WormMine: Gene WBGene00000802

• WormBase Gene ID: WBGene00000802
• Gene Name: crt-1
• Sequence Name: Y38A10A.5
• Brief Description: crt-1 encodes an ortholog of calreticulin (a calcium-binding molecularchaperone of the endoplasmic reticulum); crt-1 is dispensable forviability, but required for normal sperm development, male matingefficiency, some forms of necrotic cell death, and hermaphrodite fertilityat high temperatures (which may reflect a stress response); crt-1expression is induced by stress; CRT-1 protein binds Ca(2+) and cansuppress heat-induced protein aggregation in vitro; crt-1(bz29) andcrt-1(bz30) mutants suppress necrotic cell death induced either bymec-4(d) or by a constitutively activated Gas subunit; crt-1(bz29);crt-1's suppression of necrosis is itself partly reversed by thapsigargin,which enhances calcium release from the endoplasmic reticulum;crt-1(bz30), and crt-1(jh101) mutants grow more slowly, and have havereduced broods at 25 deg. C.; crt-1(jh101) mutants are slightly shorterthan normal and have defective sperm; CRT-1 and ITR-1 serve partlyredundant functions in vivo, since crt-1;itr-1(sa73) are highly infertileand slow-growing with greatly slowed defecation; a number of proteins,notably HSP-3/4 and PDI-2/3, are over-expressed in crt-1(jh101) mutantsand crt-1(jh101);cnx-1(nr2009) double mutants.
• Organism: Caenorhabditis elegans
• Automated Description: Enables calcium ion binding activity. Involved in several processes, including determination of adult lifespan; hemidesmosome assembly; and response to stress. Located in cytoplasm. Expressed in several structures, including coelomocyte; excretory system; intestine; neurons; and pharynx. Used to study Parkinson's disease. Human ortholog(s) of this gene implicated in several diseases, including endocrine gland cancer (multiple); gastrointestinal system cancer (multiple); and hematologic cancer (multiple). Is an ortholog of human CALR (calreticulin).
• Biotype: SO:0001217
• Genetic Position: V :-0.354153 ±0.004638
• Length (nt): 1551

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000802

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y38A10A.5.1	Y38A10A.5.1	1401	V: 6098992-6100542

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y38A10A.5	Y38A10A.5	1188	V: 6099172-6099414

25 RNAi Result

• WBRNAi00083111
• WBRNAi00009306
• WBRNAi00055972
• WBRNAi00055973
• WBRNAi00109151
• WBRNAi00061159
• WBRNAi00061161
• WBRNAi00093399
• WBRNAi00076768
• WBRNAi00093398
• WBRNAi00109554
• WBRNAi00080521
• WBRNAi00109165
• WBRNAi00083100
• WBRNAi00083125
• WBRNAi00083124
• WBRNAi00075498
• WBRNAi00108500
• WBRNAi00109263
• WBRNAi00065372
• WBRNAi00109457
• WBRNAi00108767
• WBRNAi00109360
• WBRNAi00110983
• WBRNAi00108753

34 Allele

• gk963301
• gk963591
• gk963553
• gk963042
• gk963041
• gk964259
• gk964351
• gk963850
• gk962696
• WBVar00246957
• gk948405
• bz29
• bz30
• bz31
• bz50
• gk236521
• jh101
• gk236522
• gk236520
• gk236525
• gk236526
• gk236523
• gk236524
• gk434463
• gk480641
• gk649304
• gk501705
• gk522985
• gk748310
• gk645381

1 Chromosome

• WormBase ID: V
• Organism: Caenorhabditis elegans
• Length (nt): 20924180

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000802
• Start: 6098992
• End: 6100542
• Strand: -1

4 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)
• Panther orthologue and paralogue predictions

0 Downstream Intergenic Region

199 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
	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
	mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis.	Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05.	WBPaper00045420:fertilization_downregulated_transcript
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
	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 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
	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
	Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:pharynx_expressed
	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 expressed in vulva.	FPKM >= 1.	WBPaper00064122:vulva_transcriptome
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 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_6h
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 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_6h
	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
	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 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 changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals.	Sleuth	WBPaper00051558:aging_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 that showed differential expression between 24 and 26 hours post hatching L2d and dauer committed larvae of daf-9(dh6), triggered by the dafachronic acid (DA) growth hormone. Cluster 3 genes increased expression transiently at 26 hour post hatching.	Benjamini Hochberg corrected q-value < 0.01.	WBPaper00053388:dauer_regulated_Cluster3
	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 detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
	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

12 Expression Patterns

• Primary Identifier: Expr1030500
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr2414
• Remark: Reporter gene fusion type not specified. Weak signals in the nervous system might reflect the fact that the reporter construct, which lacks crt-1 introns and 3' untranslated regions, could be missing sequences critical for high level expression in neurons.
• Pattern: pcrt-1GFP fusion protein is strongly expressed in many tissues throughout development and into adulthood, including intestine, uterus, pharynx, hypodermis, body wall muscle, and coelomocytes. Although some fluorescent neurons was observed in animals genetically mosaic for the pcrt-1GFP transgene, crt-1 did not appear strongly expressed in nervous system.

