosome biogenesis in eukaryotes)

Best hit

Source	Best Hit ID	Description
TAIR	AT2G47990.1	transducin family protein / WD-40 repeat family protein. Encodes a transducin family nucleolar protein with six WD40 repeats that is most likely involved in 18S rRNA biogenesis. The slow progression of the gametophytic division cycles in swa1 suggested that the SWA1 protein is required for the normal progression of mitotic division cycles through the regulation of cell metabolism. Ubiquitously expressed throughout the plant.
RefSeq	XP_017252301.1	PREDICTED: protein SLOW WALKER 1 [Daucus carota subsp. sativus]
Swiss-Prot	O82266	Protein SLOW WALKER 1 OS=Arabidopsis thaliana OX=3702 GN=SWA1 PE=2 SV=1
TrEMBL	A0A161YMZ3	UTP15_C domain-containing protein OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_018371 PE=4 SV=1

Expression

BioProject	Accession	TPM	Cultivar	Tissue	Development Stage	Sample Name	Description
PRJNA723697	SRX10692252	16.941271	Shengqin NO.2	seed	S1-1	S1-1	initial formation stage (S1)
PRJNA723697	SRX10692254	10.325122	Shengqin NO.2	seed	S1-3	S1-3	initial formation stage (S1)
PRJNA723697	SRX10692255	9.78004	Shengqin NO.2	seed	S3-1	S3-1	middle development stage (S3)
PRJNA723697	SRX10692256	13.148544	Shengqin NO.2	seed	S3-2	S3-2	middle development stage (S3)
PRJNA723697	SRX10692257	13.12062	Shengqin NO.2	seed	S3-3	S3-3	middle development stage (S3)
PRJNA723697	SRX10692258	16.772598	Shengqin NO.2	seed	S5-1	S5-1	maturation stage (S5)
PRJNA723697	SRX10692259	11.947455	Shengqin NO.2	seed	S5-2	S5-2	maturation stage (S5)
PRJNA723697	SRX10692260	11.811652	Shengqin NO.2	seed	S5-3	S5-3	maturation stage (S5)
PRJNA884666	SRX17729272	15.811896	celery	anther		W99A-r1	male sterile lineÂ
PRJNA884666	SRX17729273	18.230383	celery	anther		W99A-r2	male sterile lineÂ
PRJNA884666	SRX17729274	21.201088	celery	anther		W99A-r3	male sterile lineÂ
PRJNA884666	SRX17729275	22.666325	celery	anther		W99B-r1	maintainer line
PRJNA884666	SRX17729276	19.745857	celery	anther		W99B-r2	maintainer line
PRJNA884666	SRX17729277	17.548237	celery	anther		W99B-r3	maintainer line
PRJNA884180	SRX17743889	4.313314	var. secalinum Yablochny	collenchyma		Col_S1_rep1-1
PRJNA884180	SRX17748056	5.618744	var. secalinum Yablochny	collenchyma		Col_S1_rep3	biological replicate 3
PRJNA884180	SRX17748057	6.18136	var. secalinum Yablochny	collenchyma		Col_S1_rep4	biological replicate 4
PRJNA884180	SRX17748678	10.036191	var. secalinum Yablochny	parenchyma		Par_S1_rep1	Biological replicate 1
PRJNA884180	SRX17748679	8.483635	var. secalinum Yablochny	parenchyma		Par_S1_rep2	Biological replicate 2
PRJNA884180	SRX17748680	16.341757	var. secalinum Yablochny	parenchyma		Par_S1_rep3	Biological replicate 3
PRJNA884180	SRX17748681	15.306135	var. secalinum Yablochny	parenchyma		Par_S1_rep4	Biological replicate 4
PRJNA884180	SRX17748898	13.033305	var. secalinum Yablochny	vascular bundle		Vas_S1_rep1	Biological replicate 1
