WormMine: Gene WBGene00006940

• WormBase Gene ID: WBGene00006940
• Gene Name: wee-1.3
• Sequence Name: Y53C12A.1
• Brief Description: wee-1.3 encodes one of two C. elegans homologs of the Wee1 family of dual-specificity protein kinases (wee-1.1 encodes the second homolog; wee-1.2 is a pseudogene); in particular, WEE-1.3 is related to the membrane-associated vertebrate MYT1 kinases.
• Organism: Caenorhabditis elegans
• Automated Description: Enables cyclin-dependent protein serine/threonine kinase inhibitor activity. Involved in several processes, including negative regulation of reproductive process; nematode larval development; and sexual reproduction. Acts upstream of or within nematode male tail tip morphogenesis. Located in several cellular components, including condensed chromosome; nuclear envelope; and perinuclear endoplasmic reticulum. Expressed in several structures, including germ line; intestine; oocyte; somatic cell; and spermatheca. Is an ortholog of human PKMYT1 (protein kinase, membrane associated tyrosine/threonine 1).
• Biotype: SO:0001217
• Genetic Position: II :1.66787 ±0.00494
• Length (nt): 2731

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00006940

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y53C12A.1.1	Y53C12A.1.1	2404	II: 9713737-9716467

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y53C12A.1	Y53C12A.1	2034	II: 9714102-9714134

19 RNAi Result

• WBRNAi00009375
• WBRNAi00085319
• WBRNAi00108292
• WBRNAi00008141
• WBRNAi00037401
• WBRNAi00057112
• WBRNAi00057250
• WBRNAi00001545
• WBRNAi00071198
• WBRNAi00108291
• WBRNAi00024312
• WBRNAi00024313
• WBRNAi00108293
• WBRNAi00023365
• WBRNAi00023878
• WBRNAi00024165
• WBRNAi00024240
• WBRNAi00086485
• WBRNAi00106671

49 Allele

• gk963801
• gk963053
• gk962682
• gk962798
• q89
• WBVar02123499
• gk964269
• gk963142
• WBVar01696199
• tm681
• h9208
• h9209
• e1947
• hc144
• hc145
• WBVar02099352
• WBVar01989264
• WBVar01309897
• gk151408
• gk151407
• gk151410
• gk151409
• gk151406
• gk151405
• lz5
• eb61
• WBVar01895108
• eb62
• WBVar01895109
• eb60

1 Chromosome

• WormBase ID: II
• Organism: Caenorhabditis elegans
• Length (nt): 15279421

1 Chromosome Location

• Feature . Primary Identifier: WBGene00006940
• Start: 9713737
• End: 9716467
• 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_chrII_9713297..9713736
• Length (nt): 440
• Chromosome Location: II: 9713297-9713736
• Organism: Caenorhabditis elegans

155 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 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
	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
Osmotic stress	Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when no food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_NoFood
	Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_expressed
	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 day 1 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_fem-3(q20)
	Transcripts that showed significantly increased expression in day 3 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_upregulated_fem-3(q20)
Bacteria diet: Escherichia coli HB101. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria E. coli HB101 for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:HB101_downregulated
Bacteria diet: Sphingomonas aquatilis Yellow. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria Sphingomonas aquatilis (Yellow) for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:S.aquatilis_downregulated
	Transcripts that showed significantly decreased expression in hsp-6(mg585) comparing to in N2 at L4 larva stage.	EdgeR, fold change > 2, FDR < 0.001.	WBPaper00056290:hsp-6(mg585)_downregulated
	mRNAs that showed differential expression in activated AAK-2(uthIs202[aak-2 (intron 1)::aak-2(aa1-aa321)::Tomato::unc-54 3'UTR + rol-6(su1006)]), activiated CRTC-1 (uthEx222[crtc-1p::crtc-1 cDNA (S76S, S179A)::tdTomato::unc-54 3'UTR + rol-6(su1006)]), or AAK-2;CRTC-1 comparing to in N2.	Genes were tested for differential expression between each mutant strain and wild-type using edgeRs glm method. Briefly, negative binomial models were fitted and dispersion estimates obtained. These were then used to calculate average levels of change between conditions and determine differential expression, using the generalized linear model likelihood ratio test. For each comparison, genes with less than 5 CPM were filtered and those with at least 50% change and False Discovery Rate (FDR) of 1% or less were considered differentially expressed.	WBPaper00046499:AMPK_regulated
	Transcripts that showed significantly increased expression in animals exposed to 400uM tamoxifen from L1 to L4 larva stage.	DEseq2, fold change > 2	WBPaper00064505:tamoxifen_upregulated
	Transcripts that showed significantly changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals.	Sleuth	WBPaper00051558:aging_regulated
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
	Genes down regulated by mir-243(n4759).	RNAs that changed at least 2-fold with a probability of p > 0.05 in three biological replicates were considered differentially regulated between wild-type and mir-243.	WBPaper00036130:mir-243_down_regulated
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
	Transcripts that showed significantly decreased expression in tetraploid N2 comparing to diploid N2 animals at L4 larva stage.	DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05.	WBPaper00066110:tetraploid_vs_diploid_downregulated
	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:hypodermis_L3-L4-larva_expressed
	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 50uM Rifampicin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin_downregulated
Bacteria: B.thuringiensis	Transcripts in elt-2(RNAi) animals that were significantly differentially expressed at least for one time point and one pathogenic strain Bt247 and Bt679 compared to the non pathogenic strain Bt407.	Cuffdiff	WBPaper00060358:B.thuringiensis_pathogen_regulated_elt-2(RNAi)
	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 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 significantly decreased expression in the neurons of bcat-1(RNAi) animals at 5-days post L4 adult hermaphrodite stage, comparing to animals injected with empty vector.	DESeq2. FDR < 0.05.	WBPaper00060459:bcat-1(RNAi)_downregulated
	Transcripts that showed significantly decreased expression in nhl-2(ok818) comparing to in N2 at 25C.	EdgeR, FDR < 0.05, fold change < 0.5.	WBPaper00055971:nhl-2(ok818)_25C_upregulated

