WormMine: Gene WBGene00004057

• WormBase Gene ID: WBGene00004057
• Gene Name: pmk-3
• Sequence Name: F42G8.4
• Brief Description: pmk-3 encodes a homolog of p38, a mitogen-activated protein kinase (MAPK), activated in vitro by MEK6, indicating that it does respond like p38 to physiological stress; PMK-3 is expressed in nuclei throughout the intestine; PMK-3 is activated by osmotic stresses when heterologously expressed in mammalian cells; null mutants do not exhibit observable growth defects or hypersensitivity to several tested known stresses.
• Organism: Caenorhabditis elegans
• Automated Description: Enables protein kinase binding activity and protein serine/threonine kinase activity. Involved in several processes, including behavioral response to nicotine; regulation of axon extension; and response to stress. Located in cytoplasm and nucleus. Expressed in several structures, including amphid neurons; gonad; and intestine.
• Biotype: SO:0001217
• Genetic Position: IV :3.6306 ±0.002334
• Length (nt): 3936

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004057

Genomics

4 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F42G8.4a.1	F42G8.4a.1	1860	IV: 8139219-8143151
Transcript:F42G8.4a.2	F42G8.4a.2	1781	IV: 8139219-8143137
Transcript:F42G8.4a.3	F42G8.4a.3	1783	IV: 8140242-8143154
Transcript:F42G8.4b.1	F42G8.4b.1	903	IV: 8141599-8142800

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F42G8.4a	F42G8.4a	1425	IV: 8140246-8140497
CDS:F42G8.4b	F42G8.4b	903	IV: 8141599-8141669

19 RNAi Result

• WBRNAi00113182
• WBRNAi00047126
• WBRNAi00047127
• WBRNAi00014843
• WBRNAi00076415
• WBRNAi00064203
• WBRNAi00113151
• WBRNAi00113097
• WBRNAi00112752
• WBRNAi00087940
• WBRNAi00112754
• WBRNAi00112755
• WBRNAi00112758
• WBRNAi00064177
• WBRNAi00112756
• WBRNAi00112757
• WBRNAi00112952
• WBRNAi00081148
• WBRNAi00075946

54 Allele

• gk964278
• gk964500
• gk963722
• gk963417
• gk963416
• tm732
• tm745
• WBVar01650026
• h4048
• WBVar01668791
• WBVar02057876
• WBVar02057875
• WBVar01853764
• gk309994
• ju1010
• gk956167
• ju592
• WBVar01966683
• gk206745
• gk818702
• gk206746
• gk631161
• gk412125
• gk370554
• gk916481
• gk588108
• gk410980
• gk807572
• gk397956
• gk453790

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004057
• Start: 8139219
• End: 8143154
• 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_chrIV_8143155..8143499
• Length (nt): 345
• Chromosome Location: IV: 8143155-8143499
• Organism: Caenorhabditis elegans

