WormMine: Gene WBGene00003391

• WormBase Gene ID: WBGene00003391
• Gene Name: mog-3
• Sequence Name: F52C9.7
• Brief Description: mog-3 encodes a conserved nuclear protein which shares homology to a yeast splicing factor: MOG-3 contains two motifs in its N-terminus that are fully conserved from yeasts to vertebrates; necessary for oogenesis and robust germ line proliferation; mog-3 and gld-3 functions synergistically to promote meiosis progression; MOG-3, MEP-1 and CIR-1 belong to single complex; MOG-3 interacts with N-terminus but not the conserved N-terminus motifs of MEP-1 and that is necessary and sufficient for nuclear zinc-finger MEP-1 protein binding; MOG-3 interacts with CIR-1 and with MEP-1 via two distinct domains; MOG proteins represses fem-3 via MEP-1 binding; mog-3 is expressed at steady state levels throughout embryogenesis and during larval development when hermaphrodites switch to oogenesis and also in adults; MOG-3 is a ubiquitous nuclear protein mainly expressed in oocyte lineage; similar to CIR-1, MOG-3 is also detected in somatic and meiotic nuclei as well as developing L4 vulva.
• Organism: Caenorhabditis elegans
• Automated Description: Involved in feminization of hermaphroditic germ-line and meiotic cell cycle. Located in nucleus. Expressed in germ line. Is an ortholog of human CWC25 (CWC25 spliceosome associated protein homolog).
• Biotype: SO:0001217
• Genetic Position: III :-1.83752±
• Length (nt): 2545

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003391

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F52C9.7.2	F52C9.7.2	1425	III: 5308596-5311140
Transcript:F52C9.7.1	F52C9.7.1	1415	III: 5308602-5311136

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F52C9.7	F52C9.7	1356	III: 5308602-5308765

9 RNAi Result

• WBRNAi00007714
• WBRNAi00067605
• WBRNAi00047954
• WBRNAi00110123
• WBRNAi00108014
• WBRNAi00015390
• WBRNAi00005621
• WBRNAi00077843
• WBRNAi00032602

40 Allele

• q74
• WBVar02067528
• WBVar01263557
• WBVar00056316
• WBVar00056321
• WBVar00056326
• WBVar00056331
• WBVar01644652
• WBVar01644653
• WBVar01644654
• WBVar01445699
• oz146
• WBVar01445701
• gk826397
• gk320779
• gk757489
• gk895099
• gk834377
• gk851076
• oz152
• gk406195
• gk174458
• gk174457
• gk746867
• WBVar01893358
• gk667644
• gk720435
• gk867958
• gk335916
• gk625938

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003391
• Start: 5308596
• End: 5311140
• 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_5311141..5311239
• Length (nt): 99
• Chromosome Location: III: 5311141-5311239
• Organism: Caenorhabditis elegans