13 Expression Patterns

• Primary Identifier: Expr2258
• Remark: Northern hybridization experiments reveal that the wee-1.3-encoded 2.4 kb mRNA was found in fem-1(hc17lf) hermaphrodites, which do not make sperm, as well as fem-3(q23gf) hermaphrodites, which make sperm but no oocytes.
• Pattern: Seven stable transgenic lines all consistently showed GFP during early embryonic development, in the distal region of the larval, but not adult, germline, and in some larval neurons and hypodermal cells.

• Primary Identifier: Expr2303
• Remark: Reporter gene fusion type not specified.
• Pattern: Seven stable transgenic lines all consistently showed GFP during early embryonic development, in the distal region of the larval, but not adult, germline, and in some larval neurons and hypodermal cells.

• Primary Identifier: Expr2036198
• 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: Expr1032954
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr12384
• Pattern: The spermatheca of hermaphrodites of avEx148 exhibit GFP::WEE-1.3 within sperm. In the somatic tissues of the adult, perinuclear WEE-1.3::GFP expression is observed throughout the adult, including nuclei of the head and tail. The nuclei of many cell types in the developing larvae, including the cells of the developing intestine, also exhibit WEE-1.3::GFP expression.

• Primary Identifier: Expr12372
• Subcellular Localization: WEE-1.3 was observed in cytoplasm throughout the germline cells of wild-type animals.

• Primary Identifier: Expr12383
• Pattern: WEE-1.3::GFP expression is perinuclear throughout the adult soma, germline, and within developing embryos. Perinuclear expression is observed from the distal tip of the germline to the mature proximal oocytes. It then continues to be expressed in developing embryos within the uterus of the animal. In addition to the perinuclear expression within the germline, there is some diffuse cytoplasmic expression within developing oocytes and embryos, expression on the membrane within developing oocytes and embryos, and distinct punctae on the surface of the oocytes and within embryos.
• Subcellular Localization: WEE-1.3 is localized to the nuclear envelope and a portion of the endoplasmic reticulum.

• Primary Identifier: Expr2302
• Pattern: Northern hybridization experiments reveal that the wee-1.3-encoded 2.4 kb mRNA was found in fem-1(hc17lf) hermaphrodites, which do not make sperm, as well as fem-3(q23gf) hermaphrodites, which make sperm but no oocytes.

• Primary Identifier: Expr12385
• Subcellular Localization: The WEE-1.3 expression is observed within the nucleus of mature oocytes and appears to surround the individual diakinetic chromosomes.

• Primary Identifier: Expr2018061
• 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: Expr1160683
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr15226
• Pattern: The endogenous C-terminal WEE-1.3::GFP strain (WDC8) exhibits a perinuclear and cytoplasmic punctate localization expression pattern that is identical to that observed in the WEE-1.3 antibody stained germ lines, transgenic WEE-1.3::GFP animals and in endogenous gfp::wee-1.3 (WDC2) strains. This expression is ubiquitous throughout the soma, in the germ line from the distal tip to the proximal oocytes, in developing embryos, and in sperm stored in the spermatheca.

• Primary Identifier: Expr1018768
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

40 GO Annotation

6 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00006940
• Start: 9713737
• End: 9716467
• Strand: -1

40 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 2731

1 Sequence Ontology Term