halophFGD

Basic Information

Locus ID: Ag10G00540

Species & Taxonomic ID: Apium graveolens & 4045

Genome Assembly: GCA_009905375.1

Description: RNA binding (RRM RBD RNP motifs) family protein

Maps and Mapping Data

Chromosome	Start	End	Strand	ID
chr10	111146434	111156643	-	Ag10G00540

Protein Data

Protein Properties:

Theoretical pI	Molecular Weight	Instability Index	Aliphatic Index	GRAVY
6.34	110,352.96 Da	50.79	66.46	-0.65

Protein Domain:

Category	ID	Description	Start	End	Evalue/Score	InterPro ID
CDD	cd12438	RRM_CNOT4	104	203	5.02863E-48	IPR034261
CDD	cd16618	mRING-HC-C4C4_CNOT4	9	58	2.8632E-22	IPR039515
Pfam	PF14570	RING/Ubox like zinc-binding domain	9	61	7.4E-20	-
Pfam	PF00076	RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)	111	189	4.9E-6	IPR000504
SUPERFAMILY	SSF57850	RING/U-box	4	67	7.85E-14	-
SUPERFAMILY	SSF54928	RNA-binding domain, RBD	103	189	5.24E-14	IPR035979
Gene3D	G3DSA:3.30.40.10	Zinc/RING finger domain, C3HC4 (zinc finger)	1	77	2.8E-24	IPR013083
Gene3D	G3DSA:3.30.70.330	-	110	191	5.7E-25	IPR012677
SMART	SM00361	rrm2_1	110	191	4.0E-9	IPR003954
SMART	SM00360	rrm1_1	110	191	1.6E-4	IPR000504
ProSiteProfiles	PS50089	Zinc finger RING-type profile.	9	57	9.509172	IPR001841
ProSiteProfiles	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	109	195	11.110626	IPR000504
MobiDBLite	mobidb-lite	consensus disorder prediction	502	518	-	-
MobiDBLite	mobidb-lite	consensus disorder prediction	328	353	-	-
MobiDBLite	mobidb-lite	consensus disorder prediction	494	523	-	-

Gene Ontology

Molecular Function:

GO:0003676 (nucleic acid binding)

KEGG Pathway

KO Term:

K10643 (CCR4-NOT transcription complex subunit 4 [EC:2.3.2.27])

Pathway:

ko03018 (RNA degradation) map03018 (RNA degradation)

Best hit

Source	Best Hit ID	Description
TAIR	AT3G45630.1	RNA binding (RRM/RBD/RNP motifs) family protein.
RefSeq	XP_017247294.1	PREDICTED: uncharacterized protein LOC108218725 isoform X1 [Daucus carota subsp. sativus]
Swiss-Prot	Q09818	Putative general negative regulator of transcription C16C9.04c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=SPAC16C9.04c PE=3 SV=1
TrEMBL	A0A162A8K3	CCR4-NOT transcription complex subunit 4 OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_015568 PE=4 SV=1

