WormMine

WS295

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00023417 Gene Name  swm-1
Sequence Name  ? C25E10.9 Brief Description  swm-1 encodes a putative secreted TIL-domain protease inhibitor that, inmales, inhibits unpolarized round spermatids from remodelling themselvesinto motile spermatozoa until their transfer to a hermaphrodite; SWM-1is also required for efficient sperm transfer, and thus for malefertility; SWM-1 is biologically active from spermatogenesis in L4larvae onward into adulthood, and functions non-autonomously, probablybeing expressed in germline; SWM-1-inhibited spermatid activationrequires SPE-8, SPE-12, and SPE-27; SWM-1 is active in hermaphroditesbut is not strongly required for fertility; SWM-1 is paralogous toC25E10.8, ISL-1, and the products of 11 other C. elegans genes; SWM-1and its relatives are collectively similar to other TIL-domain proteaseinhibitors from nematodes, insects, and vertebrates, including theDrosophila melanogaster seminal fluid protein Acp62F; SWM-1 contains twotandem TIL domains, missense mutations of which partially complement oneanother in vivo, and which therefore may inhibit two differentproteases; mutant swm-1 males can trans-activate hermaphroditespermatids by mating, but prematurely remodel their own spermatids,which then generally fail to be transferred to hermaphrodites;sporadically or artificially transferred swm-1 mutant sperm do, however,fertilize hermaphrodite eggs normally.
Organism  Caenorhabditis elegans Automated Description  Predicted to enable serine-type endopeptidase inhibitor activity. Involved in spermatid development. Located in extracellular space and secretory vesicle. Expressed in body wall musculature; coelomocyte; reproductive tract; and in male.
Biotype  SO:0001217 Genetic Position  V :1.9142 ±0.000661
Length (nt)  ? 761
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00023417

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:C25E10.9.1 C25E10.9.1 604   V: 9054111-9054871
 

Other

1 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:C25E10.9 C25E10.9 408   V: 9054268-9054552

3 RNAi Result

WormBase ID
WBRNAi00041191
WBRNAi00011166
WBRNAi00029198

21 Allele

Public Name
gk963301
gk964351
gk962860
gk964052
gk963442
gk963441
gk963163
me86
me66
me87
WBVar00213530
WBVar00213529
ok1193
WBVar01742500
WBVar01742501
gk457364
gk638354
gk567391
gk824442
gk380770
gk467822

1 Chromosome

WormBase ID Organism Length (nt)
V Caenorhabditis elegans 20924180  

1 Chromosome Location


Feature . Primary Identifier
Start End Strand
WBGene00023417 9054111 9054871 -1

4 Data Sets

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

1 Downstream Intergenic Region

WormBase ID Name Sequence Name Length (nt) Chromosome Location Organism
intergenic_region_chrV_9054070..9054110   41 V: 9054070-9054110 Caenorhabditis elegans

181 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  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
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
  Transcripts that showed significantly increased expression in csr-1a(tor159) comparing to in N2 at 25C. DESeq2, fold change > 2, p-value < 0.05. WBPaper00061753:csr-1(tor159)_upregulated_25C
  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
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours. Transcripts that showed significantly decreased expression in N2 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_N2
  Proteins interacting with NHR-49-GFP according to co-IP and LC-MS. N.A. WBPaper00064071:NHR-49_interacting
  Developmentally modulated gene cluster. self-organizing map cgc4386_cluster_1_5
  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
  Genes that are significantly up regulated in tdp-1(ok803) poly(A) RNA-seq verses in N2. DESeq v1.14, with cut-off p-value < 0.05 and FDR < 0.1. WBPaper00046012:tdp-1(ok803)_upregulated
  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 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)
Bacteria infection: Staphylococcus aureus MW2. 4 hours of exposure. Transcripts that showed significantly increased expression after N2 animals had 4 hours of infection by Staphylococcus aureus (MW2). DEseq 1.18.0, adjusted p-value < 0.05. WBPaper00056471:S.aureus-4h_upregulated_N2
  Genes that showed significantly increased expression in daf-2(e1370) comparing to in N2. 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_N2-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 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 daf-2(e1370;mes-1(bn84ts) comparing to in mes-1(bn84ts). DESeq2 was used for differential expression analysis. A BenjaminiHochberg multiple hypothesis-corrected P-value cutoff of 0.05 was used as a significance cutoff. WBPaper00049368:daf-2(e1370)_upregulated
  Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy. Cufflinks WBPaper00065120:body-muscle-transcriptome
  Genes with increased RNA expression after 24 hours rotenone treatment EdgeR provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting p-values were adjusted using the Benjamini and Hochbergs approach for controlling the false discovery rate (FDR). Transcripts with an adjusted p-value smaller 0.05 were assigned as differentially expressed. WBPaper00044426:rotenone_24h_upregulated
Starvation Starvation-induced transcripts that showed significantly increased expression in post dauer animals comparing to wild type control. edgeR WBPaper00053713:Starvation-induced_postdauer_vs_control_upregulated
  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
  Transcripts that showed significantly increased expression in daf-2(e1370) comparing to in N2. Differential gene expression analysis was performed using the quasi-likeli-hood framework in edgeR package v. 3.20.1 in R v. 3.4.1. WBPaper00053810:daf-2(e1370)_upregulated
  Transcripts that showed significantly increased expression in isp-1(qm150) comparing to in N2. Differential gene expression analysis was performed using the quasi-likeli-hood framework in edgeR package v. 3.20.1 in R v. 3.4.1. WBPaper00053810:isp-1(qm150)_upregulated
  Transcripts that showed significantly increased expression in nuo-6(qm200) comparing to in N2. Differential gene expression analysis was performed using the quasi-likeli-hood framework in edgeR package v. 3.20.1 in R v. 3.4.1. WBPaper00053810:nuo-6(qm200)_upregulated

