WormMine: Gene WBGene00004032

• WormBase Gene ID: WBGene00004032
• Gene Name: pkc-1
• Sequence Name: F57F5.5
• Brief Description: pkc-1 encodes a serine/threonine protein kinase that is orthologous to mammalian protein kinase C epsilon (PRKCE), a member of the nPKC subgroup of the protein kinase C superfamily; together with UNC-13, PKC-1 may act downstream of goa-1 to modulate phorbol ester-induced stimulation of acetylcholine release at NMJs; PKC-1 positively regulates locomotion, and affects thermotaxis and chemotaxis together with kin-11; PKC-1 is required for regulating several behaviors including sensation of volatile and soluble compounds, osmolarity, and temperature (thermosensation); PKC-1 is also required for phorbolester-induced stimulation of acetylcholine release at neuromuscular junctions; PKC-1 localizes to the processes and cell bodies of approximately 75 sensory neurons and interneurons, and pkc-1 mRNA is detectable at varying levels during larval and adult stages.
• Organism: Caenorhabditis elegans
• Automated Description: Enables diacylglycerol-dependent serine/threonine kinase activity. Involved in several processes, including nervous system process; regulation of presynaptic dense core granule exocytosis; and signaling. Located in cholinergic synapse and neuron projection. Expressed in ganglia; linker cell; and neurons. Human ortholog(s) of this gene implicated in cerebral infarction. Is an ortholog of human PRKCE (protein kinase C epsilon).
• Biotype: SO:0001217
• Genetic Position: V :3.59318 ±0.006692
• Length (nt): 17778

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004032

Genomics

5 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F57F5.5a.2	F57F5.5a.2	3394	V: 12014383-12032160
Transcript:F57F5.5a.3	F57F5.5a.3	3365	V: 12014383-12032079
Transcript:F57F5.5b.1	F57F5.5b.1	3006	V: 12014385-12019710
Transcript:F57F5.5a.1	F57F5.5a.1	3217	V: 12014385-12024160
Transcript:F57F5.5c.1	F57F5.5c.1	2292	V: 12015456-12032131

Other

3 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F57F5.5a	F57F5.5a	2124	V: 12015456-12015602
CDS:F57F5.5b	F57F5.5b	1863	V: 12015456-12015602
CDS:F57F5.5c	F57F5.5c	2292	V: 12015456-12015602

28 RNAi Result

• WBRNAi00107738
• WBRNAi00107737
• WBRNAi00107736
• WBRNAi00048887
• WBRNAi00013037
• WBRNAi00013038
• WBRNAi00015900
• WBRNAi00076500
• WBRNAi00027586
• WBRNAi00060223
• WBRNAi00060225
• WBRNAi00060226
• WBRNAi00060227
• WBRNAi00060228
• WBRNAi00060222
• WBRNAi00060224
• WBRNAi00060229
• WBRNAi00060230
• WBRNAi00083405
• WBRNAi00083428
• WBRNAi00083434
• WBRNAi00092932
• WBRNAi00092538
• WBRNAi00083388
• WBRNAi00083437
• WBRNAi00083441
• WBRNAi00085043
• WBRNAi00106260

284 Allele

• gk963271
• gk963301
• gk964458
• gk964459
• gk963618
• WBVar02061240
• WBVar02061241
• WBVar02061242
• WBVar02061238
• WBVar02061239
• otn8951
• gk964502
• h7653
• tm11993
• ok563
• tm712
• gk248685
• gk248684
• tm540
• gk320907
• ok5794
• gk838390
• gk359277
• gk670079
• gk731052
• gk674742
• tm11468
• gk323463
• gk885565
• gk567933

1 Chromosome

• WormBase ID: V
• Organism: Caenorhabditis elegans
• Length (nt): 20924180

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004032
• Start: 12014383
• End: 12032160
• 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_chrV_12013407..12014382
• Length (nt): 976
• Chromosome Location: V: 12013407-12014382
• Organism: Caenorhabditis elegans

