WormMine: Gene WBGene00001689

• WormBase Gene ID: WBGene00001689
• Gene Name: gpr-2
• Sequence Name: C38C10.4
• Brief Description: gpr-2 encodes a protein containing a GPR (G Protein Regulator)/GoLoco motif characteristic of guanine nucleotide exchange factors specific for G-alpha GTPases; GPR-2 appears to function redundantly during early embryogenesis and germ-line development to regulate chromosome and spindle movements during cell division; GPR-2 likely acts as a positive regulator of G protein signaling and specifically, may regulate GOA-1 signaling in the embryo; GPR-2 forms a protein complex with the nearly identical GPR-1 and with LIN-5, a coiled-coil protein that is required for proper localization of GPR-2 to the cell cortex and spindle asters of the early embryo; in addition, proper GPR-2/GPR-1/LIN-5 localization between the P2 and EMS blastomeres at the four-cell stage, which may contribute to spindle positioning in EMS, requires the MES-1/SRC-1 tyrosine kinase signaling pathway; GPR-2 is believed to act downstream of, or in parallel to, PAR-3, a PDZ domain-containing protein, in mitotic spindle positioning in the early embryo.
• Organism: Caenorhabditis elegans
• Automated Description: Enables GDP-dissociation inhibitor activity. Predicted to be involved in cell division. Located in aster and cell cortex. Expressed in P lineage cell.
• Biotype: SO:0001217
• Genetic Position: III :0.469922 ±0.005225
• Length (nt): 1835

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001689

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C38C10.4.1	C38C10.4.1	1680	III: 9391330-9393164

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C38C10.4	C38C10.4	1578	III: 9391409-9391629

55 RNAi Result

• WBRNAi00079125
• WBRNAi00063517
• WBRNAi00079126
• WBRNAi00112450
• WBRNAi00088409
• WBRNAi00024776
• WBRNAi00082386
• WBRNAi00099910
• WBRNAi00100370
• WBRNAi00029651
• WBRNAi00086697
• WBRNAi00071862
• WBRNAi00076386
• WBRNAi00078200
• WBRNAi00086689
• WBRNAi00069692
• WBRNAi00110350
• WBRNAi00063511
• WBRNAi00069693
• WBRNAi00042134
• WBRNAi00045289
• WBRNAi00088423
• WBRNAi00063505
• WBRNAi00100744
• WBRNAi00071333
• WBRNAi00071346
• WBRNAi00101236
• WBRNAi00101293
• WBRNAi00099304
• WBRNAi00099506

23 Allele

• gk964518
• gk963887
• tm964
• WBVar01267069
• gk555602
• gk577157
• gk668850
• gk655839
• WBVar01893644
• gk475149
• gk568338
• WBVar01447527
• snx4530
• WBVar01447530
• WBVar01447528
• snx831
• gk182036
• WBVar01645858
• ok1179
• gk182037
• otn5874
• otn5875
• snx2690

1 Chromosome

• WormBase ID: III
• Organism: Caenorhabditis elegans
• Length (nt): 13783801

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001689
• Start: 9391330
• End: 9393164
• Strand: -1

3 Data Sets

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

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrIII_9390108..9391329
• Length (nt): 1222
• Chromosome Location: III: 9390108-9391329
• Organism: Caenorhabditis elegans

