WormMine: Gene WBGene00003864

• WormBase Gene ID: WBGene00003864
• Gene Name: oma-1
• Sequence Name: C09G9.6
• Brief Description: oma-1 encodes a zinc finger protein of the TIS11 finger type that is paralogous to OMA-2; while either oma-1 or oma-2 individually have no obvious mutant phenotype, oma-1 and oma-2 doubly mutant animals show defects in oocyte maturation, indicating that the two genes function redundantly in this process; whereas normal oocytes are released from meiotic prophase I arrest during oocyte maturation, oma-1;oma-2 mutant oocytes initiate, but fail to complete, maturation, arresting at a defined point in meiotic prophase I; the meiotic arrest of oma-1;oma-2 mutant oocytes is suppressed by wee-1.3(RNAi), implying that progression through meiotic prophase I is critically dependent on inhibition of WEE-1.3 by either OMA-1 or OMA-2; OMA-1 is expressed primarily in maturing oocytes, is cytoplasmic and visible prior to cellularization.
• Organism: Caenorhabditis elegans
• Automated Description: Enables mRNA 3'-UTR AU-rich region binding activity and mRNA regulatory element binding translation repressor activity. Involved in several processes, including meiotic nuclear membrane disassembly; oocyte development; and regulation of reproductive process. Located in P granule and centrosome. Expressed in several structures, including head muscle; intestine; neurons; somatic nervous system; and vulva. Is an ortholog of human ZFP36L1 (ZFP36 ring finger protein like 1) and ZFP36L2 (ZFP36 ring finger protein like 2).
• Biotype: SO:0001217
• Genetic Position: IV :3.99916 ±0.001096
• Length (nt): 2024

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003864

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C09G9.6.1	C09G9.6.1	1801	IV: 8888976-8890999

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C09G9.6	C09G9.6	1224	IV: 8889086-8889123

29 RNAi Result

• WBRNAi00083346
• WBRNAi00001622
• WBRNAi00040248
• WBRNAi00040249
• WBRNAi00024310
• WBRNAi00007531
• WBRNAi00010556
• WBRNAi00110294
• WBRNAi00085815
• WBRNAi00110296
• WBRNAi00028746
• WBRNAi00110297
• WBRNAi00093710
• WBRNAi00083347
• WBRNAi00083348
• WBRNAi00101307
• WBRNAi00101308
• WBRNAi00078444
• WBRNAi00078447
• WBRNAi00078448
• WBRNAi00083445
• WBRNAi00083444
• WBRNAi00077779
• WBRNAi00083447
• WBRNAi00083446
• WBRNAi00083449
• WBRNAi00024309
• WBRNAi00083448
• WBRNAi00083458

56 Allele

• gk964278
• gk964500
• gk962765
• gk962666
• gk963722
• te21
• te26
• te22
• te27
• te30
• te28
• te35
• te33
• te41
• te36
• ne3800
• gk563605
• gk771058
• red118
• gk361073
• gk719120
• red20
• gk727392
• red35
• gk824360
• red40
• red57
• tm1396
• zu450
• gk207993

1 Chromosome

• WormBase ID: IV
• Organism: Caenorhabditis elegans
• Length (nt): 17493829

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003864
• Start: 8888976
• End: 8890999
• 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_chrIV_8891000..8891461
• Length (nt): 462
• Chromosome Location: IV: 8891000-8891461
• Organism: Caenorhabditis elegans

212 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
	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
	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:bodywall-muscle_L1-larva_expressed
	Genes that showed significantly increased expression in wrn-1(gk99) comparing to in N2, according to RNAseq.	DESeq was used to calculate the fold changes, log fold changes, and significance of the changes for each comparison.	WBPaper00045934:wrn-1(gk99)_upregulated
	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 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 increased expression in day 1 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_daf-16(mu86);glp-1(e2141)
	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)
	Genes with expression level regulated by genotype (N2 vs CB4856) 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_regulated_developing
	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: 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
	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 alg-1(gk214), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-1(gk214)_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

16 Expression Patterns

• Primary Identifier: Expr1031820
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr7830
• Remark: Picture: Fig. 1. The OMA-1a, OMA-1b and OMA-2a signals in oocytes were completely abolished by absorption using their corresponding antigenic peptides. Furthermore, RNAi treatment of oma-1 and oma-2 abolished the fluorescence signals from anti-OMA-1b, anti-OMA-1a and anti-OMA-2a antibodies.
• Pattern: Anti-OMA antibodies strongly and exclusively stained wild-type developing oocytes.

• Primary Identifier: Expr7831
• Remark: Picture: Fig. 1. The OMA-1a, OMA-1b and OMA-2a signals in oocytes were completely abolished by absorption using their corresponding antigenic peptides. Furthermore, RNAi treatment of oma-1 and oma-2 abolished the fluorescence signals from anti-OMA-1b, anti-OMA-1a and anti-OMA-2a antibodies.
• Pattern: Anti-OMA antibodies strongly and exclusively stained wild-type developing oocytes.

• Primary Identifier: Expr7427
• Remark: Clone: pUL#JS6A2 No detailed description on cellular expression patterns in other life stages..
• Pattern: GFP expression was seen in many nerves, including nerves of the head, tail and ventral nerve cord, with high level of expression in the nerve ring. L4 and young adult show expression in cells either side of the vulva. There is also expression in the head muscles and weak expression in the anterior and posterior intestine.