Expression

BioProject	Accession	TPM	Cultivar	Tissue	Development Stage	Sample Name	Description
PRJNA723697	SRX10692252	27.518465	Shengqin NO.2	seed	S1-1	S1-1	initial formation stage (S1)
PRJNA723697	SRX10692254	17.685061	Shengqin NO.2	seed	S1-3	S1-3	initial formation stage (S1)
PRJNA723697	SRX10692255	19.850811	Shengqin NO.2	seed	S3-1	S3-1	middle development stage (S3)
PRJNA723697	SRX10692256	21.406725	Shengqin NO.2	seed	S3-2	S3-2	middle development stage (S3)
PRJNA723697	SRX10692257	21.458536	Shengqin NO.2	seed	S3-3	S3-3	middle development stage (S3)
PRJNA723697	SRX10692258	22.399927	Shengqin NO.2	seed	S5-1	S5-1	maturation stage (S5)
PRJNA723697	SRX10692259	20.700567	Shengqin NO.2	seed	S5-2	S5-2	maturation stage (S5)
PRJNA723697	SRX10692260	17.026514	Shengqin NO.2	seed	S5-3	S5-3	maturation stage (S5)
PRJNA884666	SRX17729272	22.728237	celery	anther		W99A-r1	male sterile lineÂ
PRJNA884666	SRX17729273	22.391212	celery	anther		W99A-r2	male sterile lineÂ
PRJNA884666	SRX17729274	25.064627	celery	anther		W99A-r3	male sterile lineÂ
PRJNA884666	SRX17729275	24.436337	celery	anther		W99B-r1	maintainer line
PRJNA884666	SRX17729276	24.822762	celery	anther		W99B-r2	maintainer line
PRJNA884666	SRX17729277	19.222761	celery	anther		W99B-r3	maintainer line
PRJNA884180	SRX17743889	21.866165	var. secalinum Yablochny	collenchyma		Col_S1_rep1-1
PRJNA884180	SRX17748056	18.93128	var. secalinum Yablochny	collenchyma		Col_S1_rep3	biological replicate 3
PRJNA884180	SRX17748057	19.490767	var. secalinum Yablochny	collenchyma		Col_S1_rep4	biological replicate 4
PRJNA884180	SRX17748678	20.027449	var. secalinum Yablochny	parenchyma		Par_S1_rep1	Biological replicate 1
PRJNA884180	SRX17748679	13.323387	var. secalinum Yablochny	parenchyma		Par_S1_rep2	Biological replicate 2
PRJNA884180	SRX17748680	20.655727	var. secalinum Yablochny	parenchyma		Par_S1_rep3	Biological replicate 3
PRJNA884180	SRX17748681	24.713476	var. secalinum Yablochny	parenchyma		Par_S1_rep4	Biological replicate 4
PRJNA884180	SRX17748898	23.645561	var. secalinum Yablochny	vascular bundle		Vas_S1_rep1	Biological replicate 1
PRJNA884180	SRX17748899	22.455482	var. secalinum Yablochny	vascular bundle		Vas_S1_rep2	Biological replicate 2
PRJNA884180	SRX17748900	18.815359	var. secalinum Yablochny	vascular bundle		Vas_S1_rep3	Biological replicate 3
PRJNA884180	SRX17748901	21.59791	var. secalinum Yablochny	vascular bundle		Vas_S1_rep4	Biological replicate 4
PRJNA884180	SRX17749129	22.898842	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep1	Biological replicate 1
PRJNA884180	SRX17749130	16.260162	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep2	Biological replicate 2
PRJNA884180	SRX17749131	20.165602	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep3	Biological replicate 3
PRJNA884180	SRX17749132	20.993769	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep4	Biological replicate 4
PRJNA1124269	SRX24936411	10.731083		leaf		CK1	replicate=biological replicate1
PRJNA1124269	SRX24936412	14.899714		leaf		CK2	replicate=biological replicate2
PRJNA1124269	SRX24936413	12.139977		leaf		CK3	replicate=biological replicate3
