WormMine: Gene WBGene00001596

• WormBase Gene ID: WBGene00001596
• Gene Name: gld-2
• Sequence Name: ZC308.1
• Brief Description: gld-2 encodes the catalytic subunit of a cytoplasmic poly(A) polymerase (PAP) associated with P granules in early embryos, which encodes the central catalytic domain but lacks the normal RNA-binding (RRM) domain of eukaryotic PAPs; GLD-2 regulates the switch from mitosis to meiosis in the germline, is necessary for formation of functional sperm or oocytes, requires activation by GLD-3 for PAP activity in vitro, and contains a glutamine/asparagine-rich domain perhaps involved in epigenetic gene control.
• Organism: Caenorhabditis elegans
• Automated Description: Enables poly(A) RNA polymerase activity. Involved in several processes, including cytosolic mRNA polyadenylation; positive regulation of meiosis I; and regulation of cell division. Located in P granule and protein-containing complex. Part of RNA-directed RNA polymerase complex. Expressed in germ line and oocyte. Is an ortholog of human TENT2 (terminal nucleotidyltransferase 2).
• Biotype: SO:0001217
• Genetic Position: I :1.06665 ±0.00142
• Length (nt): 16447

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001596

Genomics

6 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:ZC308.1a.1	ZC308.1a.1	4668	I: 6369748-6386194
Transcript:ZC308.1a.2	ZC308.1a.2	4547	I: 6369934-6386194
Transcript:ZC308.1e.1	ZC308.1e.1	2544	I: 6371389-6385084
Transcript:ZC308.1c.1	ZC308.1c.1	4253	I: 6376660-6386189
Transcript:ZC308.1f.1	ZC308.1f.1	2265	I: 6377619-6385084
Transcript:ZC308.1b.1	ZC308.1b.1	3778	I: 6381375-6386187

Other

5 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:ZC308.1a	ZC308.1a	3342	I: 6370029-6370068
CDS:ZC308.1c	ZC308.1c	3111	I: 6376697-6377466
CDS:ZC308.1f	ZC308.1f	2265	I: 6377619-6377679
CDS:ZC308.1b	ZC308.1b	2616	I: 6381434-6382151
CDS:ZC308.1e	ZC308.1e	2544	I: 6371389-6371506

44 RNAi Result

• WBRNAi00095822
• WBRNAi00106574
• WBRNAi00058829
• WBRNAi00075133
• WBRNAi00075135
• WBRNAi00075134
• WBRNAi00075136
• WBRNAi00075139
• WBRNAi00113595
• WBRNAi00075137
• WBRNAi00075138
• WBRNAi00075140
• WBRNAi00105925
• WBRNAi00085397
• WBRNAi00072794
• WBRNAi00027000
• WBRNAi00027004
• WBRNAi00000653
• WBRNAi00058827
• WBRNAi00004878
• WBRNAi00105917
• WBRNAi00064342
• WBRNAi00064343
• WBRNAi00058828
• WBRNAi00070996
• WBRNAi00116717
• WBRNAi00004877
• WBRNAi00004879
• WBRNAi00027001
• WBRNAi00027002

184 Allele

• gk962858
• gk962706
• gk963902
• otn10669
• otn10670
• otn9322
• tm8652
• q535
• q540
• q497
• gk793987
• gk460250
• WBVar01431874
• WBVar01431873
• WBVar01431875
• gk486172
• gk497441
• gk505187
• gk582160
• gk487941
• gk530047
• gk592416
• gk904816
• gk736990
• gk855234
• gk442867
• gk923484
• gk922851
• gk402728
• gk478288

1 Chromosome

• WormBase ID: I
• Organism: Caenorhabditis elegans
• Length (nt): 15072434

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001596
• Start: 6369748
• End: 6386194
• Strand: 1

4 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)
• Panther orthologue and paralogue predictions

0 Downstream Intergenic Region

161 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 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:bodywall-muscle_L1-larva_expressed
	Transcripts that showed significantly higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc).	DESeq2, fold change >= 2, FDR <= 0.01.	WBPaper00056826:SGP_biased
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	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 seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_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 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 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
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
	Proteins that showed significantly decreased expression in 1-day-old sek-1(km4) adults comparing to in wild type animals, both with 6 hours of cisplatin treatment.	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:sek-1(km4)_downregulated_cisplatin
	Genes that showed expression levels higher than the corresponding reference sample (L2 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:coelomocytes_L2-larva_expressed
	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 that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00066594:ilc-17.1(syb5296)_upregulated
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)
	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 altered expression from P0 to F2 generation animals after N2 parental generation were treated with antimycin, but not in damt-1(gk961032) P0 to F2 animals after the parenal generaton were treated with antimycin.	N.A.	WBPaper00055862:antimycin_damt-1(gk961032)_regulated
	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
Starvation 48 hours at L1 arrest	Transcripts that showed significantly increased expression in starved N2 animals (48 hours at L1 arrest)	Fold change > 2.	WBPaper00064005:starvation_upregulated_N2_mRNA
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 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:coelomocytes_L1-larva_expressed
	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
	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:hypodermis_L1-larva_expressed