• Primary Identifier: Expr8516
• Remark: Picture: Figure S2.
• Pattern: The level of OMA-1 protein is high in one-cell embryos soon after meiosis but decreases during the first mitotic cycle. In two-cell embryos, although the majority of OMA-1 protein has been degraded, a low level (<10%) can still be detected.

• Primary Identifier: Expr2582
• Subcellular Localization: The OMA-1::GFP fluorescence in the developing oocytes and one-cell embryos recapitulated the wild-type spatial and temporal patterns of OMA-1 antibody staining. The punctate staining appeared more pronounced and resembled the characteristic pattern of germline P granules. Starting with the onset of the first mitotic division, the intensity of OMA-1-GFP fluorescence rapidly decreased, and by the time the division was complete, only approximately 10% remained. Interestingly, that remaining 10% of the GFP signal in the two-cell embryo was predominantly found in the germline precursor, P1, associated with what appeared to be P granules. The GFP signal continued to decrease in two-cell embryos and again was asymmetric after the next division, with most of the remaining fluorescence segregated to P2, where it was also predominantly associated with granules. The OMA-1-GFP signal became too weak to detect in the embryo after the four-cell stage.

• Primary Identifier: Expr2222
• Pattern: In situ experiments revealed that the gene is specifically and exclusively expressed in the female gonad. There is essentially no signal in the spermatheca. Although gonadal staining is not absolutely quantitative, it was evident that moe-1 gene transcript is widely distributed throughout gonadal oocytes from the mitotic stage to the developing diakinesis stage.

• Primary Identifier: Expr2225
• Remark: Immunocytochemical staining using anti-MOE-1-specific antibodies revealed cytoplasmic expression in oocytes in the proximal region of the gonads. The distribution of MOE-1 protein in proximal oocytes corresponds to that of the MOE-2 protein. An interesting finding is the characteristic timing of MOE protein appearance during the course of oogenesis. Despite the fact that mRNAs of the MOE family are expressed from the most-distal region of the female gonads, the corresponding proteins start to accumulate only after the diakinesis stage. This finding indicates the existence of posttranscriptional regulation of moe mRNAs translation. Picture: Fig. 6A, 6C.
• Pattern: Immunocytochemical staining revealed cytoplasmic expression in oocytes in the proximal region of the gonads. Immunocytochemical staining using anti-MOE-1 antibody revealed cytoplasmic expression in oocytes in the proximal region of the gonads. The distribution of MOE-1 protein in proximal oocytes corresponds to that of the MOE-2 protein. An interesting finding is the characteristic timing of MOE protein appearance during the course of oogenesis. Despite the fact that mRNAs of the MOE family are expressed from the most-distal region of the female gonads, the corresponding proteins start to accumulate only after the diakinesis stage. This finding indicates the existence of posttranscriptional regulation of moe mRNAs translation.
• Subcellular Localization: cytoplasmic expression

• Primary Identifier: Expr9127
• Subcellular Localization: Expressed in the cytoplasm with increasing levels in growing oocytes, peaking in the oocyte undergoing maturation. The level of OMA-1 protein remain very high following fertilization as well as throughout the first mitotic cycle. The antibody staining often included a slight punctate pattern of fluorescence. Immediately after the first mitotic division, the levels of OMA-1 protein rapidly decreased and became difficult to detect with antibody staining.

• Primary Identifier: Expr1850
• Pattern: OMA-1 expression is detectable prior to oocyte cellularization. Expression is not detected in sperm or the spermatheca, nor are they detected in oma-1(te33);oma-2(te51) mutant oocytes. The expression of OMA-1 continues in the 1-cell embryo, but is not detected in 2-cell or older embryos.
• Subcellular Localization: Expression is cytoplasmic and increases as the oocytes develop, peaking in the maturing oocyte.

• Primary Identifier: Expr1848
• Pattern: Assay 1: A developmental Western blot using synchronized populations indicates that OMA-1 was expressed only in the adult with very little, if any, expression detectable in L1 through L4 larval stages. Assay 2: Extracts were prepared from three temperature-sensitive mutant strains that are defective in different aspects of germline development. At the permissive temperature (15 Centigrades) in all three strains, OMA-1 was expressed. At the nonpermissive temperature (25 Centigrades), glp-4(bn2) mutant worms do not produce a germline and do not express OMA-1. fem-3(e2006) mutant worms produce only oocytes and no sperm at 25 C and express OMA-1. Semidominant mutants fem-3(q20sd) at 25 C produce only sperm and no oocytes and do not express OMA-1. Thus, OMA-1 protein is expressed primarily in adult oocytes but not in sperm, consistent with the functional assay.

• Primary Identifier: Expr2014626
• 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: Expr12000
• Subcellular Localization: OMA-1 is a component of riboncleoprotein particles (RNPs).

• Primary Identifier: Expr1018409
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2032859
• 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: Expr1144318
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

41 GO Annotation

16 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003864
• Start: 8888976
• End: 8890999
• Strand: 1

41 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 2024

1 Sequence Ontology Term

• Name: gene

8 Strains

• WBStrain00035066
• WBStrain00035069
• WBStrain00035068
• WBStrain00035067
• WBStrain00040434
• WBStrain00040433
• WBStrain00048324
• WBStrain00052677

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIV_8888568..8888975
• Length (nt): 408
• Chromosome Location: IV: 8888568-8888975
• Organism: Caenorhabditis elegans