WormMine: Gene WBGene00004336

• WormBase Gene ID: WBGene00004336
• Gene Name: ret-1
• Sequence Name: W06A7.3
• Organism: Caenorhabditis elegans
• Automated Description: Located in endomembrane system. Expressed in several structures, including gonad and nervous system. Human ortholog(s) of this gene implicated in hereditary spastic paraplegia 12. Is an ortholog of human RTN3 (reticulon 3).
• Biotype: SO:0001217
• Genetic Position: V :6.94542 ±0.012678
• Length (nt): 18237

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004336

Genomics

8 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:W06A7.3f.1	W06A7.3f.1	10331	V: 14829177-14847312
Transcript:W06A7.3c.1	W06A7.3c.1	10407	V: 14829190-14847413
Transcript:W06A7.3d.2	W06A7.3d.2	2299	V: 14829191-14838548
Transcript:W06A7.3a.1	W06A7.3a.1	1197	V: 14829192-14831621
Transcript:W06A7.3g.1	W06A7.3g.1	1889	V: 14829192-14834572
Transcript:W06A7.3b.1	W06A7.3b.1	1260	V: 14829193-14831027
Transcript:W06A7.3d.1	W06A7.3d.1	2179	V: 14829193-14838372
Transcript:W06A7.3e.1	W06A7.3e.1	682	V: 14829596-14830618

Other

7 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:W06A7.3a	W06A7.3a	759	V: 14829596-14829662
CDS:W06A7.3d	W06A7.3d	1713	V: 14829596-14829662
CDS:W06A7.3f	W06A7.3f	9912	V: 14829596-14829662
CDS:W06A7.3e	W06A7.3e	615	V: 14829596-14829662
CDS:W06A7.3b	W06A7.3b	669	V: 14829596-14829662
CDS:W06A7.3c	W06A7.3c	9900	V: 14829596-14829662
CDS:W06A7.3g	W06A7.3g	1485	V: 14829596-14829662

4 RNAi Result

• WBRNAi00054859
• WBRNAi00019646
• WBRNAi00036323
• WBRNAi00114780

278 Allele

• gk963271
• gk963301
• gk964458
• gk964459
• gk963796
• gk963805
• gk938220
• gk821377
• gk578598
• gk471937
• WBVar00246645
• WBVar01975543
• WBVar01975542
• tm390
• WBVar01543168
• WBVar02024677
• WBVar02024676
• gk949288
• WBVar01828354
• WBVar01828355
• WBVar01828351
• WBVar01828352
• WBVar01828353
• h9871
• h17299
• h10426
• h7040
• h17189
• h9454
• gk953090

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004336
• Start: 14829177
• End: 14847413
• 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

224 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 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 expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons.	DESeq. False discovry rate (FDR) < 0.1.	WBPaper00048988:neuron_expressed
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:all-neurons_L1-larva_expressed
	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
	Genome-wide analysis of developmental and sex-regulated gene expression profile.	self-organizing map	cgc4489_group_18
	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
	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 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
	Genes with expression level regulated by genotype (N2 vs CB4856) and age at old adults stage (214 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_aging
	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 sin-3(tm1276) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:sin-3(tm1276)_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
	Significantly upregulated genes from clk-1(qm30) microarrays using SAM algorithm with an FDR < 0.1 from adult-only chips.	SAM algorithm with an FDR < 0.1.	WBPaper00033065:clk-1(qm30)_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 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 detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
	Genes that showed expression levels higher than the corresponding reference sample (L2 all cell reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:A-class-motor-neurons_L2-larva_expressed

11 Expression Patterns

• Primary Identifier: Expr1032154
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr13182
• Pattern: Fluorescence in the transcriptional ret- 1prom::GFP reporter strain was diffuse during early embryogenesis then robustly detected in several head neurons in the 2-fold stage of the embryo. Postembryonically, ret-1 is extensively expressed in the nervous system, with prominent expression in the nerve ring and VNC motor neurons and other VNC neurons, including the HSNs.

• Primary Identifier: Expr1909
• Remark: These results suggest that mRNA of nRTN-C is expressed maternally and throughout embryogenesis. Under the same conditions, a sense probe showed no signals. W06A7.3b = nRTN-C
• Pattern: mRNA of nRTN-C was detected in the early embryos and the expression was maintained at later embryonic stages. Moreover, nRTN-C mRNA was detected in the gonads of larvae: the gonadal primordium in L1 larvae, and developing gonads and oocytes at later larval stages. No signal was detected in the other larval tissues.

• Primary Identifier: Expr1158404
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1011649
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2015301
• 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: Expr13054
• Subcellular Localization: Endogenous RET-1 localized to the ER. Like its vertebrate and yeast homologues (Voeltz et al., 2006), RET-1 concentrates in the peripheral ER and is largely excluded from the nuclear envelope.

• Primary Identifier: Expr1906
• Remark: ret-1 = W06A7.3b = nRTN-C
• Pattern: Immunofluorescent staining of aged worms indicated that nRTN-C protein was expressed in some embryos in the uterus but not in oocytes or somatic tissues. nRTN-C protein was produced throughout embryogenesis after fertilization. All blastomeres seemed to express the protein evenly. However, no staining was observed in hatched worms nor even in gonadal primordium.
• Subcellular Localization: nRTN-C seemed to be localized in ER surrounding the nucleus in each blastomere although it was not clear in vivo.

• Primary Identifier: Expr1907
• Remark: Type: mammalian cell transfection. Plamid pCMV/nRTN-C was contructed and transfected it to CV-1 cells. W06A7.3b = nRTN-C
• Subcellular Localization: Immunocytochemical analysis of the cells expressing nRTN-C showed a typical ER-localization.

• Primary Identifier: Expr1908
• Remark: W06A7.3b = nRTN-C
• Pattern: N26-GFP was not expressed in the early embryos, but began to appear in the late embryos (late gastrulation stage). In worms, even larvae at the L1 stage, the GFP signal was very weak or mostly absent. Only some embryos in the uterus of adult worms showed the signal of N26-GFP. These observations also suggested the embryonic expression of nRTN-C. The expression of N26-GFP was delayed compared to that of endogenous nRTN-C because transgenes are usually silenced in the gonad.

• Primary Identifier: Expr2033535
• 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).

8 GO Annotation

15 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004336
• Start: 14829177
• End: 14847413
• Strand: -1

8 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 18237

1 Sequence Ontology Term