12 Expression Patterns

• Primary Identifier: Expr1030957
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1162265
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr443
• Remark: Other strain-- UL725 died out
• Pattern: Expression is confined to adults. It is located in intestinal cells and in the pharynx. Expression is generally weak, and in the pharynx consists of several nuclei around the terminal bulb, some of which may be neuronal.

• Primary Identifier: Expr11999
• Pattern: GLD-2 is poorly expressed in the distal half of the proliferative zone, becomes more abundant further proximal, and is most abundant in cells that have entered meiosis. Intriguingly, the protein expression pattern of GLD-2 does not match its ubiquitous mRNA expression pattern in the distal proliferative zone. This suggests translational regulation of GLD-2 expression.

• Primary Identifier: Expr2217
• Pattern: In situ hybridization showed that it was abundant in the meiotic pachytene region and in oogenesis, but decreased during spermatogenesis.

• Primary Identifier: Expr2218
• Pattern: By immunocytochemistry, GLD-2 was found to be predominantly cytoplasmic in both germ line and early embryo. Within the germ line, GLD-2 was detectable in the mitotic region and became abundant during pachytene and oogenesis. GLD-2 decreased during spermatogenesis in both sexes, and was undetectable in mature sperm. In early embryos, GLD-2 was diffuse in the cytoplasm of early P0 embryos, co-localized with P granules in late P0 embryos and remained associated with P granules in germline blastomeres. In 100-cell embryos, GLD-2 was undetectable.
• Subcellular Localization: cytoplasmic and colocalized with P granules.

• Primary Identifier: Expr2030323
• 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: Expr2012087
• 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: Chronogram1250
• Remark: Original chronogram file: chronogram.2373.xml
• Reporter Gene: [ZC308.1:gfp] transcriptional fusion.

• Primary Identifier: Chronogram1251
• Remark: Original chronogram file: chronogram.2374.xml
• Reporter Gene: [ZC308.1:gfp] transcriptional fusion.

• Primary Identifier: Expr2216
• Pattern: Northern analysis showed that gld-2 4.7kb mRNA was abundant in embryos, fourth larval stages (L4s) and adults

• Primary Identifier: Expr1011501
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

23 GO Annotation

7 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001596
• Start: 6369748
• End: 6386194
• Strand: 1

23 Ontology Annotations

3 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Genes that showed significantly decreased expression in gld-2(RNAi) comparing with control RNAi, according to RNAseq.	Using the DESeq package (R 3.0.2, DESeq version 1.14.0), the count data were normalized by the size factor to estimate the effective library size. After calculating the gene dispersion across all samples, the comparison of two different conditions resulted in a list of differentially expressed genes. Genes with a normalized read count smaller than 100 were ignored in the final analysis. A pre-filtering step was used to calculate the number of genes showing a high probability of being differentially regulated. In this step, genes with a probability (unadjusted P-value) above 0.003 were excluded from the differential expression analysis. Genes with a fold-change higher or equal to two, as well as an adjusted P-value of <= 0.05 was then defined as differentially expressed. The P-values are being adjusted to the multiple testing hypotheses to reduce the false discovery rate (FDR).	WBPaper00045729:gld-2(RNAi)_downregulated
	GLD-2-associated transcripts, based on microarray experiments.	Two-class unpaired SAM (median-centered).	WBPaper00037611:GLD-2-associated
	Genes that showed significantly increased expression in gld-2(RNAi) comparing with control RNAi, according to RNAseq.	Using the DESeq package (R 3.0.2, DESeq version 1.14.0), the count data were normalized by the size factor to estimate the effective library size. After calculating the gene dispersion across all samples, the comparison of two different conditions resulted in a list of differentially expressed genes. Genes with a normalized read count smaller than 100 were ignored in the final analysis. A pre-filtering step was used to calculate the number of genes showing a high probability of being differentially regulated. In this step, genes with a probability (unadjusted P-value) above 0.003 were excluded from the differential expression analysis. Genes with a fold-change higher or equal to two, as well as an adjusted P-value of <= 0.05 was then defined as differentially expressed. The P-values are being adjusted to the multiple testing hypotheses to reduce the false discovery rate (FDR).	WBPaper00045729:gld-2(RNAi)_upregulated

1 Sequence

• Length: 16447

1 Sequence Ontology Term