WormMine: Gene WBGene00011376

• WormBase Gene ID: WBGene00011376
• Gene Name: gla-3
• Sequence Name: T02E1.3
• Brief Description: gla-3 encodes a TIS11-like protein with two CCCH-like zinc-fingerdomains that inhibits apoptosis in the germline, and weakly inhibitsRAS signalling in vulval development along with RAS-induced muscleprotein degradation; GLA-3 inhibits physiological apoptosis inoocytes, keeping it down to a normal level of ~50% in hermaphroditegonads; gla-3 is expressed in the germline of L4 larvae and adults,and interacts with mpk-1 both genetically and physically; gla-3requires core apoptotic proteins (CED-3 and CED-4) for its excessapoptotic mutant phenotype, but not others (CEP-1, CLK-2, or HUS-1)required for DNA damage-induced apoptosis; gla-3 mutants haveincreased germline apoptosis and reduced brood size due to defectivepachytene exit from meiosis I, and also show weak enhancment of themultivulva phenotype of let-60(gf) or lip-1(zh15) mutations; gla-3mutants have temperature-sensitive progressive muscle dystrophy,consistent with hyperactivation of the RAS/MAPK pathway in musclecells; gla-3(RNAi) hermaphrodites display elevated levels ofphysiological germline apoptosis, independent of CEP-1.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable metal ion binding activity. Located in cell cortex. Expressed in germ line; muscle cell; and somatic cell.
• Biotype: SO:0001217
• Genetic Position: I :2.67909 ±0.008301
• Length (nt): 3621

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00011376

Genomics

3 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T02E1.3c.1	T02E1.3c.1	2391	I: 8214376-8217995
Transcript:T02E1.3a.1	T02E1.3a.1	2392	I: 8214382-8217996
Transcript:T02E1.3b.1	T02E1.3b.1	2040	I: 8214698-8217573

Other

3 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T02E1.3a	T02E1.3a	1941	I: 8214410-8214444
CDS:T02E1.3c	T02E1.3c	1935	I: 8214410-8214444
CDS:T02E1.3b	T02E1.3b	2040	I: 8214698-8214748

23 RNAi Result

• WBRNAi00052210
• WBRNAi00000423
• WBRNAi00004104
• WBRNAi00004105
• WBRNAi00087669
• WBRNAi00098593
• WBRNAi00098592
• WBRNAi00065422
• WBRNAi00064200
• WBRNAi00065425
• WBRNAi00035058
• WBRNAi00111681
• WBRNAi00061557
• WBRNAi00116815
• WBRNAi00098590
• WBRNAi00064174
• WBRNAi00065421
• WBRNAi00097927
• WBRNAi00098145
• WBRNAi00098146
• WBRNAi00098591
• WBRNAi00097729
• WBRNAi00097867

50 Allele

• gk962858
• gk962706
• gk963902
• gk963849
• gk964316
• gk963044
• gk963043
• gk387134
• gk578019
• gk408904
• gk442392
• gk745226
• gk749373
• gk804575
• gk831220
• op216
• op212
• gk484870
• gk442709
• gk403335
• gk2779
• gk793672
• gk677196
• gk405920
• gk116474
• gk513033
• gk116479
• gk116480
• gk514029
• gk638026

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00011376
• Start: 8214376
• End: 8217996
• Strand: 1

3 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)