127 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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
Osmotic stress	Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_Food
	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
	Transcripts that showed significantly increased expression after animals were treated with 100uM Psora and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Psora-Allantoin_upregulated
Heat shock: 35C for 1 hour.	Transcripts that showed significantly increased expression immediately after 1-day post L4 adult hermaphrodite endu-2(tm4977) animals were exposed to 35C for 1 hour.	The DESeq2 (GalaxyVersion 2.11.40.6 + galaxy1) was used to determine differentiallyexpressed features from count tables of differential transcript abundances. log2FC > 1, FDR < 0.01.	WBPaper00065749:Heat-Shock_upregulated_endu-2(tm4977)
	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
	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
	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 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 decreased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_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)
	Transcripts that showed significantly decreased expression in daf-16(mgDf50) comparing to in N2 at L1 larva stage.	DESeq v1.20.0 was used to analyze differential gene expression. Transcripts with adjusted p-value < 0.05 were considered differentialled expressed.	WBPaper00048971:daf-16(mgDf50)_downregulated_L1
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
	Transcripts depleted in purified oocyte P bodies comparing to in whole oocytes.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00065975:P-body_vs_oocyte_depleted
	Transcripts depleted in purified oocyte P bodies comparing to in the whole animal.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00065975:P-body_vs_WholeAnimal_depleted
	Transcripts that showed significantly decreased expression in dissected female germline comparing to in dissected male germline.	Log2 Fold change > 2 or <-1, p-value < 0.05.	WBPaper00053599:female_vs_male_downregulated
Temprature shift to 28C for 24 hours.	Transcripts that showed significantly decreased expression after animals were exposed to 28C temperature for 24 hours.	Differentially expressed genes wereidentified using DESeq (v.1.18.0) by normalizing readsbased on the negative binomial distribution method andcomparing each HS timepoint to the 0-h control.	WBPaper00061341:28C_24h_downregulated
	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 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 the neurons of bcat-1(RNAi) animals at 5-days post L4 adult hermaphrodite stage, comparing to animals injected with empty vector.	DESeq2. FDR < 0.05.	WBPaper00060459:bcat-1(RNAi)_downregulated
	Genes regulated by DAF-12, according to whole transcriptome profiling to compare genome-wide regulatory influences of DPY-21 and SET-4 to those of the key transcription factors controlling dauer arrest in eak-7;akt-1 animals, DAF-16 and DAF-12.	Authors identified genes differentially expressed between wild-type and eak-7;akt-1 double mutant animals [fold change >= 1.5 and false discovery rate (FDR) < 0.05]. Authors then compared the transcriptomes of eak-7;akt-1 double mutants to those of eak-7;akt-1 animals harboring mutations in dpy-21, set-4, daf-16, or daf-12, and identified genes that are differentially expressed in the opposite direction as in wild-type relative to eak-7;akt-1. Annotated gene expression data output from CuffDiff v2.2.1 was read into R version 3.2.1 for six comparisons: eak-7;akt-1 compared to (1) wild-type, (2) daf-16(mu86);eak-7;akt-1, (3) daf-12;eak-7;akt-1, (4) set-4(n4600);eak-7;akt-1, (5) set-4(dp268);eak-7;akt-1, and (6) dpy-21;eak-7;akt-1. Authors filtered genes by the following criteria: (1) status = OK for wild-type vs. eak-7;akt-1, (2) fold change (FC) >= 1.5 or FC <= 1/1.5 for wild-type vs. eak-7;akt-1 and (3) FDR < 0.05 for at least two separate comparisons.	WBPaper00050801:DAF-12_dauer_regulome
	Genes regulated by DAF-16, according to whole transcriptome profiling to compare genome-wide regulatory influences of DPY-21 and SET-4 to those of the key transcription factors controlling dauer arrest in eak-7;akt-1 animals, DAF-16 and DAF-12.	Authors identified genes differentially expressed between wild-type and eak-7;akt-1 double mutant animals [fold change >= 1.5 and false discovery rate (FDR) < 0.05]. Authors then compared the transcriptomes of eak-7;akt-1 double mutants to those of eak-7;akt-1 animals harboring mutations in dpy-21, set-4, daf-16, or daf-12, and identified genes that are differentially expressed in the opposite direction as in wild-type relative to eak-7;akt-1. Annotated gene expression data output from CuffDiff v2.2.1 was read into R version 3.2.1 for six comparisons: eak-7;akt-1 compared to (1) wild-type, (2) daf-16(mu86);eak-7;akt-1, (3) daf-12;eak-7;akt-1, (4) set-4(n4600);eak-7;akt-1, (5) set-4(dp268);eak-7;akt-1, and (6) dpy-21;eak-7;akt-1. Authors filtered genes by the following criteria: (1) status = OK for wild-type vs. eak-7;akt-1, (2) fold change (FC) >= 1.5 or FC <= 1/1.5 for wild-type vs. eak-7;akt-1 and (3) FDR < 0.05 for at least two separate comparisons.	WBPaper00050801:DAF-16_dauer_regulome
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 found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014.	N.A.	WBPaper00026929:sir-2.1_overexpression_regulated
	TGF- Dauer pathway adult transcriptional targets. Results obtained by comparing the microarray results of the dauer-constitutive mutants daf-7(e1372), daf-7(m62), and daf-1(m40) with dauer-defective mutants daf-3(mgDf90), daf-5(e1386), and daf-7(e1372);daf-3(mgDf90) double mutants at the permissive temperature, 20C, on the first day of adulthood.	SAM	WBPaper00031040:TGF-beta_adult_downregulated
	Germline-intrinsic transcripts.	Comparisons were made between genotypes by subtracting the mean log value of one ratio from another, and the significance of the difference was evaluated using Student t-test for two populations. For the fem-3(gf) versus fem-1(lf) direct comparison, authors performed the same analysis, except they used a Students t-test for one population. Author chose a combination of a twofold difference with a t value exceeding 99% confidence (P < 0.01), because these criteria allowed the inclusion of essentially all genes that had previously been identified as germline-enriched in a wt/glp-4 hermaphrodite comparison. Additionally, requiring a twofold difference reduced false positives, as the number of genes with two-fold difference and a P<0.01 only included ~100 genes more than with P < 0.001, and almost all genes showed germline expression by in situ hybridization.	[cgc6390]:intrinsic
	Transcripts down regulated in hpl-2(tm1489) embryo comparing to N2 in tiling array analysis.	Oligos from the tiling array were mapped to chromosome coordinates of the exons from Wormbase WS180. Any oligo that mapped to a gene on both the Watson and Crick strands was excluded. The remaining oligos were then grouped together (perfect match and mismatch) into probe sets and written out into an Affymetrix CDF file. The CDF file was converted into an R-package and loaded into R. The expression values were calculated using the justRMA function from Bioconductor. This used a Benjamini and Hochberg false discovery rate correction.	WBPaper00040560:hpl-2_embryo_downregulated
	Transcripts that showed significantly increased expression in set-2(tm1630) animals at embryo stage, comparing to in N2 animals.	DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction.	WBPaper00060014:set-2(tm1630)_upregulated

