WormMine: Gene WBGene00004041

• WormBase Gene ID: WBGene00004041
• Gene Name: plg-1
• Sequence Name: F44E2.11
• Brief Description: plg-1 is defined by a single, autosomal dominant mutation that results in formation of a gelatinous copulatory plug over the vulva by males after mating; analysis of natural isolates of C. elegans indicates that formation of a copulatory plug does not occur in the standard laboratory strain, N2, but does occur in other isolates; in N2, the plg-1 gene, which can encode a protein with similarity to mucin glycoproteins, is disrupted by a gypsy/Ty3 type retrotransposon, Cer1; a stable plg-1 transcript is absent in non-plugging strains such as N2, but a spliced transcript from the gene is present in RNA from adult males of plugging strains; the conserved 5' region of plg-1, when fused to a GFP reporter, directs expression exclusively in males in 12 cells of the vas deferens at the L4 stage prior to the adult molt.
• Organism: Caenorhabditis elegans
• Automated Description: Expressed in vas deferens and in male.
• Biotype: SO:0001217
• Genetic Position: III :-0.044±
• Length (nt): 746

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004041

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F44E2.11.1	F44E2.11.1	654	III: 8852261-8853006

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F44E2.11	F44E2.11	351	III: 8852264-8852339

0 RNAi Result

37 Allele

• gk964518
• gk963887
• gk561242
• WBVar02123385
• WBVar02124475
• WBVar02122460
• WBVar02121004
• WBVar02122944
• WBVar02121875
• WBVar02120686
• gk962661
• WBVar02121596
• gk963259
• gk964169
• gk963749
• WBVar02123911
• WBVar02121415
• gk963589
• WBVar02123466
• gk962693
• gk963239
• gk964494
• gk964153
• WBVar02124691
• WBVar02121174
• gk962770
• gk963195
• gk962586
• WBVar02121755
• gk962585

1 Chromosome

• WormBase ID: III
• Organism: Caenorhabditis elegans
• Length (nt): 13783801

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004041
• Start: 8852261
• End: 8853006
• Strand: 1

2 Data Sets

• WormBaseAcedbConverter
• C. elegans genomic annotations (GFF3 Gene)

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrIII_8853007..8853816
• Length (nt): 810
• Chromosome Location: III: 8853007-8853816
• Organism: Caenorhabditis elegans

