WormMine: Gene WBGene00003229

• WormBase Gene ID: WBGene00003229
• Gene Name: mex-3
• Sequence Name: F53G12.5
• Brief Description: mex-3 encodes two KH domain-containing RNA binding proteins; in the early embryo, maternally provided MEX-3 is required for specifying the identities of the anterior AB blastomere and its descendants, as well as for the identity of the P3 blastomere and proper segregation of the germline P granules; mex-3 mRNA is distributed uniformly in the syncytial core of the adult distal gonad, mature oocytes, and early 1-cell stage embryos, but then becomes more prominent in the AB blastomere and its daughters by the 4-cell stage after which it is rapidly degraded save for the D and P4 blastomeres; MEX-3 protein is also detected uniformly in the cytoplasm of oocytes and 1-cell stage embryos, but like the mRNA, becomes more abundant in AB and its daughters at the 2- and 4-cell stages, respectively, before disappearing; MEX-3 is also detected in association with P granules from the 2-cell stage until the late stages of embryogenesis.
• Organism: Caenorhabditis elegans
• Automated Description: Enables single-stranded RNA binding activity. Involved in several processes, including negative regulation of muscle cell differentiation; organelle inheritance; and regulation of gene expression. Located in P granule. Expressed in distal tip cell and embryonic cell. Is an ortholog of human MEX3A (mex-3 RNA binding family member A) and MEX3B (mex-3 RNA binding family member B).
• Biotype: SO:0001217
• Genetic Position: I :-19.1652 ±0.00806
• Length (nt): 6986

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003229

Genomics

5 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F53G12.5b.1	F53G12.5b.1	2032	I: 127285-134270
Transcript:F53G12.5a.2	F53G12.5a.2	2039	I: 127286-134269
Transcript:F53G12.5a.3	F53G12.5a.3	1989	I: 127384-134269
Transcript:F53G12.5a.1	F53G12.5a.1	1934	I: 128697-134267
Transcript:F53G12.5c.1	F53G12.5c.1	543	I: 132262-133582

Other

3 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F53G12.5b	F53G12.5b	1332	I: 127297-127336
CDS:F53G12.5a	F53G12.5a	1248	I: 128698-128896
CDS:F53G12.5c	F53G12.5c	543	I: 132262-132553

64 RNAi Result

• WBRNAi00114291
• WBRNAi00114056
• WBRNAi00114135
• WBRNAi00114214
• WBRNAi00106575
• WBRNAi00106590
• WBRNAi00110443
• WBRNAi00066938
• WBRNAi00066948
• WBRNAi00066981
• WBRNAi00067085
• WBRNAi00067681
• WBRNAi00067704
• WBRNAi00048170
• WBRNAi00083279
• WBRNAi00110449
• WBRNAi00081382
• WBRNAi00083265
• WBRNAi00114251
• WBRNAi00114095
• WBRNAi00097397
• WBRNAi00116728
• WBRNAi00000185
• WBRNAi00000063
• WBRNAi00114016
• WBRNAi00077277
• WBRNAi00077291
• WBRNAi00087359
• WBRNAi00087358
• WBRNAi00087361

133 Allele

• gk963902
• gk963701
• WBVar01929805
• WBVar01929804
• WBVar01929807
• WBVar01929806
• WBVar01929809
• WBVar01929808
• WBVar02068048
• WBVar01602722
• WBVar00245023
• WBVar01711237
• WBVar01947157
• WBVar02039064
• WBVar01402711
• WBVar00146965
• WBVar02086927
• WBVar00146963
• WBVar00146964
• WBVar00146969
• WBVar00146970
• WBVar00146967
• WBVar00146968
• WBVar01402699
• zu142
• zu171
• zu155
• zu166
• zu176
• h9492

1 Chromosome

• WormBase ID: I
• Organism: Caenorhabditis elegans
• Length (nt): 15072434

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003229
• Start: 127285
• End: 134270
• 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_chrI_134271..134336
• Length (nt): 66
• Chromosome Location: I: 134271-134336
• Organism: Caenorhabditis elegans

218 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Genes with expression altered >= 3-fold in dpy-10(e128) mutants.	Data across the wild type series was analyzed using the Significance analysis of Microarrays (SAM) algorithm (to calculate the False Discovery Rate (FDR)).	WBPaper00035873:dpy-10_regulated
	Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons.	DESeq. False discovry rate (FDR) < 0.1.	WBPaper00048988:neuron_expressed
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr 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:all-neurons_L1-larva_expressed
adult vs dauer larva	Transcripts that showed differential expression in adult vs dauer lava in N2 animals at 20C.	N.A.	WBPaper00050488:adult_vs_dauer_regulated_N2_20C
	mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis.	Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05.	WBPaper00045420:fertilization_downregulated_transcript
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr 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:AVE-neuron_L1-larva_expressed
Osmotic stress	Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when no food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_NoFood
	Transcripts that showed significantly higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc).	DESeq2, fold change >= 2, FDR <= 0.01.	WBPaper00056826:SGP_biased
	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
	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 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
	Genes with expression level regulated by genotype (N2 vs CB4856) and age at L3 larva and Late reproduction stage (96 hours at 24 centigrade).	For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR).	WBPaper00040858:eQTL_age_regulated_developing
	Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_glp-1(e2141)
Bacteria diet: Escherichia coli HB101. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria E. coli HB101 for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:HB101_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
Bacteria diet: Sphingomonas aquatilis Yellow. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria Sphingomonas aquatilis (Yellow) for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:S.aquatilis_downregulated
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_6h
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_6h
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
	Transcripts that showed significantly decreased expression in hsp-6(mg585) comparing to in N2 at L4 larva stage.	EdgeR, fold change > 2, FDR < 0.001.	WBPaper00056290:hsp-6(mg585)_downregulated
	Transcripts that showed significantly increased expression in hrde-1(tm1200) animals, comparing to in N2, after growing at 25C for five generations (late generation).	CuffDiff2	WBPaper00051265:F4_hrde-1(tm1200)_upregulated
Bacteria infection: Staphylococcus aureus MW2. 4 hours of exposure.	Transcripts that showed significantly increased expression after N2 animals had 4 hours of infection by Staphylococcus aureus (MW2).	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:S.aureus-4h_upregulated_N2
	Transcripts that showed significantly increased expression in animals exposed to 400uM tamoxifen from L1 to L4 larva stage.	DEseq2, fold change > 2	WBPaper00064505:tamoxifen_upregulated

