WormMine

WS295

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00019747 Gene Name  ipla-1
Sequence Name  ? M03A1.6 Brief Description  ipla-1 encodes a phospholipase that is a member of the Group VIA subgroup of the phospholipase A2 superfamily; in C. elegans, ipla-1 functions cell autonomously in hypodermal seam cells to regulate membrane trafficking and the asymmetric, anterior cortical localization of WRM-1/beta-catenin that, in turn, regulates asymmetric cell division; ipla-1 mutations are suppressed by mutations in mon-2 and tbc-3, which encode an Arf-GEF-like protein and a Rab GTPase GAP, respectively, involved in endosome-to-Golgi retrograde trafficking; IPLA-1, which can oligomerize, binds to a number of acidic phospholipids and exhibits calcium-independent phospholipase A2 activity in vitro that can be stimulated by the presence of acidic phospholipids; IPLA-1 is expressed in intestine, three rectal gland cells, the hypodermal syncytium and seam cells, with cytosolic localization seen in the intestine, gland cells, and syncytium, but nuclear localization seen in the seam cells.
Organism  Caenorhabditis elegans Automated Description  Enables identical protein binding activity; phospholipase activity; and phospholipid binding activity. Involved in glycerophospholipid metabolic process; regulation of asymmetric cell division; and regulation of protein localization. Located in cytosol; endoplasmic reticulum; and nucleus. Part of phosphatase complex. Expressed in pharyngeal-intestinal valve; rectum; and spermatheca. Human ortholog(s) of this gene implicated in hereditary spastic paraplegia 28. Is an ortholog of human DDHD1 (DDHD domain containing 1).
Biotype  SO:0001217 Genetic Position  II :-3.84405 ±0.004399
Length (nt)  ? 10418
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00019747

Genomics

9 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:M03A1.6a.1 M03A1.6a.1 2967   II: 4590939-4596729
Transcript:M03A1.6b.4 M03A1.6b.4 2819   II: 4590941-4597999
Transcript:M03A1.6b.3 M03A1.6b.3 3016   II: 4590941-4599008
Transcript:M03A1.6b.2 M03A1.6b.2 2875   II: 4590941-4600022
Transcript:M03A1.6b.1 M03A1.6b.1 3048   II: 4590950-4601354
Transcript:M03A1.6f.1 M03A1.6f.1 2007   II: 4591461-4595492
Transcript:M03A1.6c.1 M03A1.6c.1 2490   II: 4591461-4599002
Transcript:M03A1.6d.1 M03A1.6d.1 2334   II: 4591461-4600001
Transcript:M03A1.6e.1 M03A1.6e.1 2539   II: 4591461-4601356
 

Other

6 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:M03A1.6a M03A1.6a 2298   II: 4591461-4591604
CDS:M03A1.6b M03A1.6b 2262   II: 4591461-4591604
CDS:M03A1.6e M03A1.6e 2523   II: 4591461-4591604
CDS:M03A1.6c M03A1.6c 2340   II: 4591461-4591604
CDS:M03A1.6d M03A1.6d 2334   II: 4591461-4591604
CDS:M03A1.6f M03A1.6f 2007   II: 4591461-4591604

3 RNAi Result

WormBase ID
WBRNAi00050845
WBRNAi00050846
WBRNAi00014319

146 Allele

Public Name
gk963801
gk963053
h15402
WBVar01603729
WBVar01603728
WBVar01603730
WBVar01603731
tm471
WBVar01437545
WBVar01437546
gk963512
WBVar01372045
WBVar01372022
WBVar01372033
WBVar01719579
WBVar02029202
WBVar02070664
WBVar02076346
WBVar01982409
WBVar01982407
WBVar01982408
gk141129
gk141130
gk141131
gk141132
gk141127
gk141128
gk141126
gk141137
gk141138

