WormMine: Gene WBGene00003588

• WormBase Gene ID: WBGene00003588
• Gene Name: nex-1
• Sequence Name: ZC155.1
• Brief Description: nex-1 encodes an annexin, a member of a family of calcium-dependent phospholipid binding proteins; NEX-1 is required for efficient engulfment of apoptotic cell corpses in the pharynx, and may also function in other membrane fusion events, such as exocytosis; NEX-1 in vitro can bind phosphatidylserine, phosphatidylinositol, heparin, heparan sulfate, and chondroitin sulfate; NEX-1 is expressed in the pharynx, hypodermal cells, the vulva, the uterus, the spermathecal valve, and yolk granules of maturing oocytes.
• Organism: Caenorhabditis elegans
• Automated Description: Enables heparin binding activity and phospholipid binding activity. Involved in engulfment of apoptotic cell. Located in intracellular membrane-bounded organelle and plasma membrane. Expressed in hypodermis; pharynx; spermathecal-uterine junction; uterine toroidal epithelial cell; and vulva.
• Biotype: SO:0001217
• Genetic Position: III :-1.97258 ±0.014291
• Length (nt): 1184

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003588

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:ZC155.1.1	ZC155.1.1	1131	III: 5225621-5226804

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:ZC155.1	ZC155.1	969	III: 5225624-5226136

10 RNAi Result

• WBRNAi00107729
• WBRNAi00107730
• WBRNAi00067291
• WBRNAi00041886
• WBRNAi00058747
• WBRNAi00021578
• WBRNAi00005118
• WBRNAi00087553
• WBRNAi00027665
• WBRNAi00080498

23 Allele

• gk174276
• gk174275
• gk174277
• gk473094
• gk865386
• gk889391
• gk731503
• gk601944
• gk325218
• gk558787
• gk761462
• gk624248
• gk369442
• gk604152
• gk671789
• gk756699
• gk849386
• gk148
• WBVar00056211
• gk174274
• gk174273
• tm3545
• WBVar00056216

1 Chromosome

• WormBase ID: III
• Organism: Caenorhabditis elegans
• Length (nt): 13783801

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003588
• Start: 5225621
• End: 5226804
• Strand: 1

4 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)
• Panther orthologue and paralogue predictions

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrIII_5226805..5226817
• Length (nt): 13
• Chromosome Location: III: 5226805-5226817
• Organism: Caenorhabditis elegans

236 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	oocyte proteins identified by two or more unique peptides during proteomics study.	In the pooled data set, 1453 C. elegans proteins were identified with a probability >= 0.9 according to ProteinProphet, of which 1165 proteins were identified by more than one unique peptide.	WBPaper00038289:oocyte_protein
	Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons.	DESeq. False discovry rate (FDR) < 0.1.	WBPaper00048988:neuron_expressed
	TGF- Dauer pathway adult transcriptional targets. Results obtained by comparing the microarray results of the dauer-constitutive mutants daf-7(e1372), daf-7(m62), and daf-1(m40) with dauer-defective mutants daf-3(mgDf90), daf-5(e1386), and daf-7(e1372);daf-3(mgDf90) double mutants at the permissive temperature, 20C, on the first day of adulthood.	SAM	WBPaper00031040:TGF-beta_adult_upregulated
	Transcripts that showed significantly increased expression glp-1(e2141); TU3401 animals comparing to in TU3401 animals.	Fold change > 2, FDR < 0.01.	WBPaper00065993:glp-1(e2141)_upregulated
Fungi infection: Myzocytiopsis humicola	Transcripts that showed significantly altered expression 12 hours after animals were infected by M. humicola.	Differentially expressed genes as determined by Kallisto and Sleuth (pval<0.01, qval<0.1).	WBPaper00060871:M.humicola-infection_12h_regulated
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	Transcripts expressed in the epithelial tissues surrounding the pharynx that includes the arcade and intestinal valve (AIV) cells, according to PAT-Seq analysis using Pbath-15-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:arcade_intestinal-valve_expressed
	Transcripts expressed in body muscle, according to PAT-Seq analysis using Pmyo-3-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:body-muscle_expressed
	Transcripts expressed in GABAergic neuron, according to PAT-Seq analysis using Punc-47-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:GABAergic-neuron_expressed
	Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:hypodermis_expressed
	Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_expressed
	Transcripts expressed in NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:NMDA-neuron_expressed
	Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:pharynx_expressed
	Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_daf-16(mu86);glp-1(e2141)
	Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
	Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_fem-3(q20)
	Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_glp-1(e2141)
	Transcripts that showed significantly increased expression in day 3 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_upregulated_fem-3(q20)
	Maternal class (M): genes that are called present in at least one of the three PC6 replicates.	A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing.	[cgc5767]:expression_class_M
	Transcripts that showed significantly decreased expression in morc-1(tm6048) animals, comparing to in N2, after growing at 25C for five generations (late generation).	CuffDiff2	WBPaper00051265:F4_morc-1(tm6048)_downregulated
	Strictly maternal class (SM): genes that are the subset of maternal genes that are not also classified as embryonic.	A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing.	[cgc5767]:expression_class_SM
	Transcripts that showed significantly increased expression in daf-2(e1370) comparing to in control animals.	NOIseq(v2.34.0), fold change > = 1.5, Differentially expressed genes (DEGs) were defined as having a probability of differentialexpression > 95%.	WBPaper00064727:daf-2(e1370)_upregulated
	Transcripts that showed significantly changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals.	Sleuth	WBPaper00051558:aging_regulated
	Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
Gamma irradiation 100 mGY per hour for 72 hours since L1 larva.	Transcripts that showed significantly increased expression after exposure to 100mGy per hour gamma irradiation from L1 to day 1 adult hermaphrodite stage.	DESeq2, FDR <= 0.05, log2 fold change >= 0.3 or <= -0.3.	WBPaper00058958:100mGy-irradiation-72h_upregulated
Starvation	Starvation-induced transcripts that showed significantly increased expression in post dauer animals comparing to wild type control.	edgeR	WBPaper00053713:Starvation-induced_postdauer_vs_control_upregulated
	Genes that showed expression levels higher than the corresponding reference sample (L2 all cell reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:A-class-motor-neurons_L2-larva_expressed
	Transcripts that showed significantly increased expression in daf-2(e1370) comparing to in N2.	Differential gene expression analysis was performed using the quasi-likeli-hood framework in edgeR package v. 3.20.1 in R v. 3.4.1.	WBPaper00053810:daf-2(e1370)_upregulated
	Transcripts that showed significantly increased expression in nuo-6(qm200) comparing to in N2.	Differential gene expression analysis was performed using the quasi-likeli-hood framework in edgeR package v. 3.20.1 in R v. 3.4.1.	WBPaper00053810:nuo-6(qm200)_upregulated
	Transcripts that showed significantly increased expression in ngn-1(ok2200) embryos comparing to in N2.	DESeq2 ver.3.4.1	WBPaper00059537:ngn-1(ok2200)_upregulated

