WormMine: Gene WBGene00003395

• WormBase Gene ID: WBGene00003395
• Gene Name: mom-2
• Sequence Name: F38E1.7
• Brief Description: mom-2 encodes a member of the Wnt family of secreted signaling glycoproteins that is required for induction of endodermal (gut) tissue in the 4-cell stage embryo; MOM-2, required in the inducing blastomere (P2) at the 4-cell stage, may be the ligand for MOM-5, a Frizzled homolog, thought to act in the receiving blastomere (EMS); MOM-2 genetically interacts in the same pathway as KIN-19, but parallel to APR-1; MOM-2 also may be a ligand for LIN-18, a Ryk homolog.
• Organism: Caenorhabditis elegans
• Automated Description: Enables receptor tyrosine kinase binding activity. Involved in several processes, including cell differentiation; left/right axis specification; and neuroblast migration. Predicted to be located in extracellular space. Expressed in several structures, including HSN; P5.ppp; P7.paa; anchor cell; and epithelial cell.
• Biotype: SO:0001217
• Genetic Position: V :1.32369 ±0.00238
• Length (nt): 2198

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003395

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F38E1.7.1	F38E1.7.1	1537	V: 8355988-8358185

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F38E1.7	F38E1.7	1089	V: 8356098-8356174

152 RNAi Result

• WBRNAi00114299
• WBRNAi00114064
• WBRNAi00114143
• WBRNAi00114222
• WBRNAi00070924
• WBRNAi00070926
• WBRNAi00070928
• WBRNAi00091591
• WBRNAi00091593
• WBRNAi00098871
• WBRNAi00091566
• WBRNAi00091568
• WBRNAi00065950
• WBRNAi00106564
• WBRNAi00106592
• WBRNAi00008766
• WBRNAi00065339
• WBRNAi00101892
• WBRNAi00101345
• WBRNAi00067241
• WBRNAi00067247
• WBRNAi00067303
• WBRNAi00067342
• WBRNAi00067418
• WBRNAi00067429
• WBRNAi00067449
• WBRNAi00067485
• WBRNAi00067764
• WBRNAi00067965
• WBRNAi00068181

43 Allele

• gk963301
• gk964351
• gk962860
• gk964052
• WBVar01974420
• t2180
• tm615
• gk241254
• gk241255
• gk241256
• gk241257
• gk241258
• ne3371
• or33
• WBVar01460932
• or42
• or48
• gk482137
• gk312642
• or77
• gk906333
• gk647281
• gk912421
• gk653380
• ne141
• or85
• tm11888
• WBVar00213347
• ok591
• WBVar01274871

1 Chromosome

• WormBase ID: V
• Organism: Caenorhabditis elegans
• Length (nt): 20924180

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003395
• Start: 8355988
• End: 8358185
• 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_chrV_8358186..8358202
• Length (nt): 17
• Chromosome Location: V: 8358186-8358202
• Organism: Caenorhabditis elegans

211 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 of coding genes that showed significantly decreased expression in muscle.	DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed.	WBPaper00062325:muscle_depleted_coding-RNA
	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
	Genes that were upregulated in lin-15B(n744).	For each gene in each microarray hybridization experiment, the ratio of RNA levels from the two samples was transformed into a log2 value and the mean log2 ratio was calculated. The log2 ratios were normalized by print-tip Loess normalization (Dudoit and Yang, 2002). All genes with a false discovery rate of <= 5% (q <= 0.05) (Storey and Tibshirani, 2003) and a mean fold-change ratio of >= 1.5 were selected for further analysis.	WBPaper00038168:lin-15B(n744)_upregulated
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly decreased expression in N2 after animals were exposed to E. faecalis OG1RF for 16 hours comparing to exposure to E. Coli OP50.	Cuffcompare and Cuffdiff	WBPaper00056090:E.faecalis_downregulated_N2
	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
	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
	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)
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
	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
	Significantly differentially expressed genes as determined by microarray analysis of wild-type and cde-1 mutant germlines.	RNAs that changed at least 2-fold with a probability of p < 0.05 were considered differentially regulated between wildtype and cde-1.	WBPaper00035269:cde-1_regulated
Transgeneration hypoxia treatment.	Transcripts that are significantly upregulated in F1 animals after P0 parents were exposed to 0.1% oxygen for 16 hours at L4 larva stage.	For calling the significant differentially expressed genes (DEGs),the false discovery rate (FDR) after multiple testing correction was set as 0.05 and analyzed in edgeR.	WBPaper00064871:hypoxia_upregulated_F1
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

14 Expression Patterns

• Primary Identifier: Expr1031567
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr11177
• Pattern: The expression dynamics of mom-2/Wnt are quite different throughout the worm life span. Expression of mom-2/Wnt increases 3 fold during the first 5 days of adulthood and then decreases 4 fold by day 8 of adulthood, eventually showing little or no expression in old worms. Expression localization of mom-2 differs slightly between aging and development. During development, mom-2 is expressed throughout the whole body of the worm, in muscles, hypodermal and intestinal cells, vulva precursor cells, as well as in ventral cord motor neurons (Gleason et al. 2006). In young (day1 and 2) and middle-aged (day 5) adults, mom-2/Wnt expression was observed only in posterior intestinal and intestinal rectal valve cells. The authors were not able to detect any mom-2 expression in any other tissues.

