halophFGD

Basic Information

Locus ID: Ag8G00829

Species & Taxonomic ID: Apium graveolens & 4045

Genome Assembly: GCA_009905375.1

Description: RimM N-terminal domain

Maps and Mapping Data

Chromosome	Start	End	Strand	ID
chr8	67006329	67013987	-	Ag8G00829

Protein Data

Protein Properties:

Theoretical pI	Molecular Weight	Instability Index	Aliphatic Index	GRAVY
5.82	74,492.89 Da	45.93	85.89	-0.35

Protein Domain:

Category	ID	Description	Start	End	Evalue/Score	InterPro ID
Pfam	PF01782	RimM N-terminal domain	86	175	1.8E-20	IPR002676
Pfam	PF05239	PRC-barrel domain	182	275	1.5E-9	IPR027275
SUPERFAMILY	SSF50447	Translation proteins	84	178	2.47E-13	IPR009000
SUPERFAMILY	SSF53448	Nucleotide-diphospho-sugar transferases	305	660	3.94E-34	IPR029044
SUPERFAMILY	SSF50346	PRC-barrel domain	185	274	6.67E-11	IPR011033
Gene3D	G3DSA:2.30.30.240	-	180	279	3.3E-23	-
Gene3D	G3DSA:2.40.30.60	RimM	75	178	2.4E-19	IPR036976
Gene3D	G3DSA:3.90.550.10	Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A	300	662	4.6E-33	IPR029044
TIGRFAM	TIGR02273	16S_RimM: 16S rRNA processing protein RimM	85	274	8.2E-36	IPR011961
Hamap	MF_00014	Ribosome maturation factor RimM [rimM].	84	274	22.570538	IPR011961
Coils	Coil	Coil	297	317	-	-

Gene Ontology

Biological Process:

GO:0006364 (rRNA processing)

Molecular Function:

GO:0043022 (ribosome binding)

Cellular Component:

GO:0005840 (ribosome)

KEGG Pathway

KO Term:

K00972 (UDP-N-acetylglucosamine/UDP-N-acetylgalactosamine diphosphorylase [EC:2.7.7.23 2.7.7.83])

Pathway:

ko00520 (Amino sugar and nucleotide sugar metabolism) map00520 (Amino sugar and nucleotide sugar metabolism) ko01100 (Metabolic pathways) map01100 (Metabolic pathways)

Reaction:

R00416 (UTP + N-Acetyl-alpha-D-glucosamine 1-phosphate <=> Diphosphate + UDP-N-acetyl-alpha-D-glucosamine)

Best hit

Source	Best Hit ID	Description
TAIR	AT5G46420.1	16S rRNA processing protein RimM family.
RefSeq	XP_017223690.1	PREDICTED: uncharacterized protein LOC108200124 [Daucus carota subsp. sativus]
Swiss-Prot	Q0IDP0	Ribosome maturation factor RimM OS=Synechococcus sp. (strain CC9311) OX=64471 GN=rimM PE=3 SV=1
TrEMBL	A0A175YM02	Ribosome maturation factor RimM OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_027959 PE=3 SV=1

