WormMine: Gene WBGene00003891

• WormBase Gene ID: WBGene00003891
• Gene Name: osm-11
• Sequence Name: F11C7.5
• Brief Description: osm-11 encodes a protein required for normal osmosensation, osmotic resistance, and defecation rhythm, and for fully normal growth rate; OSM-11 has no clear orthologs outside of nematodes, but is paralogous to DOS-1, OSM-7, and K02F3.7, has a predicted signal sequence with 12 conserved cysteine residues, and may be secreted; osm-11 mutants have abnormally high levels of internal glycerol, defective osmotic avoidance, and slowed defecation rhythms characteristic of worms under chronic osmotic stress; osm-11 mutants are also somewhat scrawny and slow-growing; osm-11(RNAi) animals show constitutive gpdh-1 transcription.
• Organism: Caenorhabditis elegans
• Automated Description: Enables Notch binding activity. Involved in several processes, including positive regulation of Notch signaling pathway; response to osmotic stress; and vulval development. Located in apical part of cell and extracellular space. Expressed in several structures, including P3.p hermaphrodite; P4.p hermaphrodite; P5.p hermaphrodite; P8.p hermaphrodite; and hermaphrodite gonad.
• Biotype: SO:0001217
• Genetic Position: X :24.0914 ±0.001543
• Length (nt): 1372

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003891

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F11C7.5.1	F11C7.5.1	1176	X: 17420211-17421468
Transcript:F11C7.5.2	F11C7.5.2	1173	X: 17420217-17421582

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F11C7.5	F11C7.5	570	X: 17420756-17421273

23 RNAi Result

• WBRNAi00095565
• WBRNAi00088841
• WBRNAi00088843
• WBRNAi00044373
• WBRNAi00073019
• WBRNAi00073018
• WBRNAi00107614
• WBRNAi00013122
• WBRNAi00030820
• WBRNAi00096031
• WBRNAi00064455
• WBRNAi00027273
• WBRNAi00096355
• WBRNAi00096262
• WBRNAi00095879
• WBRNAi00097002
• WBRNAi00096521
• WBRNAi00096108
• WBRNAi00096619
• WBRNAi00025079
• WBRNAi00095956
• WBRNAi00096438
• WBRNAi00096185

38 Allele

• gk964260
• gk963810
• gk963581
• rt68
• rt142
• gk528547
• gk819077
• WBVar01554893
• gk684995
• gk839209
• gk958125
• gk456495
• h5891
• gk342648
• gk330836
• gk763572
• gk491809
• gk529526
• gk828783
• gk592041
• gk618068
• gk731239
• gk823110
• gk612085
• gk496326
• gk415496
• gk532031
• gk662425
• gk724049
• WBVar00603778

1 Chromosome

• WormBase ID: X
• Organism: Caenorhabditis elegans
• Length (nt): 17718942

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003891
• Start: 17420211
• End: 17421582
• Strand: -1

3 Data Sets

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

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrX_17414015..17420210
• Length (nt): 6196
• Chromosome Location: X: 17414015-17420210
• Organism: Caenorhabditis elegans

202 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	oocyte proteins identified by two or more unique peptides during proteomics study.	In the pooled data set, 1453 C. elegans proteins were identified with a probability >= 0.9 according to ProteinProphet, of which 1165 proteins were identified by more than one unique peptide.	WBPaper00038289:oocyte_protein
	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
	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_upregulated
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
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
	Transcripts that showed significantly increased expression glp-1(e2141); TU3401 animals comparing to in TU3401 animals.	Fold change > 2, FDR < 0.01.	WBPaper00065993:glp-1(e2141)_upregulated
Bacteria infection: Enterococcus faecalis	Genes with increased expression after 24 hours of infection by E.faecalis Fold changes shown are pathogen vs OP50.	For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated.	WBPaper00038438:E.faecalis_24hr_upregulated_TilingArray
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	Transcripts expressed in the epithelial tissues surrounding the pharynx that includes the arcade and intestinal valve (AIV) cells, according to PAT-Seq analysis using Pbath-15-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:arcade_intestinal-valve_expressed
	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
	Genes up regulated in alg-1(gk214) comparing to in N2.	Differential expression was assessed using an empirical Bayes statistics using the eBayes function.	WBPaper00040823:alg-1(gk214)_upregulated
	Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:pharynx_expressed
	Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_daf-16(mu86);glp-1(e2141)
	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 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)
	Single-cell RNA-Seq cell group 0_0 expressed in seam.	scVI 0.6.0	WBPaper00065841:0_0
	Genes with expression level regulated by genotype (N2 vs CB4856) at Late reproduction stage (96 hours at 24 centigrade).	Authors permuted transcript values and used a genome-wide threshold of log10 P-value = 2, which resembles a false discovery rate (FDR) of 0.0118.	WBPaper00040858:eQTL_regulated_reproductive
	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 increased expression in rrf-3(pk1426) comparing to in N2 at embryo stage.	DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01.	WBPaper00056169:rrf-3(pk1426)_upregulated_embryo
	Transcripts that showed significantly increased expression in sin-3(tm1276) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:sin-3(tm1276)_upregulated
Dietary restriction	Transcripts that showed significantly decreased expression after N2 animals were under dietary restriction (DR, OP50 OD = 0.1) from 3-day post L4 till 6-day post L4 adult hermaphrodite stage, comparing to under ad libtum (AL, OP50 OD = 3) condition.	Bioconductor package edgeR, p < 0.05.	WBPaper00056443:DietaryRestriction_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

8 Expression Patterns

• Primary Identifier: Expr1031834
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr8248
• Remark: Picture: Figure 4. The larval hypodermal expression pattern of osm-11p::gfp is reminiscent of the osm-7p::gfp expression pattern described previously, but osm-7p::gfp expression in seam cells was not reported.
• Pattern: In animals harboring this transgene, GFP expression was observed in numerous unidentified cells during embryonic development from the comma stage onward. GFP expression was observed in the VPCs during larval development, as well as various hypodermal cells during larval stages. In adult animals, osm-11p::gfp was expressed only in hypodermal seam cells in adult animals.

• Primary Identifier: Expr8249
• Remark: Picture: Figure 4.
• Pattern: OSM-11 was expressed in the VPCs of L3 larvae prior to and during cell fate specification. OSM-11 immunoreactivity was also observed in the seam cells of L1 larvae and adult animals. Hypodermal seam cell expression in adult animals was also confirmed with staining with OSM-11 antisera. OSM-11 protein was also expressed in the developing uterus of L4 larvae and in the spermatheca.

• Primary Identifier: Expr9280
• Pattern: OSM-11 immunoreactivity was detected in coelomocytes, which are endocytic cells that clear secreted proteins from the pseudocoelom. Because the osm-11 promoter does not drive expression in coelomocytes, OSM-11 is likely secreted into the pseudocoelom, diffuses, and accumulates in coelomocytes.

• Primary Identifier: Expr2014640
• 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: Expr1016420
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1148316
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2032873
• 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).

14 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003891
• Start: 17420211
• End: 17421582
• Strand: -1

14 Ontology Annotations

1 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Genes with expression altered >= 3-fold in osm-11(n1604) 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:osm-11_regulated

1 Sequence

• Length: 1372

1 Sequence Ontology Term

• Name: gene

3 Strains

• WBStrain00027087
• WBStrain00027083
• WBStrain00008296

0 Upstream Intergenic Region