WormMine: Gene WBGene00001328

• WormBase Gene ID: WBGene00001328
• Gene Name: epi-1
• Sequence Name: K08C7.3
• Brief Description: epi-1 encodes one of two C. elegans laminin alpha chains; epi-1 affects oogenesis due to its affect on gonad development, and also affects cell migrations, axon extension and GABAergic defasciculation, morphology of the VD and DD motor neurons, body morphology, locomotion, gonad sheath epithelialization, body muscle structure, and germ cell proliferation.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to be an extracellular matrix structural constituent. Involved in several processes, including basement membrane organization; generation of neurons; and response to stress. Located in basement membrane. Expressed in several structures, including anal depressor muscle; basal lamina; body wall musculature; egg-laying apparatus; and intestine. Human ortholog(s) of this gene implicated in familial nephrotic syndrome; junctional epidermolysis bullosa; and lung small cell carcinoma. Is an ortholog of human LAMA5 (laminin subunit alpha 5).
• Biotype: SO:0001217
• Genetic Position: IV :4.64394 ±0.003985
• Length (nt): 12469

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001328

Genomics

6 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:K08C7.3e.1	K08C7.3e.1	11185	IV: 10666823-10679289
Transcript:K08C7.3a.1	K08C7.3a.1	11208	IV: 10666827-10679289
Transcript:K08C7.3c.1	K08C7.3c.1	11147	IV: 10666827-10679291
Transcript:K08C7.3d.1	K08C7.3d.1	11087	IV: 10666827-10679291
Transcript:K08C7.3f.1	K08C7.3f.1	11233	IV: 10666833-10679287
Transcript:K08C7.3b.1	K08C7.3b.1	11106	IV: 10666833-10679289

Other

6 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:K08C7.3a	K08C7.3a	11115	IV: 10666833-10667028
CDS:K08C7.3d	K08C7.3d	10992	IV: 10666833-10667028
CDS:K08C7.3e	K08C7.3e	11088	IV: 10666833-10667028
CDS:K08C7.3b	K08C7.3b	11019	IV: 10666833-10667028
CDS:K08C7.3c	K08C7.3c	11052	IV: 10666833-10667028
CDS:K08C7.3f	K08C7.3f	11148	IV: 10666833-10667028

48 RNAi Result

• WBRNAi00085154
• WBRNAi00085156
• WBRNAi00093780
• WBRNAi00008971
• WBRNAi00066996
• WBRNAi00067018
• WBRNAi00067041
• WBRNAi00067048
• WBRNAi00067229
• WBRNAi00067282
• WBRNAi00067305
• WBRNAi00067782
• WBRNAi00068223
• WBRNAi00050236
• WBRNAi00099937
• WBRNAi00100445
• WBRNAi00085493
• WBRNAi00062567
• WBRNAi00061455
• WBRNAi00061457
• WBRNAi00061458
• WBRNAi00061459
• WBRNAi00061460
• WBRNAi00071908
• WBRNAi00062569
• WBRNAi00061456
• WBRNAi00093783
• WBRNAi00100819
• WBRNAi00071457
• WBRNAi00099331

147 Allele

• gk964278
• gk964078
• gk964500
• gk962765
• gk963382
• rh27
• rh92
• rh152
• rh191
• rh199
• rh200
• rh233
• gk211273
• gk211274
• gk211271
• WBVar01730851
• gk211272
• WBVar01795388
• gk211269
• gk211270
• gk211267
• gk211268
• WBVar01730849
• WBVar01730850
• gk211275
• WBVar01730848
• h3393
• h5443
• h5571
• gk502200

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001328
• Start: 10666823
• End: 10679291
• 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