11 Expression Patterns

• Primary Identifier: Expr1031526
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1151985
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr8097
• Remark: Picture: Figure 3.
• Subcellular Localization: The GFP::MEX-3 strain was used to visualize the distribution of MEX-3 in proximal oocytes of hermaphrodites over time; GFP accumulation changed from evenly distributed throughout the cytoplasm of oocytes, to concentrated in discrete foci at 89 to 91 h after the fourth larval stage at 23 centigrades (referred to as post-L4) (n = 28).

• Primary Identifier: Expr12977
• Pattern: The mex-3 3'UTR reporter is unique in that it showed strong GFP expression in the oocytes, with expression peaking in the most mature oocytes. Little expression was observed in the distal germline or in the syncytial region. Expression was also observed in the anterior cells of early embryos, but not in the posterior.

• Primary Identifier: Expr697
• Remark: This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope).
• Pattern: MEX-3 is present as a cytoplasmic protein. MEX-3 protein is first detected in oocytes shortly after cellularlization and the amount of protein appears to increase in oocytes as they mature. After fertilization, MEX-3 protein is evenly distributed throughout the cytoplasm of the 1 cell stage embryo. By the end of the 2-cell stage, MEX-3 protein appears more abundant in the AB blastomere than in P1 blastomere. In the 4-cell stage, the protein appears more abundant in the AB daughters than the P1 daughters. After 4-cell stage MEX-3 protein disappears from the embryo. In addition to general cytoplasmic staining, each of the MEX-3 antisera specifically stained distinct particles in P1 and in the P1 descendants P2, P3 and P4. Simultaneous staining with an anti-MEX-3 antibody and anti-P granule antibody, shows the particles stained by the MEX-3 antisera coincide with P granules in the blastomeres P1, P2, P3 and P4. However, the MEX-3 antisera do not stain P granules in the gonad or P granules in the germ cells of late stage embryos.

• Primary Identifier: Expr573
• Remark: early embryo(author) = 1-cell + 2-cell + 4-cell embryo(curator).
• Pattern: mex-3 mRNA is detected in the syncytial core of gonad arm and distribute uniformly in oocyte and early 1-cell embryo. mex-3 mRNA is more abundant in AB and its daughter cells than P1 and its daughter cells. After 4-cell stage, mex-3 mRNA disappears. MEX-3 protein is present in oocytes and uniformly distributed until the first division, when they become more abundant in the anterior AB cell. At the 4-cell stage, AB daughters have more MEX-3. Both the mRNA and protein disappear after the 4-cell stage.
• Subcellular Localization: MEX-3 is cytoplasmic, and in the P cells, MEX-3 is associated with P granules.

• Primary Identifier: Expr14398
• Pattern: AB-enriched

• Primary Identifier: Expr2013542
• 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: Expr14280
• Pattern: GFP::3xFLAG::MEX-3 protein expression was restricted to the distal tip and oocytes.

• Primary Identifier: Expr1013996
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2031776
• 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).

20 GO Annotation

14 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003229
• Start: 127285
• End: 134270
• Strand: 1

20 Ontology Annotations

6 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased expression in mex-3(eu149) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult.	RPKM fold change > 2.	WBPaper00058598:mex-3(eu149)_upregulated
	Transcripts that showed significantly decreased expression in mex-3(eu149) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult.	RPKM fold change > 2.	WBPaper00058598:mex-3(eu149)_downregulated
	Transcripts that showed significantly decreased expression in mex-3(spr9) comparing to in N2 animals.	DESeq2_1.28.1, FDR < 0.05, fold change > 2.	WBPaper00061823:mex-3(spr9)_downregulated
	Transcripts that showed significantly increased expression in mex-3(spr9) comparing to in N2 animals.	DESeq2_1.28.1, FDR < 0.05, fold change > 2.	WBPaper00061823:mex-3(spr9)_upregulated
	Transcripts that showed significantly decreased expression in mex-3(spr10) comparing to in N2 animals.	DESeq2_1.28.1, FDR < 0.05, fold change > 2.	WBPaper00061823:mex-3(spr10)_downregulated
	Transcripts that showed significantly increased expression in mex-3(spr10) comparing to in N2 animals.	DESeq2_1.28.1, FDR < 0.05, fold change > 2.	WBPaper00061823:mex-3(spr10)_upregulated

1 Sequence

• Length: 6986

1 Sequence Ontology Term