WormMine: Gene WBGene00001248

• WormBase Gene ID: WBGene00001248
• Gene Name: elp-1
• Sequence Name: F38A6.2
• Brief Description: elp-1 encodes a WD repeat-containing protein that is the sole C. elegans EMAP (echinoderm microtubule-associated protein) homolog; loss of elp-1 activity in a dys-1/dystrophin mutant background results in locomotion defects, disorganized and hypercontracted muscle, and abnormal cholinergic signaling; ELP-1 binds microtubules in vitro; ELP-1 is expressed in many tissues, including body wall muscle, male-specific sex muscles, the vulva, spermatheca, sensory neurons, and intestinal cells.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable microtubule binding activity. Predicted to be involved in microtubule cytoskeleton organization. Located in dendrite; neuromuscular junction; and neuronal cell body. Expressed in several structures, including hypodermal cell; intestine; mechanosensory neurons; spermatheca; and vulval muscle. Used to study Duchenne muscular dystrophy. Human ortholog(s) of this gene implicated in subcortical band heterotopia. Is an ortholog of human EML2 (EMAP like 2).
• Biotype: SO:0001217
• Genetic Position: V :25.1481 ±0.019355
• Length (nt): 5191

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001248

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F38A6.2a.1	F38A6.2a.1	2743	V: 20764971-20770161
Transcript:F38A6.2b.1	F38A6.2b.1	2667	V: 20765009-20769144

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F38A6.2b	F38A6.2b	2667	V: 20765009-20765131
CDS:F38A6.2a	F38A6.2a	2676	V: 20765009-20765131

16 RNAi Result

• WBRNAi00084817
• WBRNAi00000527
• WBRNAi00046679
• WBRNAi00084823
• WBRNAi00014534
• WBRNAi00107914
• WBRNAi00031946
• WBRNAi00084824
• WBRNAi00084822
• WBRNAi00084825
• WBRNAi00084819
• WBRNAi00084818
• WBRNAi00084820
• WBRNAi00070726
• WBRNAi00084821
• WBRNAi00070727

98 Allele

• gk963271
• gk964176
• gk962705
• gk963489
• gk963304
• gk963809
• WBVar01756719
• WBVar01756720
• WBVar01756721
• WBVar01756722
• WBVar00073888
• WBVar00073887
• WBVar00073886
• WBVar00073885
• WBVar00073889
• WBVar00073891
• WBVar00073890
• WBVar00073895
• WBVar00073894
• WBVar00073893
• WBVar00073892
• WBVar01710529
• tm637
• tm638
• WBVar01544398
• WBVar01978796
• WBVar01978795
• WBVar01978794
• WBVar02026482
• ok347

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001248
• Start: 20764971
• End: 20770161
• 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_chrV_20763834..20764970
• Length (nt): 1137
• Chromosome Location: V: 20763834-20764970
• Organism: Caenorhabditis elegans

142 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 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
	Transcripts that showed significantly decreased expression in AGP22 [nhr-49(nr2041)I;glp-1(e2141)III] comparing to in CF1903 [glp-1(e2144)III] at Day 2 adults.	Fold change > 2, p Value of < 0.05 and a false discovery rate (FDR) of < 0.05.	WBPaper00061530:nhr-49(e2144)_downregulated
	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
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
	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:bodywall-muscle_L1-larva_expressed
	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 after animals were treated with 50uM Rifampicin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin_upregulated
	Transcripts that showed significantly decreased expression at 11-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites.	DESeq2, fold change > 2, FDR < 0.05	WBPaper00065835:Day11_vs_Day1_downregulated
	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
	Transcripts that showed significantly increased expression in rrf-3(pk1426) comparing to in N2 at embryo stage.	DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01.	WBPaper00056169:rrf-3(pk1426)_upregulated_embryo
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 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 after four-day-old young adult worms were placed on NGM plates seeded with OP50 in the presence 5% Agaro-oligosaccharides(AGO) for 24 h, comparing to animals grown in the absence of AGO.	Fold change > 2.	WBPaper00064306:Agaro-oligosaccharides_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 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
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
	Transcripts that showed significantly increased expression in mrg-1(qa6200) comparing to in control animals in primordial germ cells (PGCs) at L1 larva stage.	DESeq2(v1.32.0), FDR < 0.05.	WBPaper00064315:mrg-1(qa6200)_upregulated_PGCs
	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
Heat Shock: 35C 4 hours at L4 larva stage.	Transcripts that showed significantly decreased expression after L4 larva N2 animals were heat stressed at 35C for 4 hours	DESeq2	WBPaper00057154:HeatShock_downregulated_mRNA
	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 the whole animal.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00065975:P-body_vs_WholeAnimal_depleted
	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:all-neurons_L2-larva_expressed
	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
	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:dopaminergic-neurons_L3-L4-larva_expressed
	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:excretory-cell_L2-larva_expressed

