WormMine: Gene WBGene00003476

• WormBase Gene ID: WBGene00003476
• Gene Name: mtm-3
• Sequence Name: T24A11.1
• Brief Description: mtm-3 encodes, by alternative splicing, two isoforms of a myotubularin lipid phosphatase orthologous to human MTMR3 and MTMR4 and paralogous to MTM1; MTM-3 is required for normal locomotion in older adults and for normally long lifespan; MTM-3 has phosphatidylinositol 3-phosphate (PI3P) phosphatase activity; MTM-3 contains a C-terminal FYVE domain that binds PI3P in vitro; MTM-3 is expressed throughout development and adulthood, primarily in eggs and muscles, but is also expressed in head neurons.
• Organism: Caenorhabditis elegans
• Automated Description: Enables inositol bisphosphate phosphatase activity and phosphatidylinositol phosphate phosphatase activity. Involved in several processes, including determination of adult lifespan; positive regulation of autophagosome maturation; and regulation of endocytosis. Located in cytoplasm. Expressed in body wall musculature and head neurons. Is an ortholog of human MTMR3 (myotubularin related protein 3).
• Biotype: SO:0001217
• Genetic Position: III :-4.25221 ±0.000147
• Length (nt): 10489

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003476

Genomics

3 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T24A11.1b.2	T24A11.1b.2	3538	III: 3789979-3800055
Transcript:T24A11.1b.1	T24A11.1b.1	3625	III: 3789982-3800465
Transcript:T24A11.1a.1	T24A11.1a.1	3974	III: 3789982-3800467

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T24A11.1a	T24A11.1a	3021	III: 3790825-3790838
CDS:T24A11.1b	T24A11.1b	2886	III: 3790613-3790838

40 RNAi Result

• WBRNAi00098948
• WBRNAi00098945
• WBRNAi00111600
• WBRNAi00077725
• WBRNAi00077724
• WBRNAi00077726
• WBRNAi00111597
• WBRNAi00111594
• WBRNAi00111595
• WBRNAi00067845
• WBRNAi00067877
• WBRNAi00064725
• WBRNAi00053994
• WBRNAi00065075
• WBRNAi00019112
• WBRNAi00006053
• WBRNAi00111598
• WBRNAi00068481
• WBRNAi00068482
• WBRNAi00068480
• WBRNAi00068746
• WBRNAi00068747
• WBRNAi00065076
• WBRNAi00068927
• WBRNAi00068926
• WBRNAi00068928
• WBRNAi00035899
• WBRNAi00111599
• WBRNAi00078220
• WBRNAi00097612

176 Allele

• gk962532
• gk963881
• gk963882
• otn11031
• otn11032
• WBVar02036275
• WBVar02003329
• gk619604
• gk756687
• gk171534
• WBVar02010374
• WBVar01262464
• WBVar01262467
• WBVar01262469
• WBVar01262470
• WBVar01262475
• WBVar01262476
• WBVar01262477
• WBVar01262478
• WBVar01262471
• WBVar01262474
• WBVar01262479
• WBVar01262480
• WBVar01262481
• WBVar01262486
• WBVar01262483
• WBVar01262485
• WBVar01656359
• WBVar01656354
• WBVar01656358

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003476
• Start: 3789979
• End: 3800467
• 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_3786813..3789978
• Length (nt): 3166
• Chromosome Location: III: 3786813-3789978
• Organism: Caenorhabditis elegans

148 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 that showed significantly increased expression in L1 neural cells comparing to in adult neural cells.	DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction.	WBPaper00060811:L1_vs_adult_upregulated_neural
	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 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
	Genes with expression level regulated by genotype (N2 vs CB4856) and age at old adults stage (214 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_aging
	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 expressed in vulva.	FPKM >= 1.	WBPaper00064122:vulva_transcriptome
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 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
	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
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 altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_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
	Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
	Transcripts that showed significantly increased expression in xrep-4(lax137).	DESeq2. Genes were selected if their p value < 0.01.	WBPaper00066062:xrep-4(lax137)_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
	Proteins that showed significantly decreased expression after 1-day-old wild type adults were exposed to cisplatin (300ug per mL) for 6 hours.	The differential expression analysis was performed in R. Differentially expressed proteins were identified by using a two-sided t-test on log-transformed data.	WBPaper00065373:Cisplatin_downregulated_WT
	Genes that showed expression levels higher than the corresponding reference sample (L3/L4 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:hypodermis_L3-L4-larva_expressed
	Transcripts detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
Bacteria: B.thuringiensis	Transcripts in elt-2(RNAi) animals that were significantly differentially expressed at least for one time point and one pathogenic strain Bt247 and Bt679 compared to the non pathogenic strain Bt407.	Cuffdiff	WBPaper00060358:B.thuringiensis_pathogen_regulated_elt-2(RNAi)

9 Expression Patterns

• Primary Identifier: Expr1031592
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr8073
• Remark: Picture: Fig. 1, middle panel. This was further verified by staining paraffin-embedded cross-sections of adult worms. Note that the staining of paraffin-embedded cross-sections also revealed partial expression of the enzyme in the intestine. The muscle expression was further verified by co-staining the paraffin-embedded sections with an antibody against myosin, a muscle marker.
• Pattern: Staining of whole-mount gravid worms showed expression of the enzyme in body wall muscle and in eggs.

• Primary Identifier: Expr8072
• Remark: Picture: Fig. 1, upper panel.
• Pattern: On Western blotting analysis, ceMTM3 appears as a relatively broad band of 105 kDa. It is expressed at the egg and young larva (L1 and L2) stages. It decreases to near absence in the L3 to young adult stages, and then regains high expression in the egg-laying period and post-reproductive age.

• Primary Identifier: Expr1021477
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Chronogram564
• Remark: Original chronogram file: chronogram.1587.xml
• Reporter Gene: [T24A11.1:gfp] transcriptional fusion.

• Primary Identifier: Expr2013810
• 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: Expr2662
• Pattern: mtm-3::gfp was expressed predominantly in neurons in the head with a low level of expression also detected in posterior intestinal cells which is a common artifact for GFP expression vectors.

• Primary Identifier: Expr2032050
• 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: Expr1157539
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

38 GO Annotation

14 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003476
• Start: 3789979
• End: 3800467
• Strand: -1

38 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 10489

1 Sequence Ontology Term

• Name: gene

1 Strains

• WBStrain00001904

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIII_3800468..3801900
• Length (nt): 1433
• Chromosome Location: III: 3800468-3801900
• Organism: Caenorhabditis elegans