93 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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
	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 vulva.	FPKM >= 1.	WBPaper00064122:vulva_transcriptome
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 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
	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
	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 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
	Genes with increased RNA expression after 24 hours rotenone treatment	EdgeR provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting p-values were adjusted using the Benjamini and Hochbergs approach for controlling the false discovery rate (FDR). Transcripts with an adjusted p-value smaller 0.05 were assigned as differentially expressed.	WBPaper00044426:rotenone_24h_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
	Transcripts detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
	Genes that were not enriched in either spermatogenic fem-3(q96gf) nor oogenic fog-2(q71) gonads, according to RNAseq analysis.	To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq.	WBPaper00045521:Gender_Neutral
	Transcripts that showed significantly decreased expression in nhl-2(ok818) comparing to in N2 at 25C.	EdgeR, FDR < 0.05, fold change < 0.5.	WBPaper00055971:nhl-2(ok818)_25C_upregulated
	Transcripts that showed decreased expression in hlh-11(ko1) knockout strain comparing to in wild type background.	DESeq2, FDR < 0.05	WBPaper00060683:hlh-11(ko1)_downregulated
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly decreased expression in hpx-2(dg047) 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_hpx-2(dg047)
	Genes found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014.	N.A.	WBPaper00026929:sir-2.1_overexpression_regulated
	Transcripts of coding genes that showed significantly increased 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_enriched_coding-RNA
	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_downregulated
	Transcripts that showed significantly increased expression in cfp-1(tm6369) comparing to in N2 at early embryo stage.	DESeq2, FDR < 0.05	WBPaper00058691:cfp-1(tm6369)_upregulated
	Genes expressed in N2.	Expressed transcripts were identified on the basis of a Present call in 3 out of 4 N2 experiments as determined by Affymetrix MAS 5.0.	WBPaper00025141:N2_Expressed_Genes
	Transcripts that showed significantly decreased expression in aak-1(tm1944);aak-2(ok524) animals comparing to in N2.	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:aak-1(tm1944);aak-2(ok524)_downregulated
	Transcripts with significantly increased expression in isp-1(qm150) vs. N2, and in isp-1(qm150) ced-4(n1162) vs. ced-4(n1162).	Comparisons of each genotype were compared to the wild-type using the Empirical Base (Wright & Simon) algorithm and fold changes were represented on a log2 scale. A threshold of p < 0.05 and a fold change of 1.3 (log2) was set to determine differentially expressed targets.	WBPaper00045263:isp-1(qm150)_upregulated
	Genes depleted in muscle cells (24hr muscle dataset). Dissociated myo-3::GFP embryos were cultured for 24 hours before FACS sorting.	A two-class unpaired analysis was performed to identify genes that are elevated 1.7-fold or greater when compared with the reference for each dataset, at a false discovery rate of 1.8% or less for M0 and 1.2% or less for the M24 datasets.	WBPaper00031003:24hr_muscle_depleted

8 Expression Patterns

• Primary Identifier: Expr1031563
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1151775
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr9046
• Remark: Picture: Fig 2P, 2Q.
• Subcellular Localization: In the germ line, MOG-3 was found in all mitotic and meiotic nuclei, except in secondary spermatocytes and spermatids. No staining was detected in mog-3 mutants indicating that the antibody is specific. Hence, MOG-3 is a ubiquitous nuclear protein that is mainly present in the oocyte lineage.

• Primary Identifier: Expr9044
• Remark: Picture: Fig 2B to 2H, Fig S1B. The transgene partially rescued the Mog phenotype of mog-3(oz152) homozygotes grown at 25 centigrade since authors found 72% of transgenic fertile adults, while in the absence of the transgene, only 15% were fertile.
• Pattern: A mog-3::gfp transgene expressed in most tissues of the embryo but also in larvae and adults.
• Subcellular Localization: The MOG-3::GFP fusion protein was essentially present in the nucleus, as predicted by two nuclear localization signals.

• Primary Identifier: Expr9045
• Remark: Picture: Fig 2I to 2O.
• Pattern: Using antibodies against MOG-3 authors found one major 53 kD protein in extracts from wild type and masculinized fem-3(gf) animals, but not in mog-3 mutants. MOG-3 was more abundant in wild type than in fem-3(gf) animals indicating that the protein is expressed in embryos or oocytes, which are absent in the masculinized fem-3(gf) mutant.

• Primary Identifier: Expr9043
• Remark: Picture: Fig 2A.
• Pattern: The steady-state levels of the mog-3 transcript throughout embryonic and larval development indicate that mog-3 is expressed in embryos and during late larval development, when hermaphrodites switch to oogenesis.

• Primary Identifier: Expr2013650
• 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: Expr2031884
• 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

5 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003391
• Start: 5308596
• End: 5311140
• Strand: 1

14 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 2545

1 Sequence Ontology Term

• Name: gene

1 Strains

• WBStrain00022521

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIII_5306352..5308595
• Length (nt): 2244
• Chromosome Location: III: 5306352-5308595
• Organism: Caenorhabditis elegans