• Primary Identifier: Expr2411
• Remark: No signals were detected in control experiments with a sense strand probe.
• Pattern: The crt-1 transcripts, both maternal and zygotic, were detected during early embryonic stages and the expression was maintained through adult stages. The signals from the maternally transcribed messages were detected as early as two-cell stage embryo and continued through four-cell stage. As the embryo went through morphogenesis, a strong but restricted signal was detected along the midplane of the embryo indicative of intestinal precursor cell expression. During larval and adult stages, CRT-1 was shown to express strongly along the intestine, which was in conformity with the embryonic expression patterns. In addition, distinct signals were observed in the pharyngeal bulb region.

• Primary Identifier: Expr2412
• Pattern: CRT-1 was detected in the cytoplasm, presumably from the endoplasmic reticulum network, of the early embryo (~100-cell stage) and a strong intestinal staining was observed in both larval and adult worms. Signals were also observed in the terminal bulb region of the pharynx and in excretory cells in the head. Faint but specific staining was also observed in head neurons and body-wall muscle cells.
• Subcellular Localization: CRT-1 was detected in the cytoplasm, presumably from the endoplasmic reticulum network.

• Primary Identifier: Expr11239
• Pattern: Fluorescence was observed in pharyngeal muscle, excretory gland cells, body-wall muscle, intestine, and coelomocytes.

• Primary Identifier: Expr2010544
• 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: Expr1159492
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2028784
• 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: Expr3228
• Pattern: Expression level ratio in egg vs. adult determined by Western analysis and MS is 0.94.

• Primary Identifier: Expr1027238
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2410
• Pattern: A single 1.4-kb transcript was detectable at all stages of development.

• Primary Identifier: Expr2413
• Subcellular Localization: In intestinal cells, clustered signals of CRT-1 were observed around the intestinal vacuoles and intestinal granules of wild-type worms. The intestinal cells of C. elegans are characterized by the appearance of such granules and vacuoles alongside the intestinal lumen. In body-wall muscles, distinct enclosed signals of CRT-1 in the cytoplasmic regions of the muscle cells were observed. In the pharyngeal muscle cells, signals were detected in the cytoplasmic regions between muscular structures.

29 GO Annotation

10 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000802
• Start: 6098992
• End: 6100542
• Strand: -1

29 Ontology Annotations

4 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased expression in crt-1(knu358) animals comparing to in N2 animals at late L4 larva stage.	Fold-change (FC) <= 2 or>= 2 and a false discovery rate (FDR) (q-value) < 0.05	WBPaper00064957:crt-1(knu358)_upregulated
	Transcripts that showed significantly decreased expression in crt-1(knu358) animals comparing to in N2 animals at late L4 larva stage.	Fold-change (FC) <= 2 or>= 2 and a false discovery rate (FDR) (q-value) < 0.05	WBPaper00064957:crt-1(knu358)_downregulated
	Transcripts that showed significantly decreased expression in crt-1(jvp1) animals comparing to in N2 animals at late L4 larva stage.	Fold-change (FC) <= 2 or>= 2 and a false discovery rate (FDR) (q-value) < 0.05	WBPaper00064957:crt-1(jvp1)_downregulated
	Transcripts that showed significantly increased expression in crt-1(jvp1) animals comparing to in N2 animals at late L4 larva stage.	Fold-change (FC) <= 2 or>= 2 and a false discovery rate (FDR) (q-value) < 0.05	WBPaper00064957:crt-1(jvp1)_upregulated

1 Sequence

• Length: 1551

1 Sequence Ontology Term

• Name: gene

6 Strains

• WBStrain00023525
• WBStrain00031729
• WBStrain00040784
• WBStrain00040783
• WBStrain00040782
• WBStrain00040781

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrV_6100543..6100734
• Length (nt): 192
• Chromosome Location: V: 6100543-6100734
• Organism: Caenorhabditis elegans