9 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr2035289 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).  
    Expr14581   Within cuboidal cells, SWM-1::mCherry was contained within large vesicles that were closely associated with the apical membrane, which are not well-characterized but have been shown to contain seminal fluid (Smith and Stanfield, 2011; Lints and Hall, 2009; Kimble and Hirsh, 1979).
    Expr14582   In muscle cells, we observed SWM-1::mCherry at low levels that appeared to be concentrated near the cell cortex.
    Expr1012350 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012  
    Expr1145222 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015  
    Expr14584 In hermaphrodites, swm-1 was expressed in posterior body wall muscle consistent with the non-sex-specific nature of this tissue. SWM-1::mCherry protein was detectable in muscle and secreted into the body cavity, as evidenced by its presence in coelomocytes. Interestingly, swm-1 also was expressed in the spermathecae, structures that are unique to the hermaphrodite gonad, and SWM-1::mCherry surrounded sperm that were stored in the spermathecal lumen. Indeed, SWM-1::mCherry protein was present throughout the outer hermaphrodite reproductive tract and it surrounded fertilized eggs. As it can be difficult to distinguish between the body cavity and the uterus, we used GFP-labeled seminal fluid to mark the lumen of the uterus. jn62[swm-1::mCherry] hermaphrodites mated to males that expressed TRY-5::GFP showed clear colocalization of SWM-1::mCherry and TRY-5::GFP in the uterus. In similar experiments, we found that muscle-derived SWM- 1::mCherry also colocalized with GFP transferred in seminal fluid. Thus, as in males, SWM-1 is secreted into the hermaphrodite body cavity and then taken up into the gonad, in which it is present throughout the sperm migratory path.  
    Expr2017153 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).  
    Expr14579 We observed Pswm-1::mCherry::H2B reporter expression in six to eight of the 12 vas deferens cuboidal cells. We also observed Pswm-1::mCherry::H2B in posterior body wall muscle cells and in the male-specific diagonal muscle cells, both of which overlie the seminal vesicle and vas deferens region. Expression of the Pswm-1 reporter in both gonadal and muscle cells began at late larval stages and persisted in adult animals until at least 48 h post L4. In addition, we observed reporter expression at low levels in two cells in the head, which were likely neurons. These data indicate that swm-1 is not expressed in sperm. Instead, it is produced in somatic tissues: the vas deferens, which is involved in the production, release, and transfer of seminal fluid, and muscle cells, outside the gonad.  
    Expr14580 In adult males, the SWM-1::mCherry protein was present, as expected, in cells in which we observed the transcriptional reporter [Expr14579]: vas deferens cuboidal cells, diagonal muscles and body wall muscles. Within cuboidal cells, SWM-1::mCherry was contained within large vesicles that were closely associated with the apical membrane, which are not well-characterized but have been shown to contain seminal fluid (Smith and Stanfield, 2011; Lints and Hall, 2009; Kimble and Hirsh, 1979). In muscle cells, we observed SWM-1::mCherry at low levels that appeared to be concentrated near the cell cortex. Interestingly, in jn62[swm-1::mCherry], SWM-1::mCherry was also visible in anterior body wall muscles, rather than being restricted to the posterior region, corresponding to slightly higher levels of rescue and protein expression as compared with the Pswm-1 MosSCI reporter strain.  

10 GO Annotation

Annotation Extension Qualifier
  enables
  involved_in
  involved_in
  involved_in
  involved_in
  located_in
  located_in
  located_in
  located_in
  located_in

7 Homologues

Type
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue

1 Locations


Feature . Primary Identifier
Start End Strand
WBGene00023417 9054111 9054871 -1

10 Ontology Annotations

Annotation Extension Qualifier
  enables
  involved_in
  involved_in
  involved_in
  involved_in
  located_in
  located_in
  located_in
  located_in
  located_in

0 Regulates Expr Cluster

1 Sequence

Length
761

1 Sequence Ontology Term

Identifier Name Description
gene  

2 Strains

WormBase ID
WBStrain00000289
WBStrain00000293

1 Upstream Intergenic Region

WormBase ID Name Sequence Name Length (nt) Chromosome Location Organism
intergenic_region_chrV_9054872..9055325   454 V: 9054872-9055325 Caenorhabditis elegans