WormMine: Gene WBGene00003885

• WormBase Gene ID: WBGene00003885
• Gene Name: osm-5
• Sequence Name: Y41G9A.1
• Brief Description: osm-5 encodes the ortholog of the murine polycystic kidney disease gene Tg737 (which encodes the protein Polaris) and human IFT88; osm-5 is required for the proper morphology of the cilia of chemosensory neurons and is involved in intraflagellar transport; the abnormalities in cilia structure in osm-5 mutants lead to defects in several processes like osmotic avoidance, chemotaxis, dauer formation, male mating and life span; osm-5 is expressed in ciliated sensory neurons and localizes to the transition zones of the amphids, phasmids, labials and rays of the male tail; osm-5 expression is regulated by the RFX-type transcription factor, DAF-19, that also regulates the expression of other genes involved in cilia formation.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable kinesin binding activity. Involved in several processes, including dauer entry; locomotory exploration behavior; and non-motile cilium assembly. Located in ciliary basal body; neuron projection; and non-motile cilium. Part of intraciliary transport particle B. Expressed in amphid sensillum and neurons. Used to study autosomal dominant polycystic kidney disease. Is an ortholog of human IFT88 (intraflagellar transport 88).
• Biotype: SO:0001217
• Genetic Position: X :-12.6622 ±0.00141
• Length (nt): 7216

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003885

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y41G9A.1.1	Y41G9A.1.1	2605	X: 2984263-2991478

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y41G9A.1	Y41G9A.1	2463	X: 2984278-2984358

2 RNAi Result

• WBRNAi00056418
• WBRNAi00095205

145 Allele

• gk963725
• WBVar01601229
• WBVar01601232
• WBVar01601233
• WBVar01601230
• WBVar01601231
• WBVar01601236
• WBVar01601237
• WBVar01601234
• WBVar01601235
• sa126
• sa130
• WBVar02068006
• WBVar00076710
• WBVar00076700
• WBVar00076705
• WBVar00076706
• WBVar00076707
• WBVar00076708
• WBVar00076701
• WBVar00076702
• WBVar00076703
• WBVar00076704
• WBVar00076709
• WBVar00076697
• WBVar00076698
• WBVar00076699
• WBVar00076696
• WBVar02123482
• WBVar02123427

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003885
• Start: 2984263
• End: 2991478
• 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_chrX_2991479..2995821
• Length (nt): 4343
• Chromosome Location: X: 2991479-2995821
• Organism: Caenorhabditis elegans

203 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased expression in L1 neural cells comparing to in adult neural cells.	DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction.	WBPaper00060811:L1_vs_adult_upregulated_neural
	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 enriched in ASG according to single cell RNAseq.	Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched.	WBPaper00061651:ASG_enriched
	Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology.	DESEQ2, fold change > 2 and FDR < 0.01.	WBPaper00062103:neuron_enriched
	Genes that showed increased expression in wdr-5(ok1417) comparing with in N2.	Statistical analysis for misexpression was performed using a moderated t test from the package limma. All genes with a false discovery rate (FDR) of <= 5% (p <= 0.05) were selected as differentially regulated.	WBPaper00045861:wdr-5(ok1417)_upregulated
	Single-cell RNA-Seq cell group 71_0 expressed in neuron.	scVI 0.6.0	WBPaper00065841:71_0
	Transcripts that showed significantly decreased expression in atfs-1(cmh15) (null allele) animals comparing to in N2 animals at L4 larva stage.	edgeR, fold change > 2, FDR < 0.05	WBPaper00060909:atfs-1(cmh15)_downregulated
	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 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 after four-day-old young adult worms were placed on NGM plates seeded with OP50 in the presence 5% Agaro-oligosaccharides(AGO) for 24 h, comparing to animals grown in the absence of AGO.	Fold change > 2.	WBPaper00064306:Agaro-oligosaccharides_upregulated
	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
	Top 300 transcripts enriched in ABalppppppa, ABpraaapppa according to single cell RNAseq.	Top 300 enriched transcripts were determined by log2.ratio of the tpm in the cell type vs the tpm in the other cells * the log2 of the cell.type tpm.	WBPaper00061340:ASE_parent
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
	Transcripts that showed significantly decreased expression in sin-3(tm1276) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult.	DESeq2, fold change > 2, adjusted p-value < 0.01	WBPaper00058598:sin-3(tm1276)_downregulated
	Transcripts that showed significantly increased expression in hpk-1(pk1393) comparing to in N2 at adult day 2.	DESeq 2, fold change > 2, FDR < 0.05.	WBPaper00065581:hpk-1(pk1393)_upregulated
	Transcripts that showed significantly increased expression in hda-1(ne4752[3xFLAG-Degron-HDA-1]) in gonads dissected from 1-day old adult animals.	Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R.	WBPaper00061479:hda-1(ne4752)_upregulated
	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 hda-2(ok1479) comparing to in N2 animals.	DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2.	WBPaper00062159:hda-2(ok1479)_upregulated
	Transcripts that showed significantly increased expression in srbc-48(ac23);kyIs262;fer-1(b232ts) comparing to in kyIs262;fer-1(b232ts), 24h after infection with P.aeruginosa.	DESeq2, FDR <0.05, fold change > 2.	WBPaper00059664:srbc-48(ac23)_upregulated
	Transcripts that showed significantly increased expression in dpy-21(e428) comparing to in N2 during L3 stage.	DESeq v1.6.3. Fold change > 1.5.	WBPaper00050370:dpy-21(e428)_L3_upregulated
	Transcripts that showed significantly decreased 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)_downregulated
	Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(+), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_P-granule(-)GFP(+)_vs_control_day2-adult
	Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(-), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_P-granule(-)GFP(-)_vs_control_day2-adult
	Genes expressed in N2.	Expressed transcripts were identified on the basis of a Present call in 3 out of 4 N2 experiments as determined by Affymetrix MAS 5.0.	WBPaper00025141:N2_Expressed_Genes
Bacteria infection: Enterococcus faecalis OG1RF. 16 hours of exposure after L4 larva stage at 25C.	Transcripts that showed significantly increased expression in skpo-1(ok1640) animals fed by E. faecalis strain OG1RF for 16 hours after L4 larva stage at 25C.	DESeq2, fold change > 2.	WBPaper00061081:E.faecalis_upregulated_skpo-1(ok1640)
	Transcripts that showed significantly increased expression in spr-1(ok2144) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:spr-1(ok2144)_upregulated
	Transcripts that showed significantly increased expression in emb-4(hc60) comparing to in N2.	DESeq2	WBPaper00052884:emb-4(hc60)_upregulated
	Transcripts that showed significantly increased expression in sma-2(rax5) comparing to in N2 at 1-day post-L4 adult hermaphrodite	HTseq-count was used to count reads mapped to each gene and counting data was imported to EdgeR for statistical analysis. Statistical significance was defined by adjusted P value (false discovery rate, FDR) of <0.05.	WBPaper00053184:sma-2(rax5)_upregulated

