WormMine: Gene WBGene00003839

• WormBase Gene ID: WBGene00003839
• Gene Name: ocr-2
• Sequence Name: T09A12.3
• Brief Description: ocr-2 encodes a TRPV (transient receptor potential channel, vanilloid subfamily) ion channel; OCR-2 activity is required for several types of sensory transduction including olfaction, osmosensation, mechanosensation, and chemosensation; an OCR-2 fusion protein is expressed in sensory cilia and requires the OSM-9 TRPV channel protein for proper localization; likewise, OSM-9 requires OCR-2 for its cilial localization.
• Organism: Caenorhabditis elegans
• Automated Description: Enables temperature-gated cation channel activity. Involved in heat acclimation. Located in non-motile cilium and plasma membrane. Expressed in several structures, including SMDVL; body ganglion; head neurons; lumbar neurons; and uterus. Human ortholog(s) of this gene implicated in several diseases, including keratosis (multiple); motor neuron disease (multiple); and osteochondrodysplasia (multiple). Is an ortholog of human TRPV5 (transient receptor potential cation channel subfamily V member 5).
• Biotype: SO:0001217
• Genetic Position: IV :3.68122 ±0.004018
• Length (nt): 6300

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003839

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T09A12.3a.1	T09A12.3a.1	2871	IV: 8213788-8220087
Transcript:T09A12.3b.1	T09A12.3b.1	1431	IV: 8213905-8216458

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T09A12.3a	T09A12.3a	2703	IV: 8213905-8214135
CDS:T09A12.3b	T09A12.3b	1431	IV: 8213905-8214135

2 RNAi Result

• WBRNAi00052912
• WBRNAi00018482

79 Allele

• gk964278
• gk964500
• gk962765
• gk963722
• gk963417
• otn8753
• tm11320
• gk946394
• gk685618
• gk832913
• gk869770
• gk683202
• gk927683
• WBVar01839025
• gk740209
• gk697663
• gk419215
• gk375411
• gk445139
• gk504876
• gk927682
• gk506068
• gk462011
• gk432077
• gk827950
• gk608678
• gk417237
• gk637408
• WBVar00190997
• gk666598

1 Chromosome

• WormBase ID: IV
• Organism: Caenorhabditis elegans
• Length (nt): 17493829

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003839
• Start: 8213788
• End: 8220087
• 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_chrIV_8213742..8213787
• Length (nt): 46
• Chromosome Location: IV: 8213742-8213787
• Organism: Caenorhabditis elegans

89 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
	Single-cell RNA-Seq cell group 84_0 expressed in neuron.	scVI 0.6.0	WBPaper00065841:84_0
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
	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
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
	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 increased expression in aak-1(tm1944);aak-2(ok524) animals comparing to in N2.	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:aak-1(tm1944);aak-2(ok524)_upregulated
	Transcripts that showed significantly decreased expression in N2 animals exposed to 0.1mM Paraquat from hatching to reaching adult stage.	DESeq2 version 1.22.2, p < 0.05	WBPaper00064716:paraquat_downregulated
	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
	Transcripts that showed significantly increased expression in xrep-4(lax137).	DESeq2. Genes were selected if their p value < 0.01.	WBPaper00066062:xrep-4(lax137)_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 decreased expression in eat-2(ad1116) comparing to in N2 at 3-days post L4 adult hermaphrodite animals.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:eat-2(ad1116)_downregulated
	Transcripts that showed significantly decreased 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_downregulated
	Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Allantoin_downregulated
	Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin and 50mM Metformin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Metformin_downregulated
	Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin and 50uM Rifampicin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Rifampicin_downregulated
	Transcripts that showed significantly decreased expression after animals were treated with 50uM Rifampicin and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin-Allantoin_downregulated
	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 with >4.0 fold increased expression in glp-1(ts) animals comparing to in N2 control at 25 centigrade. fold change = glp-1(ts) + vector vs. N2 + vector.	Fold change > 4.0 for glp-1(ts) regulated genes, and fold change < 0.67 for skn-1(RNAi) regulated genes.	WBPaper00047132:glp-1(ts)-25C_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
	Transcripts that showed significantly increased expression in sma-4(rax3) 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-4(rax3)_upregulated

9 Expression Patterns

• Primary Identifier: Expr4976
• Remark: Picture: Figure 4A and supplemental Table S1.
• Pattern: OCR-2 reporter expression was found in sensory neurons. These sensory neurons have no known role in egg laying. In addition, OCR-2 reporter was expressed in cells of the egg-laying system. These were the four uterus-associated uv1 cells attached to the ventral surface of the uterus, as well as the syncytial uv1-associated cell utse. In adults, OCR-2 reporter expression was much stronger in uv1 than in utse; in larval animals, it was the reverse.

• Primary Identifier: Expr1031810
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr15395

• Primary Identifier: Expr1983
• Pattern: ocr-2::GFP was expressed in four pairs of amphid sensory neurons, AWA, ADL, ASH, and ADF, and the two pairs of phasmid neurons, PHA and PHB.

• Primary Identifier: Expr3165
• Remark: Whereas ocr-2(ak47) animals carrying the OCR-2::FLAG transgene restore tph-1 expression (68% show strong tph-1::gfp in ADF; n = 79), ocr-2(ak47) animals that carry OCR-2(G36E)::FLAG (n = 79) exhibit reduced tph-1::gfp expression as their nontransgenic siblings (n = 235). These data indicate that FLAG-tagged OCR-2 is localized to the cellular sites in which OCR-2 acts and that the G36E substitution does not alter the subcellular localization. These results suggest that the G36E substitution disrupts the function of the OCR-2/OSM-9 channel in the ADF neurons.
• Pattern: The immunoreactivity of OCR-2::FLAG and OCR-2(G36E)::FLAG is detected in the cilia and plasma membrane of the chemosensory neurons ADF, AWA, ASH, and ADL.
• Subcellular Localization: Expressed in cilia and plasma membrane of the chemosensory neurons ADF, AWA, ASH, and ADL.

• Primary Identifier: Expr1156513
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1025107
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2014597
• 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: Expr2032830
• 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).

18 GO Annotation

22 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003839
• Start: 8213788
• End: 8220087
• Strand: -1

18 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 6300

1 Sequence Ontology Term

• Name: gene

9 Strains

• WBStrain00023454
• WBStrain00026371
• WBStrain00026384
• WBStrain00026394
• WBStrain00026395
• WBStrain00036435
• WBStrain00040166
• WBStrain00007483
• WBStrain00005264

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIV_8220088..8222201
• Length (nt): 2114
• Chromosome Location: IV: 8220088-8222201
• Organism: Caenorhabditis elegans