150 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
	mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis.	Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05.	WBPaper00045420:fertilization_downregulated_transcript
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
	Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology.	DESEQ2, fold change > 2 and FDR < 0.01.	WBPaper00062103:neuron_enriched
	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 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 altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
	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
	Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
	Transcripts that showed significantly increased expression in xrep-4(lax137).	DESeq2. Genes were selected if their p value < 0.01.	WBPaper00066062:xrep-4(lax137)_upregulated
	Genes that showed expression levels higher than the corresponding reference sample (L3/L4 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:dopaminergic-neurons_L3-L4-larva_expressed
	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 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
	Transcripts that showed decreased expression in hlh-11(ko1) knockout strain comparing to in wild type background.	DESeq2, FDR < 0.05	WBPaper00060683:hlh-11(ko1)_downregulated
	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
	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_downregulated
	Transcripts that showed significantly increased expression in cfp-1(tm6369) comparing to in N2 at early embryo stage.	DESeq2, FDR < 0.05	WBPaper00058691:cfp-1(tm6369)_upregulated
	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

14 Expression Patterns

• Primary Identifier: Expr1031934
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr4957
• Remark: Picture: Fig 3A, 3B.
• Pattern: A pkc-1 transcriptional reporter was expressed exclusively in neurons. Strong expression was seen in the majority of ventral cord motor neurons, including both cholinergic and GABAergic motor neurons.

• Primary Identifier: Expr1529
• Remark: kin-13 is called PKC1B in this article.
• Pattern: In the head, PKC1B is expressed in the cell bodies of neurons in the anterior, dorsal, lateral, ventral, and retrovescular ganglia and in touch cell neurons. Neuronal processes are stained and can be traced into the neuropil of the nerve ring. Neuronal processes within the ventral nerve cord also contain substantial levels of PKC1B. Neuonal cell bodies and processes are readily apparent in tail ganglia and the posterior lateral ganglion. Precise identities of neurons expressing PKC1B include the touch cell neurons/interneurons, BDUL, BDUR, SDQR, ALMR, ALML, PVM, posterior lateral ganglion neurons, PDEL, PDER, SDQL, PVDL, PVDR, the lumbar ganglion neurons, PHA, PHB, PLMR, PLML. PKC1B is not detected in any other cells, including ~230 neurons.
• Subcellular Localization: Neuronal cell bodies and processes.

• Primary Identifier: Expr3286
• Remark: ttx-4 = pkc-1 = F57F5.5 in this paper.
• Pattern: ttx-4::GFP reporter construct was expressed in many sensory neurons, including neurons that sense temperature (AFD), odorants (AWA and AWC), NaCl (ASE), or high osmolality (ASH). The reporter construct was also expressed in many interneurons including AIY and AIZ.

• Primary Identifier: Expr11153
• Remark: Strain IK934.
• Pattern: pkc-1 is expressed in the linker cell.

• Primary Identifier: Expr1528
• Remark: kin-13 is called PKC1B in this article.
• Pattern: The transgene is expressed selectively and abundantly in nuclei of a group of neurons whose cell bodies lie immediately posterior to the nerve ring in the pharynx. These neurons are anterior, dorsal, ventral, lateral and retrovescular ganglia. PKC1B also expressed in tail ganglia. Expression not detected in the bulk (~75%) worm neurons or any other somatic cells.

• Primary Identifier: Expr1152632
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2014944
• 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: Expr1013668
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr3587
• Subcellular Localization: Diffuse in nerve cords.

• Primary Identifier: Expr1526
• Remark: kin-13 is called PKC1B in this article.
• Pattern: PKC1B mRNA is most abundant in embryos and L1 larva; however, its relative concentrations decline sharply during later stages of larva. Subsequently, an increase in the content of PKC1B transcript is detected in adult animals containing developmental embryos. The peak level of transcription at L1 is 7.5 folder higher than at L3 stage.

• Primary Identifier: Expr1527
• Remark: kin-13 is called PKC1B in this article.
• Pattern: The 87KD protein was at maximal level at L1 larva, the protein concentration diminished markedly as animals progress through later stages. However, only a trace level of PKC1B polypeptide was detected in developing embryos, although a maximal level of mRNA was evident.

• Primary Identifier: Expr2033179
• 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: Expr4141
• Remark: Curated by authors based on online in-situ hybridization database (Y. Kohara, personal communication; http://nematode.lab.nig.ac.jp).
• Pattern: no staining

54 GO Annotation

11 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004032
• Start: 12014383
• End: 12032160
• Strand: -1

54 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 17778

1 Sequence Ontology Term

• Name: gene

5 Strains

• WBStrain00021994
• WBStrain00021993
• WBStrain00021992
• WBStrain00023632
• WBStrain00031494

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrV_12032161..12032257
• Length (nt): 97
• Chromosome Location: V: 12032161-12032257
• Organism: Caenorhabditis elegans