WormMine: Gene WBGene00001340

• WormBase Gene ID: WBGene00001340
• Gene Name: etr-1
• Sequence Name: T01D1.2
• Brief Description: etr-1 encodes a muscle-specific ELAV-type RNA-binding protein, whose homologs include Drosophila ELAV and human CUG-BINDING PROTEIN (CUGBP1; OMIM:601074); etr-1 function is required for embryonic muscle development, which suggests that ETR-1's homology to CUG-BP (implicated in myotonic dystrophy) might reflect conserved roles in development.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable mRNA 3'-UTR binding activity. Involved in determination of adult lifespan. Located in nucleus. Expressed in body wall musculature; cloacal sphincter muscle; copulatory spicule; non-striated muscle; and somatic gonad. Human ortholog(s) of this gene implicated in developmental and epileptic encephalopathy 97. Is an ortholog of human CELF1 (CUGBP Elav-like family member 1).
• Biotype: SO:0001217
• Genetic Position: II :-15.9026 ±0.013546
• Length (nt): 8258

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001340

Genomics

32 Transcripts

Class	WormMine ID	Sequence Name	Length (nt)	Chromosome Location
MRNA	Transcript:T01D1.2a.3	T01D1.2a.3	2908	II: 162374-170630
MRNA	Transcript:T01D1.2e.1	T01D1.2e.1	2147	II: 162423-170627
MRNA	Transcript:T01D1.2f.1	T01D1.2f.1	2318	II: 163078-170166
MRNA	Transcript:T01D1.2e.3	T01D1.2e.3	2301	II: 163080-170157
MRNA	Transcript:T01D1.2e.2	T01D1.2e.2	2056	II: 163080-170627
MRNA	Transcript:T01D1.2f.3	T01D1.2f.3	2062	II: 163080-170627
MRNA	Transcript:T01D1.2a.4	T01D1.2a.4	2018	II: 163080-170630
MRNA	Transcript:T01D1.2f.2	T01D1.2f.2	2030	II: 163080-170630
MRNA	Transcript:T01D1.2g.2	T01D1.2g.2	1840	II: 163080-170630
MRNA	Transcript:T01D1.2g.1	T01D1.2g.1	2556	II: 163080-170631
MRNA	Transcript:T01D1.2a.1	T01D1.2a.1	2047	II: 163086-170630
MRNA	Transcript:T01D1.2a.2	T01D1.2a.2	2762	II: 163086-170630
MRNA	Transcript:T01D1.2g.3	T01D1.2g.3	1715	II: 163093-170553
MRNA	Transcript:T01D1.2l.1	T01D1.2l.1	2044	II: 163101-170627
MRNA	Transcript:T01D1.2e.4	T01D1.2e.4	1981	II: 163120-170627
NcPrimaryTranscript	Transcript:T01D1.2c	T01D1.2c	2283	II: 163142-169679
MRNA	Transcript:T01D1.2l.2	T01D1.2l.2	2238	II: 163142-170147
MRNA	Transcript:T01D1.2d.2	T01D1.2d.2	2086	II: 163142-170157
MRNA	Transcript:T01D1.2d.1	T01D1.2d.1	1844	II: 163142-170630
MRNA	Transcript:T01D1.2m.1	T01D1.2m.1	1395	II: 164595-169679
MRNA	Transcript:T01D1.2n.1	T01D1.2n.1	1389	II: 164595-169679
MRNA	Transcript:T01D1.2o.1	T01D1.2o.1	1170	II: 164595-169679
MRNA	Transcript:T01D1.2p.1	T01D1.2p.1	1269	II: 164641-169679
MRNA	Transcript:T01D1.2q.1	T01D1.2q.1	1263	II: 164641-169679
MRNA	Transcript:T01D1.2r.1	T01D1.2r.1	1044	II: 164641-169679
MRNA	Transcript:T01D1.2b.1	T01D1.2b.1	1059	II: 166822-169679
MRNA	Transcript:T01D1.2s.1	T01D1.2s.1	1071	II: 166822-169679
MRNA	Transcript:T01D1.2t.1	T01D1.2t.1	1065	II: 166822-169679
MRNA	Transcript:T01D1.2u.1	T01D1.2u.1	846	II: 166822-169679
MRNA	Transcript:T01D1.2v.1	T01D1.2v.1	843	II: 167930-169679