Expression

BioProject	Accession	TPM	Cultivar	Tissue	Development Stage	Sample Name	Description
PRJNA723697	SRX10692252	36.858772	Shengqin NO.2	seed	S1-1	S1-1	initial formation stage (S1)
PRJNA723697	SRX10692254	27.109781	Shengqin NO.2	seed	S1-3	S1-3	initial formation stage (S1)
PRJNA723697	SRX10692255	24.389875	Shengqin NO.2	seed	S3-1	S3-1	middle development stage (S3)
PRJNA723697	SRX10692256	26.635786	Shengqin NO.2	seed	S3-2	S3-2	middle development stage (S3)
PRJNA723697	SRX10692257	27.931355	Shengqin NO.2	seed	S3-3	S3-3	middle development stage (S3)
PRJNA723697	SRX10692258	34.485039	Shengqin NO.2	seed	S5-1	S5-1	maturation stage (S5)
PRJNA723697	SRX10692259	23.303104	Shengqin NO.2	seed	S5-2	S5-2	maturation stage (S5)
PRJNA723697	SRX10692260	16.035069	Shengqin NO.2	seed	S5-3	S5-3	maturation stage (S5)
PRJNA884666	SRX17729272	46.133774	celery	anther		W99A-r1	male sterile lineÂ
PRJNA884666	SRX17729273	43.006626	celery	anther		W99A-r2	male sterile lineÂ
PRJNA884666	SRX17729274	49.317818	celery	anther		W99A-r3	male sterile lineÂ
PRJNA884666	SRX17729275	48.637531	celery	anther		W99B-r1	maintainer line
PRJNA884666	SRX17729276	48.991535	celery	anther		W99B-r2	maintainer line
PRJNA884666	SRX17729277	37.804672	celery	anther		W99B-r3	maintainer line
PRJNA884180	SRX17743889	23.949331	var. secalinum Yablochny	collenchyma		Col_S1_rep1-1
PRJNA884180	SRX17748056	20.179117	var. secalinum Yablochny	collenchyma		Col_S1_rep3	biological replicate 3
PRJNA884180	SRX17748057	24.152826	var. secalinum Yablochny	collenchyma		Col_S1_rep4	biological replicate 4
PRJNA884180	SRX17748678	34.95636	var. secalinum Yablochny	parenchyma		Par_S1_rep1	Biological replicate 1
PRJNA884180	SRX17748679	47.519928	var. secalinum Yablochny	parenchyma		Par_S1_rep2	Biological replicate 2
PRJNA884180	SRX17748680	23.822531	var. secalinum Yablochny	parenchyma		Par_S1_rep3	Biological replicate 3
PRJNA884180	SRX17748681	30.154297	var. secalinum Yablochny	parenchyma		Par_S1_rep4	Biological replicate 4
PRJNA884180	SRX17748898	16.999531	var. secalinum Yablochny	vascular bundle		Vas_S1_rep1	Biological replicate 1
PRJNA884180	SRX17748899	19.009285	var. secalinum Yablochny	vascular bundle		Vas_S1_rep2	Biological replicate 2
PRJNA884180	SRX17748900	19.783699	var. secalinum Yablochny	vascular bundle		Vas_S1_rep3	Biological replicate 3
PRJNA884180	SRX17748901	22.58242	var. secalinum Yablochny	vascular bundle		Vas_S1_rep4	Biological replicate 4
PRJNA884180	SRX17749129	43.003925	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep1	Biological replicate 1
PRJNA884180	SRX17749130	29.770613	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep2	Biological replicate 2
PRJNA884180	SRX17749131	39.242455	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep3	Biological replicate 3
PRJNA884180	SRX17749132	31.351957	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep4	Biological replicate 4
PRJNA1124269	SRX24936411	23.489925		leaf		CK1	replicate=biological replicate1
PRJNA1124269	SRX24936412	44.055763		leaf		CK2	replicate=biological replicate2
PRJNA1124269	SRX24936413	31.636286		leaf		CK3	replicate=biological replicate3
PRJNA1124269	SRX24936414	26.773291		leaf		D1	replicate=biological replicate1
PRJNA1124269	SRX24936415	19.363344		leaf		D2	replicate=biological replicate2
PRJNA1124269	SRX24936416	29.161203		leaf		D3	replicate=biological replicate3
PRJNA1124269	SRX24936417	34.511257		leaf		MD1	replicate=biological replicate1
PRJNA1124269	SRX24936418	19.072062		leaf		MD2	replicate=biological replicate2
PRJNA1124269	SRX24936419	21.653948		leaf		MD3	replicate=biological replicate3
PRJNA387092	SRX2833309	87.695641	shanghaihuangxin	leaf	leaves between 0.5 and 1 cm in breadth, folded;	stage 2
PRJNA387092	SRX2833321	65.045486	shanghaihuangxin	leaf	leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion	stage 5
PRJNA387092	SRX2833323	103.377792	shanghaihuangxin	leaf	leaves >3 cm, unfolded, with clearstem extension	stage 7
