WormMine: Gene WBGene00003228

• WormBase Gene ID: WBGene00003228
• Gene Name: mex-1
• Sequence Name: W03C9.7
• Brief Description: mex-1 encodes a CCCH-type zinc-finger protein that is required maternally for segregation of P granules, germ cell formation, and somatic cell differentiation in the early embryo; MEX-1 is expressed cytoplasmically in germ line blastomeres, is a component of P granules, and is required for restricting PIE-1 expression and function to these cells; mex-1 mRNA transcripts are also transiently associated with P granules.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable mRNA 3'-UTR binding activity. Involved in several processes, including embryonic pattern specification; establishment of cell polarity; and formation of primary germ layer. Located in P granule. Expressed in germ line.
• Biotype: SO:0001217
• Genetic Position: II :5.15029 ±0.129562
• Length (nt): 3711

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003228

Genomics

5 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:W03C9.7a.1	W03C9.7a.1	1876	II: 11968637-11972330
Transcript:W03C9.7c.1	W03C9.7c.1	1902	II: 11968637-11972347
Transcript:W03C9.7a.2	W03C9.7a.2	1739	II: 11968637-11972320
Transcript:W03C9.7b.1	W03C9.7b.1	660	II: 11970376-11971951
Transcript:W03C9.7d.1	W03C9.7d.1	669	II: 11970376-11971951

Other

4 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:W03C9.7a	W03C9.7a	1485	II: 11968649-11968787
CDS:W03C9.7c	W03C9.7c	1494	II: 11968649-11968787
CDS:W03C9.7b	W03C9.7b	660	II: 11970376-11970687
CDS:W03C9.7d	W03C9.7d	669	II: 11970376-11970687

47 RNAi Result

• WBRNAi00110470
• WBRNAi00054668
• WBRNAi00054669
• WBRNAi00055570
• WBRNAi00020079
• WBRNAi00103582
• WBRNAi00008001
• WBRNAi00101744
• WBRNAi00079041
• WBRNAi00101748
• WBRNAi00106709
• WBRNAi00079048
• WBRNAi00079047
• WBRNAi00079049
• WBRNAi00103864
• WBRNAi00103866
• WBRNAi00101762
• WBRNAi00103865
• WBRNAi00103868
• WBRNAi00101764
• WBRNAi00103867
• WBRNAi00103870
• WBRNAi00079062
• WBRNAi00103869
• WBRNAi00103872
• WBRNAi00101768
• WBRNAi00103871
• WBRNAi00079066
• WBRNAi00103874
• WBRNAi00079065

103 Allele

• gk963801
• gk963053
• gk962684
• gk963539
• WBVar02068268
• h6792
• WBVar01312848
• WBVar01312847
• WBVar01312845
• WBVar01835451
• WBVar01312849
• WBVar02078237
• zu122
• WBVar00176409
• WBVar01312839
• WBVar00176410
• WBVar00176408
• WBVar01993991
• WBVar01312844
• WBVar01312843
• WBVar01312842
• zu120
• WBVar00176411
• WBVar01312841
• zu121
• WBVar00176412
• zu140
• or286
• WBVar01394285
• gk942344

1 Chromosome

• WormBase ID: II
• Organism: Caenorhabditis elegans
• Length (nt): 15279421

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003228
• Start: 11968637
• End: 11972347
• Strand: 1