76 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 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 increased 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_upregulated
	Transcripts that showed significantly increased 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_upregulated
	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 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 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 whole oocytes.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00065975:P-body_vs_oocyte_depleted
	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
25C vs. 20C	Transcripts that showed significantly increased expression in 1-day post L4 adult hermaphrodite N2 grown at 25C, comparing to in N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:25C_vs_20C_upregulated
	Transcripts that showed significantly increased expression in 10-days post L4 adult hermaphrodite N2 grown at 20C, comparing to in 1-day post L4 adult hermaphrodite N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:Day10_vs_Day1_upregulated
Bacteria infection: Pseudomonas aeruginosa PA14. 24 hours of exposure at 25C.	Transcripts that showed significantly increased expression in N2 animals with 24 hours of exposure to P. aeruginosa PA14 for 24 hrs at 25C, comparing to N2 animals without exposure to PA14.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00058948:PA14_upregulated
	Transcripts that showed significantly altered expression at URX, AQR, and PQR neurons in camt-1(ok515) animals comparing to in wild type AX1888-1 strain.	RNA-seq data were mapped using PRAGUI - a Python 3-based pipeline for RNA-seq data analysis.	WBPaper00061902:camt-1(ok515)_regulated_URX-AQR-PQR
Bacteria infection: Streptococcus gordonii	Transcripts that showed significantly decreased expression after L4 larva animals were exposed to wild type S. gordonii for 2-3 hours, comparing to animals exposed to S. gordonii delta-spxB.	Fold change > 2, FDR corrected p-value < 0.05.	WBPaper00055049:S.gordonii_downregulated
	Transcripts that showed significantly decreased expression in eat-2(ad1116) comparing to in N2 at 3-days post L4 adult hermaphrodite animals.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:eat-2(ad1116)_downregulated
	Transcripts that showed altered expression in cat-1(RNAi) animals comparing to control animals injected with empty vector.	p-value <= 0.05	WBPaper00066902:cat-1(RNAi)_regulated
	Transcripts that showed significantly increased expression in hda-1(RNAi) embryos comparing to control animals.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00067044:hda-1(RNAi)_upregulated
	Genes that were not enriched in either spermatogenic fem-3(q96gf) nor oogenic fog-2(q71) gonads, according to RNAseq analysis.	To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq.	WBPaper00045521:Gender_Neutral
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)
	Transcripts that showed significantly increased expression in zip-3(gk3164) comparing to in N2, after exposed to P. aeruginosa for 18 hours.	p < 0.05	WBPaper00056326:zip-3(gk3164)_upregulated_P.aeruginosa-infected
	Transcripts that showed significantly increased expression in atfs-1(et15) comparing to in N2.	EdgeR v. 3.20.2, fold change > 2.	WBPaper00055941:atfs-1(et15)_upregulated
	Transcripts that showed significantly increased expression in nuo-6(qm200);atfs-1(gk3094) comparing to in N2.	EdgeR v. 3.20.2, fold change > 2.	WBPaper00055941:nuo-6(qm200);atfs-1(gk3094)_upregulated
	Embryonic A-class motor neuron enriched genes.	A two-class unpaired analysis of the data was performed to identify genes that differ by >= 1.5-fold from the reference at a FDR of <1% for the larval pan-neural, embryonic pan-neural, and larval A-class motor neuron datasets.	WBPaper00030839:Embryo_A_Class
	Transcripts that showed significantly increased expression in smn-1(ok355) heterozygots using balancer hT2 comparing to in N2.	DESeq v1.14.0, log2FC > 1, q <= 0.05.	WBPaper00056809:smn-1(ok355)_upregulated
	Expressed transcripts enriched in embryonic motor neurons (identified by unc-4::GFP expressing cells).	Comparisons of RMA normalized intensities for unc-4::GFP vs reference cells were statistically analyzed using Significance Analysis of Microarrays software (SAM, Stanford). A two-class unpaired analysis of the data was performed to identify genes that differ by 1.7-fold from the wildtype reference at a False Discovery Rate (FDR) of 1%. These genes were considered significantly enriched.	WBPaper00025141:unc-4::GFP_Enriched_Genes
	Genes expressed in embryonic motor neurons (identified by unc-4::GFP expressing cells).	Genes called Present by MAS 5.0 in 2 out of 3 unc-4::GFP hybridizations.	WBPaper00025141:unc-4::GFP_Expressed_Genes
	Transcripts that showed significantly decreased 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_downregulated_glp-1(e2141)
	Transcripts that showed significantly decreased expression in jmjd-3.1p::jmjd-3.1 comparing to in N2.	DESeq2 Benjamini-Hochberg adjusted p-value < 0.05.	WBPaper00049545:jmjd-3.1(+)_downregulated
	Transcripts that showed significantly decreased 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)_downregulated_PA14
Bacteria infection: Bacillus thurigiensis DB27	Caenorhabditis elegans Genes with expression levels changed significantly after treatment of Bacillus thurigiensis DB27.	Differential expression were calculated by empirical eBayes method using eBayes function. P_value <= 0.01 and log2 fold change > 1 were used to call differentially expressed genes in all datasets.	WBPaper00041606:CE_B.thuringiensis-DB27_regulated

3 Expression Patterns

• Primary Identifier: Expr1151140
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr8206
• Remark: Picture: Figure 3c, Supplementary Movie 1.
• Pattern: Strong expression of GFP was observed in 12 cells of the vas deferens. Expression commences during the fourth larval stage, before the adult moult. In adult males, the cuboidal GFP-expressing cells are arranged in two rows. There is left - right asymmetry in the location of the GFP-expressing cells and in the intensity of their expression. Although there seems to be variation among individuals, typically five of the cells are on the right-hand side of the midline, whereas seven are on the left-hand side of the midline; furthermore, three posterior cells express a lower level of GFP, and two of these low-level cells are on the left-hand side.

• Primary Identifier: Marker121
• Pattern: Marker for vas deferens.

0 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004041
• Start: 8852261
• End: 8853006
• Strand: 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 746

1 Sequence Ontology Term