PRJNA543957	SRX5879598	10.899817	Zhangzhou lvqing	stem		Se3	100 ppm Na2SeO4
PRJNA543957	SRX5879599	22.559118	Zhangzhou lvqing	stem		Se2	100 ppm Na2SeO4
PRJNA543957	SRX5879600	59.122158	Zhangzhou lvqing	stem		Mock2	mock
PRJNA543957	SRX5879601	55.085228	Zhangzhou lvqing	stem		Mock1	mock
PRJNA543957	SRX5879602	12.261943	Zhangzhou lvqing	stem		Se1	100 ppm Na2SeO4
PRJNA543957	SRX5879603	53.270672	Zhangzhou lvqing	stem		Mock3	mock
PRJNA609149	SRX7815917	40.110214	Jinnan Shiqin	flower bud	early flower bud	early flower bud
PRJNA609149	SRX7815918	39.092461	Jinnan Shiqin	flower bud	middle flower bud	middle flower bud
PRJNA609149	SRX7815919	34.838478	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	jg20707
Aizoaceae	Mesembryanthemum crystallinum	1	gene_519
Amaranthaceae	Atriplex hortensis	1	Ah016669
Amaranthaceae	Salicornia bigelovii	2	Sbi_jg40519, Sbi_jg50559
Amaranthaceae	Salicornia europaea	1	Seu_jg2118
Amaranthaceae	Suaeda aralocaspica	1	GOSA_00018049
Amaranthaceae	Suaeda glauca	2	Sgl45277, Sgl50060
Amaranthaceae	Chenopodium album	3	gene:ENSEOMG00000010540, gene:ENSEOMG00000034376 ... gene:ENSEOMG00000046963
Amaranthaceae	Chenopodium quinoa	2	CQ.Regalona.r1.8AG0008460, CQ.Regalona.r1.8BG0009450
Anacardiaceae	Pistacia vera	2	pistato.v30070640, pistato.v30281860
Apiaceae	Apium graveolens	1	Ag8G00829
Arecaceae	Cocos nucifera	1	COCNU_06G006870
Arecaceae	Phoenix dactylifera	1	gene-LOC103712681
Asparagaceae	Asparagus officinalis	1	AsparagusV1_01.3627.V1.1
Asteraceae	Flaveria trinervia	1	Ftri15G06941
Brassicaceae	Arabidopsis thaliana	1	AT5G46420.1
Brassicaceae	Eutrema salsugineum	1	Thhalv10000812m.g.v1.0
Brassicaceae	Schrenkiella parvula	1	Sp2g11270.v2.2
Brassicaceae	Brassica nigra	1	BniB02g063180.2N
Casuarinaceae	Casuarina glauca	1	Cgl04G0498
Cymodoceaceae	Cymodocea nodosa	1	gene.Cymno07g07440
Dunaliellaceae	Dunaliella salina	1	Dusal.0371s00015.v1.0
Hydrocharitaceae	Thalassia testudinum	1	gene.Thate07g21110
Nitrariaceae	Nitraria sibirica	1	evm.TU.LG12.708
Plantaginaceae	Plantago ovata	1	Pov_00038419
Plumbaginaceae	Limonium bicolor	1	Lb4G25000
Poaceae	Echinochloa crus-galli	3	AH05.1380, BH05.1550, CH05.1749
Poaceae	Eleusine coracana subsp. coracana	2	gene-QOZ80_5AG0363000, gene-QOZ80_5BG0411040
Poaceae	Hordeum vulgare	1	HORVU.MOREX.r3.1HG0089000.1
Poaceae	Lolium multiflorum	1	gene-QYE76_015485
Poaceae	Oryza coarctata	2	Oco09G016940, Oco10G016780
Poaceae	Oryza sativa	1	LOC_Os05g49130.1
Poaceae	Paspalum vaginatum	1	gene-BS78_09G237100
Poaceae	Puccinellia tenuiflora	2	Pt_Chr0202779, Pt_Chr0505707
Poaceae	Sporobolus alterniflorus	3	Chr01G015710, Chr12G021060, Chr22G001130
Poaceae	Thinopyrum elongatum	1	Tel1E01G665300
Poaceae	Triticum dicoccoides	2	gene_TRIDC1AG059320, gene_TRIDC1BG068030
Poaceae	Triticum aestivum	3	TraesCS1A02G402100.1, TraesCS1B02G431200.1 ... TraesCS1D02G409700.1
Poaceae	Zea mays	4	Zm00001eb184690_P001, Zm00001eb296050_P001 ... Zm00001eb330860_P001, Zm00001eb349440_P001
Poaceae	Zoysia japonica	1	nbis-gene-24839
Poaceae	Zoysia macrostachya	1	Zma_g28813
Portulacaceae	Portulaca oleracea	2	evm.TU.LG03.1903, evm.TU.LG14.201
Posidoniaceae	Posidonia oceanica	1	gene.Posoc04g21500
Rhizophoraceae	Bruguiera sexangula	2	evm.TU.Scaffold_14_RagTag.855, evm.TU.Scaffold_14_RagTag.857
Rhizophoraceae	Carallia pectinifolia	1	nbisL1-mrna-16615
Rhizophoraceae	Ceriops tagal	1	nbisL1-mrna-5488
Rhizophoraceae	Ceriops zippeliana	1	nbisL1-mrna-17179
Rhizophoraceae	Kandelia candel	1	evm.TU.utg000025l.67
Rhizophoraceae	Kandelia obovata	1	Maker00012233
Rhizophoraceae	Rhizophora apiculata	1	nbisL1-mrna-15913
Rhizophoraceae	Rhizophora mangle	1	nbisL1-mrna-11075
Salicaceae	Populus euphratica	1	populus_peu00971
Solanaceae	Lycium barbarum	1	gene-LOC132621541
Solanaceae	Solanum chilense	1	SOLCI004243100
Solanaceae	Solanum pennellii	1	gene-LOC107010044
Tamaricaceae	Reaumuria soongarica	1	STRG.18336_chr09_+
Tamaricaceae	Tamarix chinensis	1	TC07G1865
Zosteraceae	Zostera marina	1	Zosma01g37250.v3.1