4 Data Sets

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

0 Downstream Intergenic Region

229 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
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
	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 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 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 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 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)
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
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
	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 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
	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 animals exposed to 400uM tamoxifen from L1 to L4 larva stage.	DEseq2, fold change > 2	WBPaper00064505:tamoxifen_upregulated
Heat Shock: 35C 4 hours at L4 larva stage.	Transcripts that showed significantly decreased expression after L4 larva N2 animals were heat stressed at 35C for 4 hours	DESeq2	WBPaper00057154:HeatShock_downregulated_mRNA
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
	Genes down regulated by mir-243(n4759).	RNAs that changed at least 2-fold with a probability of p > 0.05 in three biological replicates were considered differentially regulated between wild-type and mir-243.	WBPaper00036130:mir-243_down_regulated
25C vs. 20C	Transcripts that showed significantly increased expression in 1-day post L4 adult hermaphrodite N2 grown at 25C, comparing to in N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:25C_vs_20C_upregulated
	Transcripts that showed significantly increased expression in 10-days post L4 adult hermaphrodite N2 grown at 20C, comparing to in 1-day post L4 adult hermaphrodite N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:Day10_vs_Day1_upregulated
Bacteria infection: Pseudomonas aeruginosa PA14. 24 hours of exposure at 25C.	Transcripts that showed significantly increased expression in N2 animals with 24 hours of exposure to P. aeruginosa PA14 for 24 hrs at 25C, comparing to N2 animals without exposure to PA14.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00058948:PA14_upregulated
	Transcripts that showed significantly decreased expression in tetraploid N2 comparing to diploid N2 animals at L4 larva stage.	DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05.	WBPaper00066110:tetraploid_vs_diploid_downregulated

9 Expression Patterns

• Primary Identifier: Expr1031525
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1019776
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr576
• Remark: Maternal effect. early embryo(author) = blastula + gastrulating embryo(curator).
• Pattern: In adult hermaphrodites, mex-1 mRNA is detected in the syncytial core of the gonad and in oocytes at all stages of maturation. In 1 and 2-cell stage embryos, mex-1 mRNA is distributed uniformly, but then appears to be degraded rapidly in somatic blastomeres but remains in germ line blastomeres in subsequent divisions. After P4 divides, mex-1 mRNA is not detected.

• Primary Identifier: Expr9708
• Reporter Gene: We employed a transgene-based assay that tests the post-transcriptional control activity of 3' UTRs in vivo. In this assay, the GFP::H2B reporter fusion is placed upstream of the selected 3' UTR such that the entire fusion-GFP::H2B-3' UTR-is produced as a single transcript. Expression in the germline is achieved by using pie-1 promoter, which has been shown earlier to drive transgene expression in the germline.
• Pattern: The transgene containing mex-1 3' UTR expressed GFP::H2B in oocytes and the meiotic region, but was either absent or very low in the mitotic germ cells.

• Primary Identifier: Expr4130
• Remark: Curated by authors based on online in-situ hybridization database (Y. Kohara, personal communication; http://nematode.lab.nig.ac.jp).
• Pattern: Expressed in medial germline.

• Primary Identifier: Expr577
• Remark: Antisera from two different regions of MEX-1 (amino acids 74-96 and 273-296) gave the same results. early embryo(author) = blastula + gastrulating embryo(curator).
• Pattern: MEX-1 first appears at low levels in mature oocytes, and increases after fertilization. MEX-1 is most abundant in the posterior half at the late-1-cell stage, and continues in the germ line cytoplasm until P4 divides. During the early cleavage stages, MEX-1 is present in the cytoplasm of each of the germline blastomeres, and is not detected in nuclei. After each division of a germline blastomere, MEX-1 is detected initially in both daughters, but then disappears from the somatic daughter later in that cell cycle.
• Subcellular Localization: In P0 through P4, MEX-1 is associated with P granules in addition to a diffuse cytoplasmic component.

• Primary Identifier: Expr2013541
• 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: Expr1158209
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2031775
• 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).

14 GO Annotation

16 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003228
• Start: 11968637
• End: 11972347
• Strand: 1

14 Ontology Annotations

2 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly decreased expression in mex-1(or286) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult.	RPKM fold change > 2.	WBPaper00058598:mex-1(or286)_downregulated
	Transcripts that showed significantly increased expression in mex-1(or286) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult.	RPKM fold change > 2.	WBPaper00058598:mex-1(or286)_upregulated

1 Sequence

• Length: 3711

1 Sequence Ontology Term

• Name: gene

3 Strains

• WBStrain00022473
• WBStrain00023560
• WBStrain00007305

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrII_11967545..11968636
• Length (nt): 1092
• Chromosome Location: II: 11967545-11968636
• Organism: Caenorhabditis elegans