WormMine: Gene WBGene00002173

• WormBase Gene ID: WBGene00002173
• Gene Name: itr-1
• Sequence Name: F33D4.2
• Brief Description: itr-1 encodes a putative inositol (1,4,5) trisphosphate receptor that affects the defecation cycle and pharyngeal pumping, and also affects ovulation in a pathway downstream of LET-23; interacts with UNC-54 in vivo, and is expressed in the adult intestine, pharynx, excretory cell, germ line, and spermatheca, with limited neuronal expression.
• Organism: Caenorhabditis elegans
• Automated Description: Enables myosin binding activity. Involved in several processes, including determination of adult lifespan; mating behavior; and system process. Located in endoplasmic reticulum and membrane. Expressed in several structures, including egg-laying apparatus; ganglia; gonad; non-striated muscle; and tail hypodermis. Human ortholog(s) of this gene implicated in several diseases, including Alzheimer's disease; Gillespie syndrome; autosomal dominant cerebellar ataxia (multiple); and diabetes mellitus (multiple). Is an ortholog of human ITPR1 (inositol 1,4,5-trisphosphate receptor type 1); ITPR2 (inositol 1,4,5-trisphosphate receptor type 2); and ITPR3 (inositol 1,4,5-trisphosphate receptor type 3).
• Biotype: SO:0001217
• Genetic Position: IV :3.3765 ±0.003586
• Length (nt): 21757

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00002173

Genomics

6 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F33D4.2a.1	F33D4.2a.1	8906	IV: 7675174-7696930
Transcript:F33D4.2d.1	F33D4.2d.1	8511	IV: 7677568-7696703
Transcript:F33D4.2e.1	F33D4.2e.1	8862	IV: 7681357-7696923
Transcript:F33D4.2f.1	F33D4.2f.1	8827	IV: 7681359-7696923
Transcript:F33D4.2g.1	F33D4.2g.1	5142	IV: 7681425-7691446
Transcript:F33D4.2h.1	F33D4.2h.1	8824	IV: 7681425-7696923

Other

6 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F33D4.2a	F33D4.2a	8679	IV: 7675174-7675252
CDS:F33D4.2d	F33D4.2d	8511	IV: 7677568-7677581
CDS:F33D4.2g	F33D4.2g	5142	IV: 7681425-7681468
CDS:F33D4.2e	F33D4.2e	8574	IV: 7681425-7681468
CDS:F33D4.2f	F33D4.2f	8541	IV: 7681425-7681468
CDS:F33D4.2h	F33D4.2h	8604	IV: 7681425-7681468

50 RNAi Result

• WBRNAi00095605
• WBRNAi00061091
• WBRNAi00089828
• WBRNAi00066969
• WBRNAi00066993
• WBRNAi00066997
• WBRNAi00067003
• WBRNAi00067070
• WBRNAi00067099
• WBRNAi00067287
• WBRNAi00067350
• WBRNAi00067499
• WBRNAi00067723
• WBRNAi00067761
• WBRNAi00000810
• WBRNAi00046203
• WBRNAi00078895
• WBRNAi00085492
• WBRNAi00008743
• WBRNAi00025376
• WBRNAi00061437
• WBRNAi00071711
• WBRNAi00078896
• WBRNAi00078897
• WBRNAi00108178
• WBRNAi00071422
• WBRNAi00063877
• WBRNAi00110595
• WBRNAi00064376
• WBRNAi00022978

221 Allele

• gk964278
• gk964500
• gk963722
• gk963417
• gk963416
• WBVar00243138
• sa73
• gk654434
• gk874139
• WBVar02068722
• sy290
• sy291
• sy327
• sy328
• sy331
• tm902
• WBVar01542855
• gk946346
• WBVar00573506
• WBVar00573503
• h6205
• h4981
• WBVar01966630
• WBVar01966632
• WBVar01966631
• WBVar01786438
• WBVar01729911
• WBVar01729912
• WBVar01913433
• WBVar02047139

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00002173
• Start: 7675174
• End: 7696930
• 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_7696931..7696931
• Length (nt): 1
• Chromosome Location: IV: 7696931-7696931
• Organism: Caenorhabditis elegans

191 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
	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
	Transcripts that showed significantly increased expression in csr-1a(tor159) comparing to in N2 at 25C.	DESeq2, fold change > 2, p-value < 0.05.	WBPaper00061753:csr-1(tor159)_upregulated_25C
Bacteria: E.faecalis strain OG1RF	Transcripts that showed significantly increased expression after infection by E. faecalis OG1RF.	Ballgown was used to calculate differential expression of genes using FPKM data and to generate tables with fold change and P values. Genes were shortlisted with a cutoff of 2-fold change and P values of less than 0.05.	WBPaper00059754:E.faecalis_OG1RF_upregulated
	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 body muscle, according to PAT-Seq analysis using Pmyo-3-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:body-muscle_expressed
	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 expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_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
	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
	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
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h
	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
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
Bacteria infection: Staphylococcus aureus MW2. 4 hours of exposure.	Transcripts that showed significantly increased expression after N2 animals had 4 hours of infection by Staphylococcus aureus (MW2).	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:S.aureus-4h_upregulated_N2
	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
	Significantly differentially expressed genes as determined by microarray analysis of wild-type and cde-1 mutant germlines.	RNAs that changed at least 2-fold with a probability of p < 0.05 were considered differentially regulated between wildtype and cde-1.	WBPaper00035269:cde-1_regulated
	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 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 increased expression in sftb-1(cer6) deletion homozygous comparing to to in N2 animals at L4 larva stage.	DESeq2, fold change > 2	WBPaper00058725:sftb-1(cer6)_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
	Proteins that showed significantly decreased expression after 1-day-old wild type adults were exposed to cisplatin (300ug per mL) for 6 hours.	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:Cisplatin_downregulated_WT
	Transcripts that showed significantly increased expression in animals with germline-specific inx-14(RNAi) comparing to in aniamls fed with control vector, both exposed to PA14 infection.	DESeq2. Differentially-expressed genes (DEG) were identified based on two criteria: FDR (False discovery rateusing Benjamini-Hochberg adjusted p-values) < 0.01 and absolute value of log2(Fold Change) > 1.	WBPaper00066146:germline-inx-14(RNAi)_upregulated_PA14