8 Expression Patterns

• Primary Identifier: Expr1031008
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1146135
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2012214
• 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: Expr2564
• Remark: The close sequence identity of gpr-1 and gpr-2 prevented distinguishing between them in the experiments.
• Subcellular Localization: During all mitotic divisions examined, GPR-1/GPR-2 and LIN-5 were present at the cell cortex and spindle asters. GPR-1/GPR-2 and LIN-5 were detected at the spindle asters and at the membranes between germ-precursor nuclei in the distal gonad arms. During the formation and maturation of oocytes, GPR-1/GPR-2 and LIN-5 localized diffusely to the cytoplasm and more prominently to the nuclear and cytoplasmic membranes, in particular to membranes between adjacent oocytes. Following fertilization and meiosis, GPR-1/GPR-2 and LIN-5 appeared at the duplicated centrosomes associated with the sperm pronucleus. GPR-1/GPR-2 and LIN-5 both became progressively more abundant at the spindle asters during the formation of the first mitotic spindle. Both proteins also localized diffusely around the kinetochore MTs in metaphase. Although the latter localization disappeared in early anaphase, GPR-1/GPR-2 and LIN-5 persisted at the spindle asters until chromosome decondensation in telophase. On completion of cell cleavage, GPR-1/GPR-2 and LIN-5 were detected only at the cell cortex and cytoplasm. This pattern of spindle-associated localizations was repeated during subsequent mitotic divisions. The cortical localization appeared enriched between blastomeres, especially the cortical staining of LIN-5. No other asymmetries in localization were detected until the four-cell stage. At that stage, both LIN-5 and GPR-1/GPR-2 showed significant accumulation at the boundary between the EMS and P2 blastomeres. Similar asymmetries were detected during some of the subsequent divisions. Unlike LIN-5, GPR-1/GPR-2 were not detected at the meiotic spindle. In 15/18 embryos, GPR-1/GPR-2 antiserum diffusely stained the maternal pronucleus or condensed meiotic chromosomes. However, this staining is likely not specific, as similar staining was seen in 9/16 gpr-1/gpr-2(RNAi) embryos. In contrast, LIN-5 was abundantly present at the polar regions of the meiotic spindle.

• Primary Identifier: Expr10765
• Subcellular Localization: In early wild-type embryos, GPR-1/2 were localized both on the asters and the cell cortex. The cortical localization of GPR- 1/2 changed with the cell cycle. In one-cell embryos, GPR-1/2 were uniformly present at a low level on the cortex from early prophase to metaphase. The level of cortical localization of GPR-1/2 increased and became weakly enriched at the posterior pole of most embryos during anaphase. In some embryos with enriched posterior staining, GPR-1/2 also appeared to be slightly enriched at the anterior pole of the embryo, compared with lateral regions. GPR-1/2 asymmetry became more pronounced during cytokinesis and interphase of the two-cell stage. In the P1 blastomere during interphase, GPR-1/2 were highly enriched around the posterior pole of the cell, and were present at low levels uniformly around the cortex of AB. As the cell cycle progressed, GPR-1/2 asymmetry in P1 disappeared; GPR-1/2 were uniformly localized around the cortex through out prophase, metaphase and early anaphase. During late anaphase and telophase, GPR-1/2 were once again enriched at the posterior part of the P1 cell. These results indicate that GPR- 1/2 is asymmetrically localized in the P lineage.

• Primary Identifier: Expr1200200
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr1013915
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2030450
• 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).

9 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001689
• Start: 9391330
• End: 9393164
• Strand: -1

9 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 1835

1 Sequence Ontology Term