PRJNA1124269	SRX24936414	22.577972		leaf		D1	replicate=biological replicate1
PRJNA1124269	SRX24936415	16.13257		leaf		D2	replicate=biological replicate2
PRJNA1124269	SRX24936416	20.866299		leaf		D3	replicate=biological replicate3
PRJNA1124269	SRX24936417	13.692813		leaf		MD1	replicate=biological replicate1
PRJNA1124269	SRX24936418	10.848724		leaf		MD2	replicate=biological replicate2
PRJNA1124269	SRX24936419	14.616025		leaf		MD3	replicate=biological replicate3
PRJNA387092	SRX2833309	16.124344	shanghaihuangxin	leaf	leaves between 0.5 and 1 cm in breadth, folded;	stage 2
PRJNA387092	SRX2833321	14.356984	shanghaihuangxin	leaf	leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion	stage 5
PRJNA387092	SRX2833323	9.264417	shanghaihuangxin	leaf	leaves >3 cm, unfolded, with clearstem extension	stage 7
PRJNA543957	SRX5879598	25.902777	Zhangzhou lvqing	stem		Se3	100 ppm Na2SeO4
PRJNA543957	SRX5879599	27.163231	Zhangzhou lvqing	stem		Se2	100 ppm Na2SeO4
PRJNA543957	SRX5879600	39.524651	Zhangzhou lvqing	stem		Mock2	mock
PRJNA543957	SRX5879601	45.132271	Zhangzhou lvqing	stem		Mock1	mock
PRJNA543957	SRX5879602	20.694567	Zhangzhou lvqing	stem		Se1	100 ppm Na2SeO4
PRJNA543957	SRX5879603	37.238686	Zhangzhou lvqing	stem		Mock3	mock
PRJNA609149	SRX7815917	17.830114	Jinnan Shiqin	flower bud	early flower bud	early flower bud
PRJNA609149	SRX7815918	18.074625	Jinnan Shiqin	flower bud	middle flower bud	middle flower bud
PRJNA609149	SRX7815919	20.187113	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	jg16628, jg37936, jg37937
Aizoaceae	Mesembryanthemum crystallinum	1	gene_25753
Amaranthaceae	Atriplex hortensis	2	Ah037635, Ah037637
Amaranthaceae	Beta vulgaris	1	BVRB_9g207330
Amaranthaceae	Salicornia bigelovii	2	Sbi_jg2425, Sbi_jg59867
Amaranthaceae	Salicornia europaea	1	Seu_jg24119
Amaranthaceae	Suaeda aralocaspica	1	GOSA_00025989
Amaranthaceae	Suaeda glauca	2	Sgl78745, Sgl81214
Amaranthaceae	Chenopodium album	7	gene:ENSEOMG00000016030, gene:ENSEOMG00000017359 ... gene:ENSEOMG00000019106, gene:ENSEOMG00000037100, gene:ENSEOMG00000040183, gene:ENSEOMG00000052659, gene:ENSEOMG00000052970
Amaranthaceae	Chenopodium quinoa	3	CQ.Regalona.r1.9AG0005470, CQ.Regalona.r1.9BG0016740 ... CQ.Regalona.r1.9BG0016810
Anacardiaceae	Pistacia vera	2	pistato.v30059360, pistato.v30271870
Apiaceae	Apium graveolens	6	Ag10G00540, Ag11G04662, Ag11G04663, Ag2G00670, Ag2G00923 ... Ag6G02307
Arecaceae	Cocos nucifera	3	COCNU_03G013580, COCNU_04G002800, COCNU_12G007040
Arecaceae	Phoenix dactylifera	4	gene-LOC103702851, gene-LOC103715965, gene-LOC103716197 ... gene-LOC103723062
Asparagaceae	Asparagus officinalis	3	AsparagusV1_05.445.V1.1, AsparagusV1_06.1382.V1.1 ... AsparagusV1_07.374.V1.1
Asteraceae	Flaveria trinervia	4	Ftri10G26587, Ftri12G16297, Ftri17G20184, Ftri9G23169
Brassicaceae	Arabidopsis thaliana	3	AT2G28540.2, AT3G45630.1, AT5G60170.2
Brassicaceae	Eutrema salsugineum	3	Thhalv10012563m.g.v1.0, Thhalv10012567m.g.v1.0 ... Thhalv10016186m.g.v1.0
Brassicaceae	Schrenkiella parvula	4	Sp4g11360.v2.2, Sp4g11370.v2.2, Sp5g15830.v2.2 ... Sp5g15860.v2.2