14 Expression Patterns

• Primary Identifier: Expr1031268
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr826
• Remark: Authors established that itr-1 has three promoters responsible for differential tissue expression.
• Pattern: Expression of pA is observed in the vulva, rectal epithelial (Rep) cells and anterior muscle cells of the pharyngeal terminal bulb.

• Primary Identifier: Expr504
• Remark: Transgenic Marker: rol-6(su1006)
• Pattern: Expressed in intestine, pharynx, pharyngeal intestinal valve, mu_sph, and excretory cell at unspecified stage(es). Expression in ventral nerve cord, spermathecae and germ line observed with immunostaining but not GFP reporter gene. Pharyngeal results differ slightly from GFP reporter gene results (see Expression pattern 503).
• Subcellular Localization: ITR-1 present in membrane preparations by Western blotting.

• Primary Identifier: Expr503
• Remark: Transgenic Marker: rol-6(su1006)
• Pattern: Expressed in intestine, pharynx, pharyngeal terminal bulb, pharyngeal isthmus, pharyngeal intestinal valve, mu_sph, and excretory cell at unspecified stage. Not observed in the nervous system or germ line, which differs from immunostaining results (see Expression pattern 504).
• Subcellular Localization: ITR-1 present in membrane preparations by Western blotting.

• Primary Identifier: Expr828
• Remark: Authors established that itr-1 has three promoters responsible for differential tissue expression.
• Pattern: Expression of pC is observed in the intestine, pharyngeal isthmus and spermathecal (Sp) valve, uterine sheath cells and spermatheca.

• Primary Identifier: Expr1164
• Pattern: Transgenic animals that carry this construct show GFP expression in a variety of tissue types. GFP expression is observed in the intestine, and the posterior cells express GFP more intensely than the remaining intestinal cells. Other cells include the rectal epithelial cells, the pharynx, the somatic gonad, and vulval hypodermal cells. In addition, the IP3 receptor is expressed in hypodermal cells of the tail, rectum, and head. Pharyngeal expression is restricted to the muscles of the metacorpus, isthmus, and the anterior portion of the terminal bulb (m4, m5, and m6). This construct was only expressed in neurons LUA and PDA. GFP is expressed in the gonad sheath cells, spermatheca, spermathecal valve, and uterine sheath cells. GFP is expressed in the vulval hypodermal cells.

• Primary Identifier: Expr827
• Remark: Authors established that itr-1 has three promoters responsible for differential tissue expression.
• Pattern: Expression from pB is observed in the spermatheca, PDA neuron, amphid socket cells and excretory cell.

• Primary Identifier: Expr1150090
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr3391
• Pattern: Expressed in the embryonic epidermis during the process of ventral enclosure.
• Subcellular Localization: ITR-1 is expressed at significant levels in the embryonic epidermis during the process of ventral enclosure. The reticular pattern of staining within these cells suggests that ITR-1 is localized to the ER and close to the plasma membrane. Consistent with Western blot analysis, ITR-1 is also present in jc5 embryos derived from mothers grown at 15N0C, although the overall membrane staining is reduced and more signal is present in the cytoplasm.

• Primary Identifier: Expr3702
• Pattern: Expression in male-specific structures is directed by all three promoters. Promoter pA directs expression in the spicule protractor muscles of the proctodeum and in a single male-specific neuron that is likely to be CP8 or CP9. Promoter pB directs expression in the spicule retractor muscles, gubernaculum retractor muscles, posterior oblique muscles, diagonal muscles, and the vas deferens. Promoter pC also directs expression in the vas deferens, as well as the seminal vesicle and the valve that separates the seminal vesicle and vas deferens. Thus itr-1 is expressed widely in the sex-associated muscles and somatic gonad of males.

• Primary Identifier: Expr13476
• Pattern: Onset of expression: DA9: L2/L3.

• Primary Identifier: Expr2012875
• 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: Expr2031109
• 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: Expr1018824
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

47 GO Annotation

10 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00002173
• Start: 7675174
• End: 7696930
• Strand: 1

47 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 21757

1 Sequence Ontology Term

• Name: gene

11 Strains

• WBStrain00022778
• WBStrain00030832
• WBStrain00030844
• WBStrain00030856
• WBStrain00030857
• WBStrain00030866
• WBStrain00030863
• WBStrain00030862
• WBStrain00034585
• WBStrain00040665
• WBStrain00005344

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIV_7672973..7675173
• Length (nt): 2201
• Chromosome Location: IV: 7672973-7675173
• Organism: Caenorhabditis elegans