149 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased expression in L1 neural cells comparing to in adult neural cells.	DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction.	WBPaper00060811:L1_vs_adult_upregulated_neural
	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 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 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 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 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 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 sin-3(tm1276) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:sin-3(tm1276)_upregulated
	Transcripts that showed significantly increased expression in aak-1(tm1944);aak-2(ok524) animals comparing to in N2.	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:aak-1(tm1944);aak-2(ok524)_upregulated
	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 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
	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 mep-1(ne4629[MEP-1-GFP-Degron]) in gonads dissected from 1-day old adult animals.	Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R.	WBPaper00061479:mep-1(ne4629)_upregulated
	Transcripts that showed significantly increased expression in hda-2(ok1479) comparing to in N2 animals.	DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2.	WBPaper00062159:hda-2(ok1479)_upregulated
	Transcripts that showed significantly increased expression in srbc-48(ac23);kyIs262;fer-1(b232ts) comparing to in kyIs262;fer-1(b232ts), 24h after infection with P.aeruginosa.	DESeq2, FDR <0.05, fold change > 2.	WBPaper00059664:srbc-48(ac23)_upregulated
	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
Fungi infection: Haptoglossa zoospora.	Transcripts that showed significantly altered expression after L4 N2 animals were exposed to omycete Haptoglossa zoospora for 6 hours.	Kalisto abundance files were converted and analysed using Sleuth in a R pipeline. Standard Sleuth protocols were used to calculate differential expression. P value < 0.01 and FDR < 0.01.	WBPaper00062354:H.zoospora_6h_regulated
	Proteins that showed significantly increased expression in CB4856 animals growing in 15mg per mL doxycycline from L1 to L4 larva stage.	edgeR (version 3.24.3), fold change > 2, FDR < 0.05.	WBPaper00062456:doxycycline_upregulated_CB4856_protein
	Transcripts that showed significantly decreased expression in pfd-6(gk493446); daf-2(e1370) comparing to in daf-2(e1370).	Limma version 3.24.15. Fold change < 0.67 (p < 0.05).	WBPaper00055827:pfd-6(gk493446)_downregulated
	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
	Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(+), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_P-granule(-)GFP(+)_vs_control_day2-adult
	Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(-), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_P-granule(-)GFP(-)_vs_control_day2-adult
	Transcripts that showed significantly increased expression in pgl-1(ct131) animals (isolated from SS0002[pgl-1(ct131)him-3(e1147)], comparing to in control animals SS1174, at 1-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_pgl-1(ct131)_vs_control_day1-adult
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)
Heat shock: 35C for 1 hour.	Transcripts that showed significantly increased expression 4 hours after 1-day post L4 adult hermaphrodite N2 animals were exposed to 35C for 1 hour.	The DESeq2 (GalaxyVersion 2.11.40.6 + galaxy1) was used to determine differentiallyexpressed features from count tables of differential transcript abundances. log2FC > 1, FDR < 0.01.	WBPaper00065749:Heat-Shock-With-Recovery_upregulated_N2
	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
20C vs 25C	Transcripts that showed differential expression in 20C vs 25C in mir-34(OverExpression) animals at adult stage.	N.A.	WBPaper00050488:20C_vs_25C_regulated_mir-34(OverExpression)_adult

11 Expression Patterns

• Primary Identifier: Expr1031955
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr8635
• Remark: Picture: Fig 5.
• Subcellular Localization: In neurons, PMK-3::GFP was present in both the nucleus and cytoplasm.

• Primary Identifier: Expr12435
• Pattern: pmk-3 is expressed in BAG cells.

• Primary Identifier: Expr1150994
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1845
• Pattern: pmk-3 promoter is active throughout the intestine. An identical expression pattern was found with two independent reporter constructs of pmk-3; one fusion construct had GFP linked to the first three exons of pmk-3 (DA1750) and the other fused GFP to the last exon and contained 90% of the coding region of pmk-3.
• Subcellular Localization: pmk-3::GFP localizes to the nuclei of intestinal cells. This nuclear localization was independent of growth conditions.

• Primary Identifier: Expr13103
• Pattern: Refers to NEXTDB In-situ hybridization pattern in the adult gonad.

• Primary Identifier: Expr12622
• Pattern: Expression of PMK-3::GFP from its endogenous promoter using a fosmid-based construct confirmed that PMK-3::GFP is widely expressed throughout the animal. Strong PMK-3::GFP fluorescence was observed in nuclei of neurons surrounding the second pharyngeal bulb, where the cell bodies of the ciliated amphid channel neurons localize. PMK-3::GFP is mainly present in the nucleus, but was also detected in cilia and in the dendrites.

• Primary Identifier: Expr1010260
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2014971
• 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: Expr12621
• Subcellular Localization: PMK- 3::GFP was specifically expressed in ASI neurons under the control of the gpa-4 promoter. PMK-3::GFP localized mostly to the nucleus of these neurons, but was also visible in the cytoplasm, dendrites, axons and cilia.

• Primary Identifier: Expr2033206
• 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).

36 GO Annotation

22 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004057
• Start: 8139219
• End: 8143154
• Strand: 1

36 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 3936

1 Sequence Ontology Term