6 Expression Patterns

• Primary Identifier: Expr1019699
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr8965
• Remark: Picture: Fig 3, 4, 5.
• Pattern: ELP-1::GFP was associated with the nine pairs of rays of the male tale. The relatively diffuse and broad band of fluorescence appears to originate from the hypodermal cells (hyp7) and one or more of the neuronal cells of the ray (RnA, RnB). In embryos, ELP-1::GFP expression first appeared during the comma stage. As the embryo matured into the 1-1.5 fold stage, the strongest expression was seen in the hypodermal cells, with only diffuse staining throughout the rest of the embryo. During larval development, expression of the fusion protein was progressively refined to muscle, neurons and epithelial cells. In the adult, ELP-1::GFP and ELP-1(truncated)::NLS::GFP were expressed in body wall muscle, spermatheca, vulval muscle, seam cells, the intestine, touch receptor neurons (TRNs) and inner labial 1 (IL1) neurons of the head.
• Subcellular Localization: At the subcellular level, ELP-1::GFP was associated with adhesion sites in both males and hermaphrodites. In the hermaphrodite body wall muscle, ELP-1::GFP was associated with the muscle arms that terminate in neuromuscular junctions. The ELP-1::GFP fluorescence is found throughout the muscle arm. In males, ELP-1::GFP associated with repeating focal attachment points in the sex-specific muscles of the worm. ELP-1 expression was prominent at the adhesion sites located at the sarcolemma.

• Primary Identifier: Expr1150555
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr8966
• Remark: Picture: Fig 6, 7, 8, 9.
• Subcellular Localization: Affinity-purified antibodies against ELP-1 and the full-length ELP-1::GFP fusion protein localized to thin linear rows near the cell surface that were not quite parallel to the long axis of the muscle cell. At higher resolution there was a periodicity to these lines that approximated the distance between the dense body adhesion sites. The ELP-1::GFP fluorescence slightly overlaps the edges of the dense bodies but is not superimposable with the dense bodies at this angle. These results indicate that ELP-1 is unlikely to be a component of the dense bodies. Double-stained muscle cells with anti-ELP-1 antibodies and a monoclonal antibody MH25 against PAT-3 shows that integrin and ELP-1 have overlapping staining patterns at this level of resolution. Because of the relatively impenetrable cuticle that surrounds the nematode, these worms were frozen and cracked open prior to antibody staining. In areas lacking dense bodies, ELP-1::GFP was sometimes lost. However most of the ELP-1::GFP was retained in a linear pattern. These results indicate that the membrane and dense bodies can be separated from the ELP-1::GFP. Although the truncated construct and the full-length construct were expressed in the same cells and tissues, only the full length ELP-1::GFP construct localized to an elaborate array of fluorescent filaments. An obliquely striated fluorescent pattern emerges approximately 0.8 um apically from the base of the dense body. Deeper within the muscle body the filaments appear to separate from the linear track and branch out into the cytoplasm. ELP-1 was enriched in preparations of paclitaxel-stabilized microtubules in vitro. Paclitaxel-stabilized microtubules were prepared from a mixed-stage worm preparation and examined by means of Western blotting with an affinity-purified antisera against a bacterially expressed ELP-1 fusion protein. An ELP-1-reacting band co-purified with microtubules and migrated at ~100 kDa, a mass that corresponded to the Genefinder predictions for the larger ELP-1a polypeptide. Two smaller and less abundant proteins that cross-react with the ELP-1 antibodies also co-purified with microtubules. These may be isoforms generated by alternative splicing (i.e. ELP-1b) or proteolytic fragments of ELP-1a. This experiment and the one described above showed that ELP-1 is microtubule-associated both in situ and in vivo. To test the idea that the filaments decorated by ELP-1::GFP were microtubules, authors treated worms with the microtubule inhibitor, nocodazole. Worms were gently pressed between a slide and coverslip to extrude their intestines. This process was done in the presence of levamisole, an acetylcholine agonist, which was used to paralyze the worms for microscopy. The filaments in the extruded layer were stable for 30 minutes or more in the absence of nocodazole. The decorated filaments began to degrade within seconds and were entirely de-polymerized after two minutes in nocodazole. When the fluorescence disappeared the intestinal fragments noticeably flattened and the remnants of the worm contracted. This result indicates that ELP-1::GFP associates with microtubules in situ.

• Primary Identifier: Expr2011287
• 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: Expr2029523
• 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).

10 GO Annotation

13 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001248
• Start: 20764971
• End: 20770161
• Strand: -1

10 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 5191

1 Sequence Ontology Term