0 Downstream Intergenic Region

185 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
	Transcripts that showed significantly decreased expression in AGP22 [nhr-49(nr2041)I;glp-1(e2141)III] comparing to in CF1903 [glp-1(e2144)III] at Day 2 adults.	Fold change > 2, p Value of < 0.05 and a false discovery rate (FDR) of < 0.05.	WBPaper00061530:nhr-49(e2144)_downregulated
	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
Osmotic stress	Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when no food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_NoFood
	Genes that were upregulated in lin-15B(n744).	For each gene in each microarray hybridization experiment, the ratio of RNA levels from the two samples was transformed into a log2 value and the mean log2 ratio was calculated. The log2 ratios were normalized by print-tip Loess normalization (Dudoit and Yang, 2002). All genes with a false discovery rate of <= 5% (q <= 0.05) (Storey and Tibshirani, 2003) and a mean fold-change ratio of >= 1.5 were selected for further analysis.	WBPaper00038168:lin-15B(n744)_upregulated
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:hypodermis_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 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)
	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: 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 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 animals exposed to 400uM tamoxifen from L1 to L4 larva stage.	DEseq2, fold change > 2	WBPaper00064505:tamoxifen_upregulated
	Transcripts that showed significantly changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals.	Sleuth	WBPaper00051558:aging_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 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
	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
	Transcripts that showed significantly altered expression at URX, AQR, and PQR neurons in camt-1(ok515) animals comparing to in wild type AX1888-1 strain.	RNA-seq data were mapped using PRAGUI - a Python 3-based pipeline for RNA-seq data analysis.	WBPaper00061902:camt-1(ok515)_regulated_URX-AQR-PQR
	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
	Transcripts that showed significantly increased expression in hira-1(gk835598) comparing to in N2 animals at L4 larva stage.	Differential expression analysis was done with Rversion 2.15.3 using DESeq_1.10.1. Fold change > 2, p-value < 0.01.	WBPaper00059739:hira-1(gk835598)_upregulated_L4

11 Expression Patterns

• Primary Identifier: Expr1022656
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr7989
• Remark: Picture: Fig. 3A.
• Pattern: gla-3 expressed in embryos, L4-stage larvae, and adults, with the highest expression being in L4 larvae.

• Primary Identifier: Expr7990
• Remark: Picture: Fig. 3B.
• Pattern: At the nonpermissive temperature, glp-4(bn2ts) mutants produce a somatic gonad that is largely devoid of germ cells, fem-2(e2105ts) mutants make oocytes but no sperm, and fem-3(q20sd) mutants make sperm but no oocytes. gla-3 expression was detected in all three mutant backgrounds, demonstrating that gla-3 is expressed in both germline and soma.

• Primary Identifier: Expr7991
• Remark: Picture: Fig. 3C.
• Pattern: GFP expression was observed throughout the germline from the L4 stage onward and in all cells of the early embryo. Expression was also observed in muscle cells in 3-fold stage embryos.

• Primary Identifier: Expr2030280
• 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: Expr7992
• Remark: Picture: Fig. 3D.
• Pattern: Western blot analysis of synchronized wild-type worms revealed that both isoforms are expressed at the L4 and adult stages, whereas no expression was detectable from the L1 to L3 stages, nor in gla-3(op212) mutants.

• Primary Identifier: Expr13387
• Pattern: GFP::3xFLAG::GLA-3A is expressed in the germline cytoplasm from the distal tip to near the bend region of the gonad.

• Primary Identifier: Expr7993
• Remark: No detailed description on expression pattern at embryo stage. Picture: Fig. 3E.
• Pattern: GLA-3B was detectable in L4 and adult gonads. The protein was expressed in the mitotic and meiotic zones of the adult germline, and localized to the cytoplasmic compartment, with an enrichment in cortical/submembrane regions; a similar pattern of expression was observed with GLA-3A. The GLA-3B staining was absent in the gonads of gla-3(op212) mutants.
• Subcellular Localization: The protein was expressed in the mitotic and meiotic zones of the adult germline, and localized to the cytoplasmic compartment, with an enrichment in cortical/submembrane regions

• Primary Identifier: Expr2012044
• 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: Expr1155842
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1035006
• Pattern: Tiling arrays expression graphs

8 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00011376
• Start: 8214376
• End: 8217996
• Strand: 1

8 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 3621

1 Sequence Ontology Term

• Name: gene

6 Strains

• WBStrain00032710
• WBStrain00040534
• WBStrain00040533
• WBStrain00040532
• WBStrain00004784
• WBStrain00005746

0 Upstream Intergenic Region