9 Expression Patterns

• Primary Identifier: Expr1031638
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1162168
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1209
• Remark: Identical expression patterns were obtained with these plasmids, although there appeared to be more cytoplasmic staining with nex-1-GFP 1 while nex-1-GFP 2 led to more concentrated nuclear staining in the same cells. The significance of these differences is presently unknown since both plasmids should express identical proteins; however, the observations made with the two different plasmids were made at different times so uncontrolled differences, such as variance in trans-gene dosage, between the experiments may have contributed to this difference. See Expr1210 for antibody staining of this gene.
• Pattern: The GFP is diffusely localized throughout the gland cell bodies within the terminal bulb of the pharynx, immediately anterior to the autofluorescent yellow granules that fill the cells of the intestine. When the vector nex-1-GFP 2 was used, punctate staining was also seen representing the nuclei of the two g1 gland cells of the terminal bulb. GFP staining was diffuse throughout the volume of the cell. Fluorescence of the spermathecal valve was also marked in nematodes expressing nex-1-GFP 2. The spermathecal valve is a single cell with four nuclei that is the product of the fusion of four cells. A region of nex-1 expression that was identified by the nex-1-GFP markers but was not identified by immunolocalization is the hypodermal cells.
• Subcellular Localization: nuclei

• Primary Identifier: Expr1210
• Remark: See Expr1209 for the gfp expression pattern.
• Pattern: Expressed in cells and tissues identified by nex-1::gfp except not detected in the hypodermal cells.

• Primary Identifier: Expr1560
• Pattern: Significant amount of annexin was found in the pharynx, the uterine wall, the vulva, and the spermathecal valves. The intense staining of the uterine wall was seen either as an outline around the eggs in the gravid adults or as intense staining of the entire uterus and vulva in young adults that did not have eggs. The staining of spermathecal valves was most apparent in the case of uteri which had fallen out of adults during the staining procedure. The intensely staining valves were seen at the two ends of the uteri. The staining in the pharynx was of greatest intensity within the terminal bulb in the region of the grinder and the gland cells at the back of the bulb. Additional staining was seen along the length of the pharynx.

• Primary Identifier: Expr8283
• Remark: Picture: Fig 2. The expression level of nex-1 was higher than that of nex-3, as more PCR cycles were required for detection of nex-3.
• Pattern: Expressed at low level at the embryonic stage and total amounts of annexin reached to a peak at the L1 stage. The expression of nex-1 was continuous in all larval stages after hatching to the adulthood.

• Primary Identifier: Expr2013979
• Pattern: Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans).

• Primary Identifier: Expr1022217
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2032219
• Pattern: Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans).

18 GO Annotation

6 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003588
• Start: 5225621
• End: 5226804
• Strand: 1

18 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 1184

1 Sequence Ontology Term

• Name: gene

1 Strains

• WBStrain00035608

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIII_5220096..5225620
• Length (nt): 5525
• Chromosome Location: III: 5220096-5225620
• Organism: Caenorhabditis elegans