WormMine: Gene WBGene00015478

• WormBase Gene ID: WBGene00015478
• Gene Name: mapk-15
• Sequence Name: C05D10.2
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable protein serine/threonine kinase activity. Involved in dopamine uptake; protein localization to ciliary transition zone; and regulation of cilium assembly. Located in axoneme; cell-cell junction; and ciliary basal body. Expressed in neurons; oocyte; and in male. Human ortholog(s) of this gene implicated in breast cancer. Is an ortholog of human MAPK15 (mitogen-activated protein kinase 15).
• Biotype: SO:0001217
• Genetic Position: III :-1.42275±
• Length (nt): 4230

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00015478

Genomics

3 Transcripts

Class	WormMine ID	Sequence Name	Length (nt)	Chromosome Location
MRNA	Transcript:C05D10.2a.1	C05D10.2a.1	1741	III: 6067857-6072086
NcPrimaryTranscript	Transcript:C05D10.2b	C05D10.2b	1418	III: 6067891-6071792
NcPrimaryTranscript	Transcript:C05D10.2c	C05D10.2c	1417	III: 6067891-6071792

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C05D10.2a	C05D10.2a	1413	III: 6067891-6067938

14 RNAi Result

• WBRNAi00113187
• WBRNAi00039720
• WBRNAi00039721
• WBRNAi00108296
• WBRNAi00010193
• WBRNAi00076083
• WBRNAi00005930
• WBRNAi00108271
• WBRNAi00113101
• WBRNAi00113155
• WBRNAi00028488
• WBRNAi00087937
• WBRNAi00112957
• WBRNAi00103165

48 Allele

• gk964518
• gk175937
• gk175938
• gk175939
• gk175940
• gk964338
• gk964339
• WBVar01264201
• WBVar01264199
• WBVar01656784
• h10903
• WBVar01722559
• gk960143
• WBVar01837645
• gk656714
• gk590447
• gk919717
• gk622300
• gk349009
• WBVar01396874
• WBVar01918604
• gk823776
• gk800671
• gk418783
• gk572741
• gk770964
• gk879681
• gk574976
• gk935054
• gk642009

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00015478
• Start: 6067857
• End: 6072086
• 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_chrIII_6072087..6080562
• Length (nt): 8476
• Chromosome Location: III: 6072087-6080562
• Organism: Caenorhabditis elegans

178 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 of coding genes that showed significantly decreased 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_depleted_coding-RNA
	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
	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
	Transcripts that showed significantly increased expression after four-day-old young adult worms were placed on NGM plates seeded with OP50 in the presence 5% Agaro-oligosaccharides(AGO) for 24 h, comparing to animals grown in the absence of AGO.	Fold change > 2.	WBPaper00064306:Agaro-oligosaccharides_upregulated
	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
	Top 300 transcripts enriched in ABalppppppa, ABpraaapppa according to single cell RNAseq.	Top 300 enriched transcripts were determined by log2.ratio of the tpm in the cell type vs the tpm in the other cells * the log2 of the cell.type tpm.	WBPaper00061340:ASE_parent
	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 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 that showed significantly increased expression in xrep-4(lax137).	DESeq2. Genes were selected if their p value < 0.01.	WBPaper00066062:xrep-4(lax137)_upregulated
	Transcripts that showed significantly increased expression in hda-1(ne4752[3xFLAG-Degron-HDA-1]) 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:hda-1(ne4752)_upregulated
	Transcripts that showed significantly increased expression in mut-16(pk710), comparing to in N2 animals.	DESeq2 v. 1.22.2, adjusted p-value <= 0.05.	WBPaper00059605:mut-16(pk710)_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 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 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
	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
	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 animals fed with JM103 bacteria producing Cry5B, comparing to control animals fed with JM103.	ANOVA, p-value < 0.05.	WBPaper00056167:Cry5B_upregulated
	Transcripts that showed significantly increased expression in spr-1(ok2144) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:spr-1(ok2144)_upregulated
	Transcripts that showed significantly increased expression in him-17(me24) comparing to in N2 animals.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00064769:him-17(me24)_upregulated
	Transcripts that showed significantly increased expression in sma-4(rax3) comparing to in N2 at 1-day post-L4 adult hermaphrodite	HTseq-count was used to count reads mapped to each gene and counting data was imported to EdgeR for statistical analysis. Statistical significance was defined by adjusted P value (false discovery rate, FDR) of <0.05.	WBPaper00053184:sma-4(rax3)_upregulated
Bacteria infection: Pseudomonas aeruginosa PA14. 24 hours of exposure at 25C.	Transcripts that showed significantly decreased 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_downregulated

17 Expression Patterns

• Primary Identifier: Expr13483
• Pattern: Expression of mapk- 15 isoform A-fused to gfp and C-fused to mCherry was observed in non-dye-filling (ASE, BAG, CEP, IL1, IL2, and OLQ) and dye-filling (ADL, ADF, ASH, ASI, ASJ, and ASK) head CSNs, as well as in nondye filling (PQR) and dye filling (PHA, PHB) tail CSNs. Expression was also occasionally observed in mid-body neurons (PDE).
• Subcellular Localization: Isoform A localizes broadly to cell bodies, dendritic processes, and throughout the ciliary region of CSNs. Within the ciliary region, localization of both A and C isoforms occurs in a region consistent with the periciliary membrane compartment (PCMC) and along the length of the cilium.