PRJNA884180	SRX17748899	13.302052	var. secalinum Yablochny	vascular bundle		Vas_S1_rep2	Biological replicate 2
PRJNA884180	SRX17748900	13.545983	var. secalinum Yablochny	vascular bundle		Vas_S1_rep3	Biological replicate 3
PRJNA884180	SRX17748901	14.712934	var. secalinum Yablochny	vascular bundle		Vas_S1_rep4	Biological replicate 4
PRJNA884180	SRX17749129	10.597593	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep1	Biological replicate 1
PRJNA884180	SRX17749130	11.989047	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep2	Biological replicate 2
PRJNA884180	SRX17749131	10.9628	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep3	Biological replicate 3
PRJNA884180	SRX17749132	11.95411	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep4	Biological replicate 4
PRJNA1124269	SRX24936411	7.349085		leaf		CK1	replicate=biological replicate1
PRJNA1124269	SRX24936412	12.744811		leaf		CK2	replicate=biological replicate2
PRJNA1124269	SRX24936413	12.504771		leaf		CK3	replicate=biological replicate3
PRJNA1124269	SRX24936414	34.864124		leaf		D1	replicate=biological replicate1
PRJNA1124269	SRX24936415	19.707457		leaf		D2	replicate=biological replicate2
PRJNA1124269	SRX24936416	26.611603		leaf		D3	replicate=biological replicate3
PRJNA1124269	SRX24936417	19.726761		leaf		MD1	replicate=biological replicate1
PRJNA1124269	SRX24936418	14.533313		leaf		MD2	replicate=biological replicate2
PRJNA1124269	SRX24936419	14.392512		leaf		MD3	replicate=biological replicate3
PRJNA387092	SRX2833309	10.82022	shanghaihuangxin	leaf	leaves between 0.5 and 1 cm in breadth, folded;	stage 2
PRJNA387092	SRX2833321	9.002373	shanghaihuangxin	leaf	leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion	stage 5
PRJNA387092	SRX2833323	2.456592	shanghaihuangxin	leaf	leaves >3 cm, unfolded, with clearstem extension	stage 7
PRJNA543957	SRX5879598	17.785961	Zhangzhou lvqing	stem		Se3	100 ppm Na2SeO4
PRJNA543957	SRX5879599	21.448793	Zhangzhou lvqing	stem		Se2	100 ppm Na2SeO4
PRJNA543957	SRX5879600	54.30505	Zhangzhou lvqing	stem		Mock2	mock
PRJNA543957	SRX5879601	30.448078	Zhangzhou lvqing	stem		Mock1	mock
PRJNA543957	SRX5879602	28.418022	Zhangzhou lvqing	stem		Se1	100 ppm Na2SeO4
PRJNA543957	SRX5879603	16.318911	Zhangzhou lvqing	stem		Mock3	mock
PRJNA609149	SRX7815917	15.973674	Jinnan Shiqin	flower bud	early flower bud	early flower bud
PRJNA609149	SRX7815918	16.238928	Jinnan Shiqin	flower bud	middle flower bud	middle flower bud
PRJNA609149	SRX7815919	17.081654	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	jg37905, jg37908
Aizoaceae	Mesembryanthemum crystallinum	1	gene_11643
Amaranthaceae	Atriplex hortensis	1	Ah022014
Amaranthaceae	Salicornia bigelovii	2	Sbi_jg1521, Sbi_jg35029
Amaranthaceae	Salicornia europaea	1	Seu_jg3224
Amaranthaceae	Suaeda aralocaspica	1	GOSA_00011943
Amaranthaceae	Suaeda glauca	2	Sgl73790, Sgl77295