Brassicaceae	Brassica nigra	7	BniB01g015360.2N, BniB01g015370.2N, BniB02g039900.2N ... BniB05g040470.2N, BniB06g017560.2N, BniB08g011970.2N, BniB08g058510.2N
Casuarinaceae	Casuarina equisetifolia	1	Ceq08G2392
Casuarinaceae	Casuarina glauca	1	Cgl08G2596
Cymodoceaceae	Cymodocea nodosa	3	gene.Cymno18g00440, gene.Cymno18g00470, gene.Cymno18g00480
Hydrocharitaceae	Thalassia testudinum	2	gene.Thate08g12630, gene.Thate08g12670
Malvaceae	Hibiscus hamabo Siebold & Zucc.	1	nbisL1-mrna-580
Nitrariaceae	Nitraria sibirica	2	evm.TU.LG01.1374, evm.TU.LG09.982
Plantaginaceae	Plantago ovata	2	Pov_00012739, Pov_00016047
Plumbaginaceae	Limonium bicolor	3	Lb0G36780, Lb1G02544, Lb6G30938
Poaceae	Echinochloa crus-galli	3	AH08.2136, BH08.2250, CH08.2425
Poaceae	Eleusine coracana subsp. coracana	2	gene-QOZ80_5AG0406040, gene-QOZ80_5BG0454130
Poaceae	Hordeum vulgare	1	HORVU.MOREX.r3.5HG0466830.1
Poaceae	Oryza coarctata	6	Ocoptg000041lG000150, Ocoptg000061lG000100 ... Ocoptg000074lG000010, Ocoptg000092lG000070, Ocoptg000275lG000020, Ocoptg000441lG000010
Poaceae	Oryza sativa	1	LOC_Os12g01190.2
Poaceae	Paspalum vaginatum	1	gene-BS78_05G001600
Poaceae	Puccinellia tenuiflora	1	Pt_Chr0705182
Poaceae	Sporobolus alterniflorus	5	Chr07G022540, Chr17G014360, Chr19G011160, Chr27G004940 ... Chr31G000070
Poaceae	Thinopyrum elongatum	1	Tel5E01G270200
Poaceae	Triticum dicoccoides	2	gene_TRIDC5AG025990, gene_TRIDC5BG027140
Poaceae	Triticum aestivum	3	TraesCS5A02G156500.2, TraesCS5B02G154700.3 ... TraesCS5D02G161900.2
Poaceae	Zea mays	4	Zm00001eb094340_P001, Zm00001eb163140_P001 ... Zm00001eb194940_P001, Zm00001eb417060_P002
Poaceae	Zoysia japonica	2	nbis-gene-38390, nbis-gene-40104
Poaceae	Zoysia macrostachya	1	Zma_g17517
Portulacaceae	Portulaca oleracea	4	evm.TU.LG02.2094, evm.TU.LG06.1000, evm.TU.LG11.260 ... evm.TU.LG23.329
Posidoniaceae	Posidonia oceanica	1	gene.Posoc07g14430
Rhizophoraceae	Bruguiera sexangula	3	evm.TU.Scaffold_12_RagTag.319, evm.TU.Scaffold_12_RagTag.320 ... evm.TU.Scaffold_13_RagTag.765
Rhizophoraceae	Carallia pectinifolia	3	nbisL1-mrna-24477, nbisL1-mrna-30274, nbisL1-mrna-30286
Rhizophoraceae	Ceriops tagal	2	nbisL1-mrna-12662, nbisL1-mrna-19718
Rhizophoraceae	Ceriops zippeliana	3	nbisL1-mrna-16138, nbisL1-mrna-16139, nbisL1-mrna-19596
Rhizophoraceae	Kandelia candel	2	evm.TU.utg000015l.448, evm.TU.utg000027l.379
Rhizophoraceae	Kandelia obovata	2	Maker00015216, Maker00017869
Rhizophoraceae	Rhizophora apiculata	2	nbisL1-mrna-4367, nbisL1-mrna-5604
Rhizophoraceae	Rhizophora mangle	2	nbisL1-mrna-11820, nbisL1-mrna-15040
Salicaceae	Populus euphratica	6	populus_peu02677, populus_peu09199, populus_peu11743 ... populus_peu11751, populus_peu25800, populus_peu35624
Solanaceae	Lycium barbarum	4	gene-LOC132600816, gene-LOC132605924, gene-LOC132613799 ... gene-LOC132616048
Solanaceae	Solanum chilense	4	SOLCI001120100, SOLCI003343700, SOLCI003402900 ... SOLCI005076700
Solanaceae	Solanum pennellii	4	gene-LOC107004502, gene-LOC107017872, gene-LOC107018096 ... gene-LOC107023251
Tamaricaceae	Reaumuria soongarica	2	gene_13756, gene_2168
Tamaricaceae	Tamarix chinensis	2	TC01G2712, TC03G0051
Zosteraceae	Zostera marina	2	Zosma06g27440.v3.1, Zosma06g27460.v3.1