238 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
	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
	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
	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 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
	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 at 5-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites.	DESeq2, fold change > 2, FDR < 0.05	WBPaper00065835:Day5_vs_Day1_downregulated
	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 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
	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
	Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_daf-16(mu86);glp-1(e2141)
	Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_glp-1(e2141)
	Transcripts detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
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
starvation 12 hours	Transcripts that showed significantly increased expression in dissected intestines of N2 L1 larva that were starved for 12 hours, comparing to fed animals.	EdgeR, FDR < 0.05, fold change >= 2.	WBPaper00067259:starvation_upregulated_intestine
	Transcripts that showed significantly increased expression after 24-hour exposure to 10uM benzyl butyl phthalate (BBP) in col-121(nx3) animals.	DESeq2v1.38.3, FDR < 0.05	WBPaper00067417:benzyl-butyl-phthalate_regulated
Bacteria infection: Staphylococcus aureus	Transcripts that showed significantly decreased expression in animals experimentally colonised by a wild microbiota community and infected by the widespread animal pathogen, Staphylococcus aureus, comparing to animals not colonized by microbiota and not infected by pathogen.	DeSeq2 (v. 1.42.0), Wald analyses testing against a null hypothesis of < |1.5|-fold change in gene expression between treatments (BenjaminiHochberg adjusted false detection rate of p <= 0.05.	WBPaper00067479:Microbiota-Pathogen_vs_control_downregulated
Bacteria infection: Staphylococcus aureus	Transcripts that showed significantly decreased expression in animals experimentally colonised by a wild microbiota community and infected by the widespread animal pathogen, Staphylococcus aureus, comparing to animals colonized by microbiota but not infected by pathogen.	DeSeq2 (v. 1.42.0), Wald analyses testing against a null hypothesis of < |1.5|-fold change in gene expression between treatments (BenjaminiHochberg adjusted false detection rate of p <= 0.05.	WBPaper00067479:Microbiota-Pathogen_vs_Microbiota_downregulated
Bacteria infection: Staphylococcus aureus	Transcripts that showed significantly decreased expression in animals experimentally colonised by a wild microbiota community and infected by the widespread animal pathogen, Staphylococcus aureus, comparing to animals not colonized by microbiota but infected by pathogen.	DeSeq2 (v. 1.42.0), Wald analyses testing against a null hypothesis of < |1.5|-fold change in gene expression between treatments (BenjaminiHochberg adjusted false detection rate of p <= 0.05.	WBPaper00067479:Microbiota-Pathogen_vs_Pathogen_downregulated
	Genes that showed significantly increased expression in daf-2(e1370);hel-1(gk148684) comparing to in hel-1(gk148684)	To identify DEGs, Students t test and the log2 median ratio test were performed to compute t values and median ratios for all the annotated genes. The adjusted P values from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjusted P values from the individual tests were combined to compute the overall P values using Stouffers method , and genes with overall P < 0.05 and fold change > 1.5 were selected as DEGs.	WBPaper00047131:daf-2(e1370)_upregulated_hel-1(gk148684)-background
	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
	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

8 Expression Patterns

• Primary Identifier: Expr1030808
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr2623
• Pattern: Expression first detected in gastrulating embryo. Expression continues as the intestinal cells and the precursors of the pharynx form a central cylinder with the myoblasts filling in between this cylinder and the outer layer of cells. Strong expression by the myoblasts is detected. In larvae, epi-1 is expressed in the body wall, vulva and anal depressor muscles, as well as intestinal cells and in somatic cells of the gonad.
• Subcellular Localization: Expression of epi-1, the gene encoding epi-1, is first detected in the nucleus of cells entering the gastrula. As the cells arrange into the endodermal and mesodermal layers, epi-1 mRNA is detected within cytoplasm.

• Primary Identifier: Expr2622
• Remark: Colocalization Assay: In order to compare directly the distribution of lam-3 and epi-1, both subunits were co-stained using species-specific secondary antibody conjugates. As the germ layers develop, both subunits are deposited between the layers. However, the staining for laminin A is most intense around the pharyngeal and intestinal precursor cells, whereas staining for laminin B is most intense around the myoblast cells and along epidermal cells. By the onset of elongation, distinct layers of laminin A and laminin B staining can be distinguished, particularly anteriorly between the developing pharynx and the body wall. This indicates that the segregation of the laminin isoforms begins early, before or as organogenesis proceeds. In mnDf90, the two subunits remain differentially localized after elongation. lam-3 is localized to the pharyngeal basement membrane, whereas epi-1 is associated mainly with the body wall basement membranes and only weakly with the pharyngeal basement membrane. These results indicate that each laminin alpha subunit is segregated in the embryo to different adjacent basement membranes and that each membrane retains its unique subunit composition.
• Pattern: The antisera indicate that early expression occurs during gastrulation. epi-1 accumulates between the primary tissue layers near the completion of gastrulation (~250 minutes). epi-1 antiserum stains all the major basement membranes during the remainder of embryogenesis and throughout larval development and in the adult. Although epi-1 staining is weak in the basement membranes surrounding pharynx, intestine, body wall muscle and epidermis, the staining is strong in the basement membranes surrounding gonad, distal tip cell, vulval muscle, intestinal muscle, anal depressor muscle and coelomocytes. These basement membranes are notable in that they are thick and appear to have mainly the alphaB-containing laminin isoform.
• Subcellular Localization: Although the staining is diffuse within most basement membranes, at the muscle/epidermis membrane a distinct pattern is observed. On the muscle surface, a grid-like network that comprises regularly spaced bands running circumferentially and longitudinally is observed. The longitudinal bands correspond to the thin-filament-containing (I-band) region of the muscle myofilament lattice. epi-1 is also strongly detected at muscle-muscle cell boundaries.

• Primary Identifier: Expr2011350
• 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: Expr1153931
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr4055
• Remark: Curated by authors based on online in-situ hybridization database (Y. Kohara, personal communication; http://nematode.lab.nig.ac.jp).
• Pattern: Broadly expressed in soma/vulva/emb.

• Primary Identifier: Expr1024091
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2029586
• 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).

21 GO Annotation

8 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001328
• Start: 10666823
• End: 10679291
• Strand: 1

21 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 12469

1 Sequence Ontology Term

• Name: gene

3 Strains

• WBStrain00028734
• WBStrain00028750
• WBStrain00050773

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIV_10665686..10666822
• Length (nt): 1137
• Chromosome Location: IV: 10665686-10666822
• Organism: Caenorhabditis elegans