Other

19 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T01D1.2e	T01D1.2e	1761	II: 163142-163324
CDS:T01D1.2f	T01D1.2f	1767	II: 163142-163324
CDS:T01D1.2g	T01D1.2g	1542	II: 163142-163324
CDS:T01D1.2n	T01D1.2n	1389	II: 164595-164643
CDS:T01D1.2o	T01D1.2o	1170	II: 164595-164643
CDS:T01D1.2p	T01D1.2p	1269	II: 164641-164643
CDS:T01D1.2r	T01D1.2r	1044	II: 164641-164643
CDS:T01D1.2t	T01D1.2t	1065	II: 166822-166905
CDS:T01D1.2w	T01D1.2w	837	II: 167930-168047
CDS:T01D1.2a	T01D1.2a	1755	II: 163142-163324
CDS:T01D1.2b	T01D1.2b	1059	II: 166822-166905
CDS:T01D1.2d	T01D1.2d	1608	II: 163142-163324
CDS:T01D1.2l	T01D1.2l	1770	II: 163142-163324
CDS:T01D1.2m	T01D1.2m	1395	II: 164595-164643
CDS:T01D1.2q	T01D1.2q	1263	II: 164641-164643
CDS:T01D1.2s	T01D1.2s	1071	II: 166822-166905
CDS:T01D1.2u	T01D1.2u	846	II: 166822-166905
CDS:T01D1.2v	T01D1.2v	843	II: 167930-168047
CDS:T01D1.2x	T01D1.2x	618	II: 167930-168047

25 RNAi Result

• WBRNAi00009094
• WBRNAi00052116
• WBRNAi00035014
• WBRNAi00072605
• WBRNAi00072604
• WBRNAi00074641
• WBRNAi00074643
• WBRNAi00074642
• WBRNAi00074645
• WBRNAi00074644
• WBRNAi00074647
• WBRNAi00074646
• WBRNAi00091268
• WBRNAi00074648
• WBRNAi00091005
• WBRNAi00085855
• WBRNAi00102173
• WBRNAi00113335
• WBRNAi00072606
• WBRNAi00026147
• WBRNAi00113333
• WBRNAi00113332
• WBRNAi00113331
• WBRNAi00113334
• WBRNAi00092390

130 Allele

• gk964317
• h6140
• h10228
• h10229
• h10058
• gk963800
• gk964386
• gk964387
• gk131001
• gk131006
• gk131003
• gk131002
• gk131005
• gk131004
• gk131010
• gk131009
• gk131012
• gk131011
• gk131008
• gk131007
• gk131013
• WBVar01715459
• WBVar01715458
• WBVar01715457
• WBVar01715456
• WBVar01291088
• gk674378
• WBVar01762461
• gk941033
• WBVar01291087

1 Chromosome

• WormBase ID: II
• Organism: Caenorhabditis elegans
• Length (nt): 15279421

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001340
• Start: 162374
• End: 170631
• 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_chrII_170632..170845
• Length (nt): 214
• Chromosome Location: II: 170632-170845
• Organism: Caenorhabditis elegans

116 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 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
	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 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 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
	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 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 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
Gamma irradiation 100 mGY per hour for 72 hours since L1 larva.	Transcripts that showed significantly increased expression after exposure to 100mGy per hour gamma irradiation from L1 to day 1 adult hermaphrodite stage.	DESeq2, FDR <= 0.05, log2 fold change >= 0.3 or <= -0.3.	WBPaper00058958:100mGy-irradiation-72h_upregulated
Reduced humidity (98% relative humidity).	Genes that were down-regulated after one day exposure to reduced humidity (98% relative humidity) according to microarray analysis.	Multiple hypothesis testing with the Benjamini-Hochberg correction was applied on calculated p-values. A change in the expression level was considered to be significant if the adjusted p-value was less than 0.001.	WBPaper00044578:reduced-humidity_downregulated_microarray
	Genes that showed expression levels higher than the corresponding reference sample (L3/L4 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:hypodermis_L3-L4-larva_expressed
	Genes that showed expression levels higher than the corresponding reference sample (L3/L4 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:PVD-OLL-neurons_L3-L4-larva_expressed
	Proteins interacting with HA-PPM-1.D.	N.A.	WBPaper00062498:PPM-1.D_interacting
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly decreased expression in hpx-2(dg047) after animals were exposed to E. faecalis OG1RF for 16 hours comparing to exposure to E. Coli OP50.	Cuffcompare and Cuffdiff	WBPaper00056090:E.faecalis_downregulated_hpx-2(dg047)
	Genes found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014.	N.A.	WBPaper00026929:sir-2.1_overexpression_regulated
	Transcripts of coding genes that showed significantly increased 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_enriched_coding-RNA
	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_downregulated
	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
heat-shock hlh-1	Genes enriched in HLH-1 heat shock dataset.	A two-class unpaired analysis was performed to identify genes that are elevated 1.7-fold or greater when compared with the reference for each dataset, at a false discovery rate of 1.8% or less for M0 and 1.2% or less for the M24 datasets.	WBPaper00031003:hlh_1_enriched
	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 lin-22(ot269) comparing to in N2 at L3 larva.	Differences in gene expression were then calculated using the negative binomial test in the DESeq package (FDR = 0.1).	WBPaper00053295:lin-22(ot269)_upregulated