1 Chromosome

WormBase ID Organism Length (nt)
II Caenorhabditis elegans 15279421  

1 Chromosome Location


Feature . Primary Identifier
Start End Strand
WBGene00019747 4590939 4601356 -1

4 Data Sets

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

0 Downstream Intergenic Region

114 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
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 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
  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
  Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals. Fold change > 2, FDR < 0.05 WBPaper00064088:Day-1-adult_vs_L4_upregulated_glp-1(e2141)
  Genes with expression level regulated by genotype (N2 vs CB4856) at Late reproduction stage (96 hours at 24 centigrade). Authors permuted transcript values and used a genome-wide threshold of log10 P-value = 2, which resembles a false discovery rate (FDR) of 0.0118. WBPaper00040858:eQTL_regulated_reproductive
  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 sftb-1(cer6) deletion homozygous comparing to to in N2 animals at L4 larva stage. DESeq2, fold change > 2 WBPaper00058725:sftb-1(cer6)_downregulated
  Proteins that showed significantly decreased expression in 1-day-old sek-1(km4) adults comparing to in wild type animals, both with 6 hours of cisplatin treatment. The differential expression analysis was performed in R. Differentially expressed proteins were identified by using a two-sided t-test on log-transformed data. WBPaper00065373:sek-1(km4)_downregulated_cisplatin
  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
  Transcripts that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage. DESeq2, fold change > 2, FDR < 0.05. WBPaper00066594:ilc-17.1(syb5296)_upregulated
  Transcripts that showed significantly decreased expression after animals were treated with 100uM Psora and 250uM Allantoin from day 1 to day 3 adult hermaphradite. DESeq2(v1.14.1), fold change > 2, p-value < 0.05 WBPaper00055354:Psora-Allantoin_downregulated
  Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin and 50mM Metformin from day 1 to day 3 adult hermaphradite. DESeq2(v1.14.1), fold change > 2, p-value < 0.05 WBPaper00055354:Rapamycin-Metformin_downregulated
  Transcripts that showed significantly decreased expression after animals were treated with 50uM Rifampicin and 250uM Allantoin from day 1 to day 3 adult hermaphradite. DESeq2(v1.14.1), fold change > 2, p-value < 0.05 WBPaper00055354:Rifampicin-Allantoin_downregulated
  Transcripts detected in germline isolated from day-1 adult hermaphrodite animals. All three experiments have CPM >= 1. WBPaper00067147:germline_expressed
  Transcripts that showed altered expression from P0 to F2 generation animals after N2 parental generation were treated with antimycin, but not in damt-1(gk961032) P0 to F2 animals after the parenal generaton were treated with antimycin. N.A. WBPaper00055862:antimycin_damt-1(gk961032)_regulated
  Proteins identified in extracellular vesicle. N.A. WBPaper00062669:extracellular-vesicle_protein
  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
Bacteria infection: Serratia marcescens Genes with increased expression after 24 hours of infection by S.marcescens Fold changes shown are pathogen vs OP50. For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated. WBPaper00038438:S.marcescens_24hr_upregulated_TilingArray
  Transcripts that showed significantly increased expression in sin-3(tm1276) comparing to in N2 at early embryo stage. DESeq2, FDR < 0.05 WBPaper00058691:sin-3(tm1276)_upregulated
  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
  Transcripts that showed significantly increased 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_upregulated_daf-16(mu86);glp-1(e2141)
  Transcripts that showed significantly increased 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_upregulated_glp-1(e2141)
  Embryonic class (E): genes that significantly increase in abundance at some point during embryogenesis. 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_E
  WT-Pico Pan-neural Depleted Genes, with genes found multiple times in a single dataset removed (without dups). To identify differentially expressed transcripts, normalized intensity values from the pan-neural data sets were compared to a reference (from all larval cells) using Significance Analysis of Microarray software (SAM). A two class unpaired analysis of the data was performed to identify neuron-enriched genes. Pan-neural enriched transcripts in the IVT and WT-Pico-derived data set were defined as 1.5X elevated vs the reference at a False Discovery Rate (FDR) = 3%. WBPaper00031532:Larva_Pan_Neuronal_Depleted

10 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
Strain: BC14511 [M03A1.6b::gfp] transcriptional fusion. PCR products were amplified using primer A: 5' [TTCTGAGTTCTTTGGCAGTTTTC] 3' and primer B 5' [CGTTTGAGCCATCGTGTATTT] 3'. Expr6411 Adult Expression: arcade cells; intestine; rectal gland cells; Reproductive System; vulval muscle; body wall muscle; hypodermis; excretory cell; Nervous System; pharyngeal neurons; Larval Expression: arcade cells; intestine; rectal gland cells; body wall muscle; hypodermis; excretory cell; Nervous System; pharyngeal neurons;  
Picture: Figure S7, Movie 1.   Expr8105 Expression patterns of ipla-1 in the adult stage. ipla-1 is expressed in several unidentified cells in pharynx (probably gland cells of pharynx), pharyngeal-intestinal valve, spermatheca, hypodermal syncytium, seam cells, rectal grand cells and intestinal-rectal valve. Expression patterns of ipla-1 in the larval stages. ipla-1 is expressed in intestine, three rectal gland cells, hypodermal syncytium and seam cells in the L1, L2 and L3 larva. In the L1 stage, ipla-1 expression is also observed in several unidentified cells in the tail. While IPLA-1 localizes to cytosol in intestine, spermatheca and gland cells, IPLA-1 localizes to the nuclei of hypodermal syncytium and seam cells.
IPLA-1::mCherry and ACL-10::GFP rescued the phenotypes of ipla-1 mutants and acl-8 acl-9 acl-10 mutants, respectively, indicating that these fusion proteins are functional. Picture: Fig 7D, 7E.   Expr9098   IPLA-1::mCherry and ACL-10::GFP were distributed in an ER-like reticular pattern throughout the cytoplasm and were partially colocalized. Both IPLA-1 and ACL-10 partially colocalized with an ER marker, ACS-20::EGFP. Furthermore, an immunoblot analysis revealed that both IPLA-1 and ACL-10 were present in the membrane fraction. IPLA-1 was also present in the soluble fraction.
    Expr1038538 Tiling arrays expression graphs  
Original chronogram file: chronogram.2027.xml [M03A1.6:gfp] transcriptional fusion. Chronogram973    
    Expr2012806 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).  
    Expr1154539 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015  
    Expr2031045 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).  
    Expr1027158 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012  
Original chronogram file: chronogram.843.xml [M03A1.6:gfp] transcriptional fusion. Chronogram1923    

23 GO Annotation

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

5 Homologues

Type
least diverged orthologue
least diverged orthologue
least diverged orthologue
orthologue
least diverged orthologue

1 Locations


Feature . Primary Identifier
Start End Strand
WBGene00019747 4590939 4601356 -1

23 Ontology Annotations

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

0 Regulates Expr Cluster

1 Sequence

Length
10418

1 Sequence Ontology Term

Identifier Name Description
gene  

1 Strains

WormBase ID
WBStrain00003074

0 Upstream Intergenic Region