• Primary Identifier: Expr7988
• Remark: Picture: Figure 2, Figure S5.
• Pattern: mom-2 expression was observed in early embryos, at approximately 0-2 hours after egg laying, and continued throughout embryonic and larval development. mom-2 was expressed slightly earlier in embryogenesis than cwn-1 or cwn-2. Expression of mom-2 continued throughout embryonic and larval development. Expression of mom-2 was observed in body wall muscles, ventral cord neurons, intestinal cells and fused and unfused seam cells throughout larval development. mom-2 expression was also observed in head cells between the anterior and posterior bulbs of the pharynx. During the L3 and L4 stages, mom-2 was expressed in the descendants of P5.p to P7.p. No expression of mom-2 was observed in the anchor cell (8/8 lines).

• Primary Identifier: Expr13236
• Pattern: In the 8-cell embryo, when there are four AB- derived blastomeres (two ABa daughters and two ABp daughters), the smFISH signal was consistently 2-4 fold higher in the ABp-derived blastomeres. In the 14-15 cell embryo, when there are eight AB-derived blastomeres, elevated smFISH signal was detected primarily in two of the four ABa granddaughters (ABalp and ABara), in addition to all ABp-derived blastomeres.

• Primary Identifier: Expr12036
• Pattern: mom-2 expression was observed in the male blast cells B, F, Y as well as P12.p, T.a, T.p, hyp7, hyp8 and hyp10 in syEx664 males.

• Primary Identifier: Expr1150592
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr9345
• Pattern: mom-2 has previously been reported to be widely expressed along the anteroposterior axis of developing larvae, with expression in body wall muscle cells, ventral cord neurons, intestinal cells and seam cells (Gleason et al., 2006). By contrast, we found that mom- 2 shows a restricted expression pattern, with mom-2 transcripts localizing only to the germ cell precursors Z2 and Z3, their descendants and a few unidentified cells in the tail. mom-2 expression in the germ cells continued throughout larval development, whereas the tail expression reached a maximum at the mid-L1 stage and disappeared before the L1 to L2 molt. In addition, one or two mom-2 transcripts were occasionally detected in posterior seam cells in early L1 larvae. Consistent with the early embryonic function of mom-2 (Thorpe et al., 1997), we found that mom-2 transcripts were already present in the zygote. At the four-cell stage, mom-2 transcripts were enriched in the P2 blastomere. During later stages of embryonic development, mom- 2 transcripts were restricted to the posterior, with expression remaining in the tail and in the region of the Z2 and Z3 germ line precursors in comma stage embryos.

• Primary Identifier: Expr11633
• Pattern: Pmom-2::mCherry is robustly expressed in the tail and weakly expressed in the vulva and body wall muscles.

• Primary Identifier: Expr3051
• Remark: Reporter gene fusion type not specified.
• Pattern: In the vicinity of the developing vulva, consistent mom-2::gfp expression was observed in the anchor cell. Some transgenic lines also expressed GFP in ventral uterine cells near the anchor cell (VU and descendants), HSN neurons, ventral cord neurons, and VPC granddaughters P5.ppa, P5.ppp, P7.paa, and P7.pap.

• Primary Identifier: Expr15112
• Pattern: Anchor cell

• Primary Identifier: Expr2013656
• 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: Expr2031890
• 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: Expr15696
• Pattern: Using transcriptional reporters of the five Wnt ligands [cis-regulatory elements of the Wnt ligands placed upstream of a nuclear GFP (Gleason et al., 2006)], we observed that three Wnt ligands (CWN-1, CWN-2 and MOM-2) are expressed in the embryo at the time of the terminal division of the SMDD/AIY mother cell. We could not detect expression of the two remaining Wnt ligands (LIN-44 and EGL-20) at that time but start seeing expression at later stages, during elongation, in the posterior end of the embryo. Interestingly, at the time of the terminal division of the SMDD/AIY mother cell, cwn-1, cwn-2 and mom-2 are transcribed at a higher level in the posterior region of the embryo than in the anterior region. These observations are consistent with an analysis of the transcription pattern of Wnt ligands by fluorescent in situ hybridization (Harterink et al., 2011). cwn-1, cwn-2 and mom-2 are transcribed in several tissues: cwn-1 (posterior muscle), cwn-2 ( posterior neuronal progenitors, posterior epidermis, intestine and posterior muscle) and mom-2 (posterior epidermis and muscle). Their zygotic expression starts during gastrulation and remains during embryonic elongation.

• Primary Identifier: Expr1015549
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

44 GO Annotation

5 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003395
• Start: 8355988
• End: 8358185
• Strand: 1

44 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 2198

1 Sequence Ontology Term