13 Expression Patterns

• Primary Identifier: Expr1031829
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr856
• Pattern: Using either antibody, prominent OSM-5 protein staining was observed in the transition zones and cilia of the sensory neurons, including the amphids, phasmids, labials and rays of the male tail. Little or no staining was observed in the cell bodies or other areas of the worm.
• Subcellular Localization: Expressed in the transitional zone and cilia of sensory neurons.

• Primary Identifier: Expr857
• Remark: All transgenic lines were screened for dye filling of the amphid and phasmid neurons to confirm rescue of the osm-5(p813) cilia defects and show that the OSM-5GFP fusion protein was functional.
• Pattern: Analysis of OSM-5GFP expression reveals almost exclusive localization to the transition zones and cilia of amphids, phasmids, labials and rays of the male tail.
• Subcellular Localization: Expressed in the transitional zone and cilia of sensory neurons.

• Primary Identifier: Expr855
• Pattern: GFP expression in animals transgenic for pCJ3 was first observed around the 2-fold stage of embryogenesis and continued throughout development and in the adult worm. The pattern of GFP fluorescence was consistent with expression in all ciliated sensory neurons including the amphids, phasmids, and inner and outer labials. GFP expression was also observed in the sensory rays of the male tail.
• Subcellular Localization: Expressed in the transitional zone and cilia of sensory neurons.

• Primary Identifier: Expr1345
• Pattern: osm-5::gfp is expressed in ciliated sensory neurons in both hermaphrodites and males. osm-5::gfp expression coincides with the timing of ciliogenesis and continues throughout adulthood.
• Subcellular Localization: OSM-5::GFP is cytoplasmically localized in the basodendritic (cell body and dendrite) compartment of sensory neurons and has the highest concentration in ciliated endings. Axonal expression is not observed. In contrast, a nonfunctional, nonrescuing OSM-5::GFP fusion protein lacking the TPR domains (OSM-5 TPR::GFP) is not observed in sensory cilia, but rather is uniformly distributed throughout the neuron, including the axon.

• Primary Identifier: Expr10121
• Remark: Promoter::GFP fusion constructs of variable lengths were generated using PCR amplification followed by subsequent cloning into expression vectors.
• Pattern: Expressed in both the amphid and tail ciliated sensory neurons. The 60 C. elegans CSNs present in an adult hermaphrodite worm were divided into 5 subgroups or anatomical regions including, neurons that reside in the amphids (region 1 = 24 CSNs: AWAL/R, AWBL/R, AWCL/R, AFDL/R, ASEL/R, ADFL/R, ASGL/R, ASHL/R, ASIL/R, ASJLR, ASKL/R, ADLL/R) or in the tail (region 2 = 5 CSNs: PHAL/R, PHBL/R, PQR), neurons surrounding the anterior bulb (region 3 = 24 CSNs: BAGL/ R, CEPVL/R, CEPDL/R, IL1L/R, IL2L/R, IL1VL/R, IL2VL/R, IL1DL/R, IL2DL/R, OLLL/R, OLQVL/R, OLQDL/R) or the posterior bulb (region 4 = 5 CSNs: ADEL/R, FLPL/R, AQR) of the pharynx, and neurons in the midbody region of the worm (region 5=2 CSNs: PDEL/R). osm-5 was detected in all 5 regions.

• Primary Identifier: Expr1023416
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2032877
• 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: Expr2014644
• 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: Expr1159901
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr853
• Pattern: A 2.6 kb transcript was observed at highest levels during embryogenesis and early larval stages. Expression decreased, relative to actin controls, to almost undetectable levels during L4 and adult stages.

• Primary Identifier: Expr13661
• Pattern: A wild-type OSM-5::GFP fusion protein localized to cilia when expressed in ASI.

• Primary Identifier: Expr854
• Pattern: RT-PCR analysis confirmed that osm-5 is still expressed in both L4 and adult worms, albeit at very low levels.

22 GO Annotation

4 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003885
• Start: 2984263
• End: 2991478
• Strand: 1

22 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 7216

1 Sequence Ontology Term

• Name: gene

2 Strains

• WBStrain00030797
• WBStrain00035629

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrX_2984127..2984262
• Length (nt): 136
• Chromosome Location: X: 2984127-2984262
• Organism: Caenorhabditis elegans