8 Expression Patterns

• Primary Identifier: Expr1030819
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr9488
• Pattern: Transgenic animals expressed this reporter specifically in muscle. Strong expression was observed in muscle cells in embryos. Adult expression was seen in striated body-wall muscle along the length of the animal, especially in the head. Strong expression was also seen in the vulval muscles. Additional expression was observed in intestinal muscle, anal sphincter muscle and the sex-specific muscles of the male tail. No expression was observed in pharyngeal muscle.
• Subcellular Localization: Sub-cellular localization within the body wall muscle: Nucleus only

• Primary Identifier: Expr1204
• Remark: Reporter gene fusion type not specified.
• Pattern: Transgenic animals expressed this reporter specifically in muscle. Strong expression was observed in muscle cells in embryos. Adult expression was seen in striated body-wall muscle along the length of the animal, especially in the head. Strong expression was also seen in the vulval muscles. Additional expression was observed in intestinal muscle, anal sphincter muscle and the sex-specific muscles of the male tail. No expression was observed in pharyngeal muscle.

• Primary Identifier: Expr13464
• Pattern: ETR-1 is expressed in both the germline and the somatic gonadal tissue of the hermaphrodite gonad. A medial optical section through the hermaphrodite gonad shows that ETR-1 exhibits a diffuse, cytoplasmic staining throughout the entire hermaphrodite gonad. We also observed cytoplasmic expression of ETR-1 within both the female and male gametes (egg and sperm, respectively). A superficial optical section of the proximal hermaphrodite gonad shows that ETR-1 is localized specifically to the gonadal sheath cell myofilaments. This result was confirmed by colocalization with an antibody against myosin heavy chain A (MHCA) (Hubbard and Greenstein, 2000; Rose et al., 1997). Further confirmation of ETR-1 being expressed in the somatic gonadal cells emerges when imaging the surface of the distal gonad. ETR-1 exhibits a honeycomb pattern in the distal germ line that is consistent with the pattern observed by Hall et al. (1999) in their description of the individual somatic gonadal sheath cells via TEM and immunofluorescence studies (Hall et al., 1999). Analysis of embryos indicates early embryonic expression of ETR-1 that persists through the comma stage of embryonic development. In early embryos (1- to 16-cell stage), ETR-1 is diffusely cytoplasmic. In older embryos (>32-cell), while there still remains some diffuse cytoplasmic ETR-1 staining, a majority of the ETR-1 is now nuclear.
• Subcellular Localization: In early embryos (1- to 16-cell stage), ETR-1 is diffusely cytoplasmic. In older embryos (>32-cell), while there still remains some diffuse cytoplasmic ETR-1 staining, a majority of the ETR-1 is now nuclear.

• Primary Identifier: Expr2011378
• 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: Expr2029614
• 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: Expr1026122
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1155747
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

13 GO Annotation

10 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001340
• Start: 162374
• End: 170631
• Strand: 1

13 Ontology Annotations

6 Regulates Expr Cluster

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 of coding genes that showed significantly increased 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_enriched_coding-RNA
	Transcripts of noncoding genes that showed significantly increased 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_enriched_noncoding-RNA
	Transcripts that showed significantly increased expression in etr-1(lq61) comparing to in N2 animals at L1 larva stage.	DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed.	WBPaper00062325:etr-1(lq61)_upregulated
	Transcripts of noncoding 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_noncoding-RNA
	Transcripts that showed significantly decreased expression in etr-1(lq61) comparing to in N2 animals at L1 larva stage.	DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed.	WBPaper00062325:etr-1(lq61)_downregulated

1 Sequence

• Length: 8258

1 Sequence Ontology Term