• Primary Identifier: Expr13484
• Pattern: Expression of mapk- 15 isoform A-fused to gfp and C-fused to mCherry was observed in non-dye-filling (ASE, BAG, CEP, IL1, IL2, and OLQ) and dye-filling (ADL, ADF, ASH, ASI, ASJ, and ASK) head CSNs, as well as in nondye filling (PQR) and dye filling (PHA, PHB) tail CSNs. Expression was also occasionally observed in mid-body neurons (PDE).
• Subcellular Localization: Isoform C primarily localizes to cell bodies in punctate spots and throughout the ciliary region of CSNs, with only a diffuse signal along dendritic processes. Within the ciliary region, localization of both A and C isoforms occurs in a region consistent with the periciliary membrane compartment (PCMC) and along the length of the cilium. Analysis of a strain expressing the fluorescently tagged PCMC marker kap-1 demonstrated MAPK-15 isoform C colocalization with KAP-1 in the PCMC. Analysis of a strain expressing the fluorescently tagged transition-zone marker nphp-1 demonstrated that MAPK-15 isoform C does not colocalize with NPHP-1 in the transition zone, which resides between the PCMC and cilium.

• Primary Identifier: Expr14460
• Pattern: IL2, OLQ, CEPD/V, ASK, AFD, ADF, ADL, ASG, ASI, ASH, ASE, ADE, PHA, PHB, PQR

• Primary Identifier: Expr13487
• Pattern: As previously observed for the A- and C-isoform translational fusion constructs, young adults containing a wild-type copy of the daf-19 gene demonstrate robust expression of the mapk-15 transcriptional-fusion construct in head and tail CSNs of both hermaphrodite and male animals. However, expression of the mapk-15 transcriptional construct was additionally found in the head neurons AFD, ADE, and ASG, as distinguished from other neurons based on their proximity to known dye-filled neurons.

• Primary Identifier: Expr13784
• Pattern: A mapk-15 transcriptional reporter labels URX as well as many other head sensory neurons at all larval stages.

• Primary Identifier: Expr13558
• Pattern: Worms expressing mapk-15p::gfp display GFP expression in many, if not all, ciliated cells, including all amphid and phasmid neurons. Little or no GFP expression was observed in nonciliated cells, suggesting that MAPK-15 promoter activity is largely restricted to ciliated cells. It remains possible that regulatory elements present elsewhere in the genomic sequences may drive expression in other cell types.

• Primary Identifier: Expr1036618
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr13500
• Pattern: Worms expressing the Pswip-13::GFP transgene revealed GFP expression in a number of head neurons and in a pair of neurons resembling PDE, as well as expression by a small number tail neurons and by developing oocytes. Dual labeling studies with animals expressing a dopaminergic mCherry reporter (Pdat-1:: mCherry) revealed colabeling in all DA neurons (CEP, ADE, PDE).

• Primary Identifier: Expr13485
• Pattern: Males containing either the fluorescent-tagged mapk-15A isoform showed expression in tail HOB and all 9 Rn CSNs.
• Subcellular Localization: Localization of the mapk-15A isoform product was found in the cell body, dendritic projections, and ciliary regions, similar to the localization pattern observed in hermaphrodite animals.

• Primary Identifier: Expr13486
• Pattern: Males containing either the fluorescent-tagged mark-15C isoform showed expression in tail HOB and all 9 Rn CSNs.
• Subcellular Localization: Localization of the mapk-15C isoform product was found in the cell body, dendritic projections, and ciliary regions, similar to the localization pattern observed in hermaphrodite animals, with ciliary staining more discernable from dendritic process staining in the C-isoform.

• Primary Identifier: Expr1020597
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1143818
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2013380
• 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: Expr13559
• Subcellular Localization: A functional MAPK-15c fusion protein localizes at the ciliary base and along the axonemes of most or all ciliated neurons. An identical localization pattern is also found for worms with a mapk-15a::gfp transgene expressed at low levels. In cilia, MAPK-15c appears to localize preferentially to the middle segments in examined neurons. At the ciliary base, MAPK-15 is largely excluded from the transition zone marked with TMEM- 107 and NPHP-4, but colocalizes with the basal body marker GASR-8. In addition to accumulating at the basal body and axoneme, we observed a prominent pool of MAPK-15 1-2 μm proximal to the basal body, and in some images, the two pools appear to be connected by a strip of MAPK-15 signal. Based on its position, the proximal pool coincides with the proximal side of the periciliary membrane compartment (PCMC) where cell junctions (variably referred to as tight, belt, or apical junctions) connect the neuronal dendrites with a supporting sheath cell. In summary, MAPK-15 localizes to the ciliary axoneme middle segment, basal body, and apical junctions in sensory neurons.

• Primary Identifier: Expr13785
• Subcellular Localization: sfGFP-MAPK-15 localizes throughout the neuron with ~4-fold relative enrichment at the URX dendrite ending.

• Primary Identifier: Expr2031612
• 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: Expr13501
• Subcellular Localization: Confocal images of animals expressing the Pdat- 1::GFP::swip-13 translational fusion demonstrated a distribution of the fusion protein throughout the cell, including the cell bodies and processes. Colabeling for DA synapses using Pdat-1::mCherry::RAB-3 demonstrated robust colocalization with GFP::SWIP-13 in CEP, ADE, and PDE neurons, suggesting that a fraction of SWIP-13 is localized to DA synapses. Additional sites of expression include the cell body and the ciliated endings in all three types of DA neurons. In PDE, GFP::SWIP-13 is seen in the cell body and processes, including the cilia. Colabeling with synaptic marker mCherry::RAB-3 shows colocalization with GFP::SWIP-13 at putative synapses in CEP, ADE, and PDE. E, In CEP dendrites, GFP::SWIP-13 is seen along the processes, and enriches at the ciliated endings.

29 GO Annotation

4 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00015478
• Start: 6067857
• End: 6072086
• Strand: 1

29 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 4230

1 Sequence Ontology Term