Amaranthaceae	Chenopodium album	3	gene:ENSEOMG00000014984, gene:ENSEOMG00000018428 ... gene:ENSEOMG00000049350
Amaranthaceae	Chenopodium quinoa	2	CQ.Regalona.r1.2AG0008420, CQ.Regalona.r1.2BG0009330
Apiaceae	Apium graveolens	1	Ag11G04616
Arecaceae	Cocos nucifera	1	COCNU_04G005230
Arecaceae	Phoenix dactylifera	1	gene-LOC103709103
Asparagaceae	Asparagus officinalis	1	AsparagusV1_10.686.V1.1
Asteraceae	Flaveria trinervia	2	Ftri11G26437, Ftri12G11476
Brassicaceae	Arabidopsis thaliana	1	AT2G47990.1
Brassicaceae	Eutrema salsugineum	1	Thhalv10001392m.g.v1.0
Brassicaceae	Schrenkiella parvula	1	Sp4g29910.v2.2
Brassicaceae	Brassica nigra	2	BniB01g000180.2N, BniS05187g230.2N
Cymodoceaceae	Cymodocea nodosa	1	gene.Cymno05g14080
Dunaliellaceae	Dunaliella salina	2	Dusal.0343s00018.v1.0, Dusal.0343s00019.v1.0
Hydrocharitaceae	Thalassia testudinum	2	gene.Thate04g27080, gene.Thate06g05810
Malvaceae	Hibiscus hamabo Siebold & Zucc.	1	nbisL1-mrna-2599
Nitrariaceae	Nitraria sibirica	1	evm.TU.LG04.251
Plantaginaceae	Plantago ovata	1	Pov_00008191
Poaceae	Echinochloa crus-galli	3	AH03.624, BH03.754, CH03.847
Poaceae	Eleusine coracana subsp. coracana	2	gene-QOZ80_3AG0249400, gene-QOZ80_3BG0278810
Poaceae	Hordeum vulgare	1	HORVU.MOREX.r3.7HG0747280.1.CDS1
Poaceae	Lolium multiflorum	3	gene-QYE76_000111, gene-QYE76_042092, gene-QYE76_042973
Poaceae	Oryza coarctata	2	Oco13G004000, Oco14G004460
Poaceae	Oryza sativa	1	LOC_Os07g12320.1
Poaceae	Paspalum vaginatum	1	gene-BS78_06G219000
Poaceae	Sporobolus alterniflorus	4	Chr01G035260, Chr04G011990, Chr12G004340, Chr13G012160
Poaceae	Thinopyrum elongatum	2	Tel1E01G698200, Tel7E01G931100
Poaceae	Triticum dicoccoides	2	gene_TRIDC7AG074480, gene_TRIDC7BG070780
Poaceae	Triticum aestivum	3	TraesCS7A02G534500.1.cds1, TraesCS7B02G451600.1.cds1 ... TraesCS7D02G521800.1.cds1
Poaceae	Zea mays	1	Zm00001eb303580_P001
Poaceae	Zoysia japonica	1	nbis-gene-49982
Poaceae	Zoysia macrostachya	1	Zma_g3585
Portulacaceae	Portulaca oleracea	2	evm.TU.LG06.1518, evm.TU.LG22.1193
Posidoniaceae	Posidonia oceanica	2	gene.Posoc01g29740, gene.Posoc04g16550
Rhizophoraceae	Bruguiera sexangula	1	evm.TU.Scaffold_5_RagTag.921
Rhizophoraceae	Carallia pectinifolia	1	nbisL1-mrna-11422
Rhizophoraceae	Ceriops tagal	1	nbisL1-mrna-7727
Rhizophoraceae	Ceriops zippeliana	1	nbisL1-mrna-11541
Rhizophoraceae	Kandelia candel	1	add.evm.TU.utg000006l.97
Rhizophoraceae	Kandelia obovata	1	Maker00013836
Rhizophoraceae	Rhizophora apiculata	1	nbisL1-mrna-20729
Rhizophoraceae	Rhizophora mangle	1	nbisL1-mrna-7537
Salicaceae	Populus euphratica	3	populus_peu01093, populus_peu27190, populus_peu37847
Solanaceae	Lycium barbarum	1	gene-LOC132609293
Solanaceae	Solanum chilense	1	SOLCI004455100
Solanaceae	Solanum pennellii	1	gene-LOC107019796
Tamaricaceae	Reaumuria soongarica	1	gene_11921
Tamaricaceae	Tamarix chinensis	1	TC05G2052
Zosteraceae	Zostera marina	1	Zosma03g30380.v3.1