WormMine: Gene WBGene00003865

• WormBase Gene ID: WBGene00003865
• Gene Name: oma-2
• Sequence Name: ZC513.6
• Brief Description: oma-2 encodes a zinc finger protein of the TIS11 finger type that is paralogous to OMA-1; 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-2 is expressed primarily in maturing oocytes, is cytoplasmic and visible in oocytes after cellularization.
• Organism: Caenorhabditis elegans
• Automated Description: Enables 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 germ line; head muscle; intestine; oocyte; and somatic nervous system. 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: V :1.00434 ±0.000337
• Length (nt): 1776

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003865

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:ZC513.6.1	ZC513.6.1	1546	V: 8029439-8031214

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:ZC513.6	ZC513.6	1182	V: 8029509-8029546

28 RNAi Result

• WBRNAi00083346
• WBRNAi00067307
• WBRNAi00067443
• WBRNAi00067848
• WBRNAi00068066
• WBRNAi00058994
• WBRNAi00008019
• WBRNAi00021742
• WBRNAi00110295
• WBRNAi00110296
• WBRNAi00110297
• WBRNAi00093710
• WBRNAi00083347
• WBRNAi00101307
• WBRNAi00101308
• WBRNAi00078447
• WBRNAi00078448
• WBRNAi00083445
• WBRNAi00083444
• WBRNAi00083447
• WBRNAi00083446
• WBRNAi00083449
• WBRNAi00083448
• WBRNAi00083458
• WBRNAi00038093
• WBRNAi00083349
• WBRNAi00078445
• WBRNAi00024311

32 Allele

• gk963301
• gk963553
• gk964351
• gk962860
• gk964047
• gk964046
• WBVar01862885
• te51
• te50
• tm911
• gk240570
• gk240571
• gk240572
• gk240573
• gk240574
• gk240575
• gk240576
• h15480
• gk746503
• tn1760
• tn1764
• gk339843
• gk408205
• gk391211
• gk906331
• gk469467
• gk855577
• gk741756
• gk757634
• gk368200

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003865
• Start: 8029439
• End: 8031214
• 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_8031215..8031410
• Length (nt): 196
• Chromosome Location: V: 8031215-8031410
• Organism: Caenorhabditis elegans

249 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 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
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
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	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 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 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 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: 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
	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
	mRNAs that showed differential expression in activated AAK-2(uthIs202[aak-2 (intron 1)::aak-2(aa1-aa321)::Tomato::unc-54 3'UTR + rol-6(su1006)]), activiated CRTC-1 (uthEx222[crtc-1p::crtc-1 cDNA (S76S, S179A)::tdTomato::unc-54 3'UTR + rol-6(su1006)]), or AAK-2;CRTC-1 comparing to in N2.	Genes were tested for differential expression between each mutant strain and wild-type using edgeRs glm method. Briefly, negative binomial models were fitted and dispersion estimates obtained. These were then used to calculate average levels of change between conditions and determine differential expression, using the generalized linear model likelihood ratio test. For each comparison, genes with less than 5 CPM were filtered and those with at least 50% change and False Discovery Rate (FDR) of 1% or less were considered differentially expressed.	WBPaper00046499:AMPK_regulated
	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
	Top 300 transcripts enriched in excretory duct, excretory pore according to single cell RNAseq.	Top 300 enriched transcripts were determined by log2.ratio of the tpm in the cell type vs the tpm in the other cells * the log2 of the cell.type tpm.	WBPaper00061340:Excretory_duct_and_pore
	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
	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

13 Expression Patterns

• Primary Identifier: Expr1031821
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1162428
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr7832
• 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: Expr7753
• Remark: Clone: pUL#JRH7B11
• Pattern: Comma stage embryos show weak expression in ventral and dorsal regions. Late embryo to adult, expression is seen in the dorsal and ventral nerve cords and two nerves lateral to the terminal pharyngeal bulb. There is also expression in the intestine and weakly in head muscles.

• Primary Identifier: Expr4135
• 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: Expr2223
• 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-2 gene transcript is widely distributed throughout gonadal oocytes from the mitotic stage to the developing diakinesis stage.

• Primary Identifier: Expr2226
• 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.
• Subcellular Localization: cytoplasmic expression

• Primary Identifier: Expr2581
• Subcellular Localization: Expressed in the cytoplasm with increasing levels in growing oocytes, peaking in the oocyte undergoing maturation. The level of OMA-2 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 level of OMA-2 proteins rapidly decreased and became difficult to detect with antibody staining.

• Primary Identifier: Expr1851
• Pattern: OMA-2 is expressed only in fully cellularized oocytes. 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-2 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: Expr1849
• Pattern: Assay 1: A developmental Western blot using synchronized populations indicates that OMA-2 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-2 was expressed. At the nonpermissive temperature (25 Centigrades), glp-4(bn2) mutant worms do not produce a germline and do not express OMA-2. 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-2. Thus, OMA-2 protein is expressed primarily in adult oocytes but not in sperm, consistent with the functional assay.

• Primary Identifier: Expr1022790
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2014627
• 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: Expr2032860
• 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).

32 GO Annotation

16 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003865
• Start: 8029439
• End: 8031214
• Strand: 1

32 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 1776

1 Sequence Ontology Term