WormMine: Gene WBGene00001597

• WormBase Gene ID: WBGene00001597
• Gene Name: gld-3
• Sequence Name: T07F8.3
• Brief Description: gld-3 encodes two KH domain-containing RNA-binding proteins, GLD-3L and GLD-3S, that are homologous to Drosophila Bicaudal-C; gld-3 activity is required for two aspects of germ line development: the sperm/oocyte and mitosis/meiosis decisions; in regulating the sperm/oocyte switch, GLD-3L acts by binding and negatively regulating FBF's regulatory interaction with the fem-3 3'UTR; in regulating the mitosis/meiosis decision, GLD-3 functions with GLD-2, the catalytic subunit of a poly (A) polymerase, and in parallel to GLD-1 and NOS-3, to positively regulate entry into meiosis as germ cells move away from the distal, mitotic region of the gonad; in contrast to the sperm/oocyte decision, gld-3 functions downstream of FBFs, which bind specifically to elements in the gld-3S 3'-UTR to regulate GLD-3 expression, in the mitosis/meiosis decision; gld-3 activity is also required for germline survival and early embryogenesis; GLD-3 is a cytoplasmic protein that is found in the early embryo and in the germline throughout development in both sexes; in the early embryo, GLD-3 is also seen in cytoplasmic particles, some of which are coincident with P granules.
• Organism: Caenorhabditis elegans
• Automated Description: Enables polynucleotide adenylyltransferase activator activity and protein domain specific binding activity. Involved in several processes, including cytosolic mRNA polyadenylation; developmental process involved in reproduction; and positive regulation of meiotic nuclear division. Located in P granule. Part of RNA-directed RNA polymerase complex. Expressed in germ line and in male.
• Biotype: SO:0001217
• Genetic Position: II :0.495502 ±0.000121
• Length (nt): 4880

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001597

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T07F8.3a.1	T07F8.3a.1	3564	II: 7132643-7137522
Transcript:T07F8.3b.1	T07F8.3b.1	2002	II: 7132643-7135327

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T07F8.3a	T07F8.3a	2910	II: 7132643-7132767
CDS:T07F8.3b	T07F8.3b	1812	II: 7132643-7132767

26 RNAi Result

• WBRNAi00052780
• WBRNAi00062882
• WBRNAi00022762
• WBRNAi00062888
• WBRNAi00085712
• WBRNAi00077892
• WBRNAi00022760
• WBRNAi00105924
• WBRNAi00022761
• WBRNAi00022763
• WBRNAi00062831
• WBRNAi00062834
• WBRNAi00062835
• WBRNAi00062883
• WBRNAi00001745
• WBRNAi00007667
• WBRNAi00062884
• WBRNAi00062885
• WBRNAi00062886
• WBRNAi00062887
• WBRNAi00062829
• WBRNAi00062830
• WBRNAi00062832
• WBRNAi00062833
• WBRNAi00103820
• WBRNAi00106139

53 Allele

• gk963801
• gk963053
• q730
• q741
• WBVar02121138
• WBVar01438371
• WBVar01438370
• gk476022
• gk322572
• gk826810
• gk400035
• gk408582
• gk711651
• gk826811
• gk616531
• gk744572
• gk668158
• gk676229
• gk625134
• gk770438
• gk433914
• gk516747
• gk705887
• gk572610
• gk355512
• gk683035
• gk447200
• gk350719
• gk385404
• gk482885

1 Chromosome

• WormBase ID: II
• Organism: Caenorhabditis elegans
• Length (nt): 15279421

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001597
• Start: 7132643
• End: 7137522
• 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_chrII_7137523..7144606
• Length (nt): 7084
• Chromosome Location: II: 7137523-7144606
• Organism: Caenorhabditis elegans

204 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
	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
	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
	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 decreased expression in day 3 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_daf-16(mu86);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)
	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
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
	Transcripts that showed significantly increased expression in hrde-1(tm1200) animals, comparing to in N2, after growing at 25C for five generations (late generation).	CuffDiff2	WBPaper00051265:F4_hrde-1(tm1200)_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
	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
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

7 Expression Patterns

• Primary Identifier: Expr1030958
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr12329
• Pattern: In wild type animals, GLD-3 was detectable in the germ line, but only at a low level in the mitotic region, barely detectable in the transition zone, and higher in the pachytene region.

• Primary Identifier: Expr2269
• Pattern: Wild-type adults of either sex expressed both GLD-3L and GLD-3S. By contrast, adult glp-1(ts) hermaphrodites, which have virtually no germline, had no detectable GLD-3, consistent with the idea that gld-3 is expressed specifically in the germline. Furthermore, the deletion mutant, gld-3(q730), made no detectable GLD-3, confirming specificity of the antibodies.
• Subcellular Localization: The GLD-3 subcellular distribution was investigated by immunocytochemistry. Similar results were obtained using either anti-GLD-3 or anti-GLD-3L. In most experiments, antibodies to the P granule protein PGL-1 were used to highlight germ cells and P granules. The data support three main conclusions. First, GLD-3 protein is predominantly cytoplasmic. GLD-3 was found in germline cytoplasm throughout development in both sexes and in the cytoplasm of early embryos. Second, GLD-3 distribution is controlled spatially and temporally. In adult hermaphrodites, GLD-3 was detectable in the transition zone (TZ), where germ cells enter meiotic prophase; it was fainter in the early mitotic region and in pachytene germ cells; however, as germ cells entered diakinesis, GLD-3 became abundant. During spermatogenesis, GLD-3 was present in primary spermatocytes, but not in secondary spermatocytes or mature sperm. A similar pattern was observed in males. Third, GLD-3 colocalizes with P granules. GLD-3 was found in the cytoplasm of early embryos, and colocalized with P granules from the 1-cell stage through the 64-cell stage; beyond the 100-cell stage of embryogenesis, GLD-3 was no longer detected. GLD-3 also appeared in particles that were near but not coincident with P granules. In the germline, GLD-3 was found both diffusely as well as in a more granular form. The granular GLD-3 was found primarily at the cytoplasmic side of the nuclear boundary and often colocalized with PGL-1. Mutant embryos derived from gld-3(q730) homozygous mothers could contain apparently normal P granules that appeared to segregate normally to a single blastomere; however, these gld-3 mutant embryos had no detectable GLD-3, consistent with the idea that this mutant removes most gld-3 activity.

• Primary Identifier: Expr2030324
• 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: Expr2012088
• 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: Expr1156387
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1025390
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

31 GO Annotation

9 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001597
• Start: 7132643
• End: 7137522
• Strand: 1

31 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 4880

1 Sequence Ontology Term