WormMine: Gene WBGene00000387

• WormBase Gene ID: WBGene00000387
• Gene Name: cdc-25.2
• Sequence Name: F16B4.8
• Brief Description: cdc-25.2 encodes a putative homolog of Cdc25 phosphatase protein family that affects germline proliferation.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable protein tyrosine phosphatase activity. Involved in epidermal cell division. Acts upstream of or within nematode male tail tip morphogenesis. Predicted to be located in cytoplasm and nucleus. Expressed in several structures, including diagonal muscle; germ line; hypodermis; oocyte; and ventral nerve cord. Human ortholog(s) of this gene implicated in several diseases, including autosomal recessive polycystic kidney disease; endometrial hyperplasia; and reproductive organ cancer (multiple). Is an ortholog of human CDC25B (cell division cycle 25B).
• Biotype: SO:0001217
• Genetic Position: V :-18.5235 ±0.0415
• Length (nt): 18457

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000387

Genomics

4 Transcripts

Class	WormMine ID	Sequence Name	Length (nt)	Chromosome Location
NcPrimaryTranscript	Transcript:F16B4.8d	F16B4.8d	1526	V: 1567076-1584934
MRNA	Transcript:F16B4.8a.1	F16B4.8a.1	2088	V: 1577691-1585532
MRNA	Transcript:F16B4.8b.1	F16B4.8b.1	1963	V: 1582779-1585520
MRNA	Transcript:F16B4.8c.1	F16B4.8c.1	1122	V: 1583396-1584934

Other

3 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F16B4.8a	F16B4.8a	1443	V: 1577738-1577795
CDS:F16B4.8b	F16B4.8b	1377	V: 1582779-1582883
CDS:F16B4.8c	F16B4.8c	1122	V: 1583396-1583866

25 RNAi Result

• WBRNAi00008653
• WBRNAi00025120
• WBRNAi00044796
• WBRNAi00099920
• WBRNAi00031033
• WBRNAi00100769
• WBRNAi00101227
• WBRNAi00101246
• WBRNAi00101265
• WBRNAi00101284
• WBRNAi00071518
• WBRNAi00099314
• WBRNAi00099516
• WBRNAi00099718
• WBRNAi00101108
• WBRNAi00117463
• WBRNAi00106604
• WBRNAi00111935
• WBRNAi00100021
• WBRNAi00100208
• WBRNAi00100395
• WBRNAi00100582
• WBRNAi00100956
• WBRNAi00101175
• WBRNAi00106660

449 Allele

• WBVar01860496
• WBVar01584620
• WBVar01584621
• WBVar01584622
• WBVar01584623
• WBVar01584624
• WBVar01584625
• WBVar01584626
• WBVar01584627
• WBVar01584617
• WBVar01584618
• WBVar01584619
• gk963591
• gk963553
• gk964259
• gk963850
• gk963899
• gk963027
• s819
• s1613
• s1666
• WBVar01971090
• WBVar01971091
• WBVar01971092
• WBVar01971093
• WBVar01971098
• WBVar01971099
• WBVar01971094
• WBVar01971095
• WBVar01971096

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000387
• Start: 1567076
• End: 1585532
• 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_1585533..1585710
• Length (nt): 178
• Chromosome Location: V: 1585533-1585710
• Organism: Caenorhabditis elegans

202 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 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
	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 no food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_NoFood
	Transcripts that showed significantly increased 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_upregulated
	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 higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc).	DESeq2, fold change >= 2, FDR <= 0.01.	WBPaper00056826:SGP_biased
	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
	Genome-wide analysis of developmental and sex-regulated gene expression profile.	self-organizing map	cgc4489_group_18
	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 that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_daf-16(mu86);glp-1(e2141)
	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)
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
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_6h
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_6h
	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
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
	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 hrde-1(tm1200) animals, comparing to in N2, after growing at 25C for five generations (late generation).	CuffDiff2	WBPaper00051265:F4_hrde-1(tm1200)_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

10 Expression Patterns

• Primary Identifier: Expr2009780
• 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: Expr5775
• Remark: Also expressed in (comments from author) : No comments. Strain: BC14937
• Reporter Gene: [cdc-25.2::gfp] transcriptional fusion. PCR products were amplified using primer A: 5' [GAGGTTTATGATCGTTTGCCA] 3' and primer B 5' [ATGACTGTGCCCACGTGTT] 3'.
• Pattern: Adult Expression: pharynx; intestine; rectal gland cells; Nervous System; pharyngeal neurons; Larval Expression: pharynx; intestine; rectal gland cells; Reproductive System; developing vulva; Nervous System; ventral nerve cord; pharyngeal neurons

• Primary Identifier: Expr1030211
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr13197
• Pattern: Expression of Pcdc-25.2::gfp was observed in seam cells during the male larval developmental stages. Furthermore, the Pcdc-25.2::gfp signals were broadly expressed throughout development in multiple male somatic tissues, including pharynx, ventral nerve cord, body muscles, diagonal muscles, nervous system, and hypodermis.

• Primary Identifier: Expr8942
• Remark: Picture: Fig 1A.
• Pattern: cdc-25.2 mRNA was hardly detectable in glp-1(q224) hermaphrodites compared with N2 hermaphrodites, indicating that cdc-25.2 is preferentially expressed in the germ line. In N2 hermaphrodites, expression of cdc-25.2 mRNA was relatively low until L4 larval stage, but the expression increased significantly in young adult (YA; just after the L4 to adult molting but before egg laying has started) and adult (Ad; egg-laying gravid adult worms) stages, when oogenesis actively occurs in hermaphrodite worms. Furthermore, although cdc-25.2 mRNA was expressed in feminized fem-1(hc17lf) hermaphrodites, it was barely detectable in N2 males and in masculinized fem-3(q20gf) hermaphrodites. These results indicate that cdc-25.2 is expressed primarily in oocytes and not in sperm. However, compared with the robust expression in the N2 hermaphrodite germ line, the expression was much weaker in the feminized fem-1(lf) germ line, suggesting that the presence of sperm or fertilization positively affect the cdc-25.2 expression level. In conclusion, quantitative real-time RT-PCR showed that cdc-25.2 is predominantly expressed in oocytes of adult hermaphrodites.

• Primary Identifier: Expr12938
• Pattern: cdc-25.2 mRNA was expressed in the intestine at the L1 stage. In contrast, a cdc-25.2 mRNA signal was not detected in the L2- to L3-stage larvae, but reappeared after the L4 stage in the gonad. These results indicate that cdc-25.2 is transiently expressed in the intestine at the L1 stage.

• Primary Identifier: Expr16199
• Pattern: We found that not only the cdc-25.1 and cdc-25.2 genes but also the cdc-25.3 and cdc-25.4 genes were preferentially expressed in the germline.

• Primary Identifier: Expr2028020
• 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: Expr1148759
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1014180
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

18 GO Annotation

12 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000387
• Start: 1567076
• End: 1585532
• Strand: 1

18 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 18457

1 Sequence Ontology Term

• Name: gene

8 Strains

• WBStrain00035742
• WBStrain00040725
• WBStrain00049711
• WBStrain00049554
• WBStrain00000598
• WBStrain00008414
• WBStrain00007843
• WBStrain00008413

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrV_1558146..1567075
• Length (nt): 8930
• Chromosome Location: V: 1558146-1567075
• Organism: Caenorhabditis elegans