WormMine: Gene WBGene00000386

• WormBase Gene ID: WBGene00000386
• Gene Name: cdc-25.1
• Sequence Name: K06A5.7
• Brief Description: cdc-25.1 encodes a CDC25 phosphatase homolog that affects embryonic viability, meiosis, mitosis, proliferation of the intestine (E cell lineage), and germ line proliferation; it is expressed in the developing germline, in the nuclei of oocytes, embryonic nuclei, nuclei of embryonic cortical membranes, and sperm pronuclei, and in the germline precursors Z2 and Z3.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable protein tyrosine phosphatase activity. Involved in meiotic spindle organization and positive regulation of mitotic cell cycle. Located in nucleus. Expressed in several structures, including Z2; Z3; germ line; oocyte; and sperm.
• Biotype: SO:0001217
• Genetic Position: I :1.13944 ±0.00404
• Length (nt): 2537

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000386

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:K06A5.7.1	K06A5.7.1	2261	I: 6469386-6471922

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:K06A5.7	K06A5.7	1815	I: 6469812-6470066

56 RNAi Result

• WBRNAi00065119
• WBRNAi00106583
• WBRNAi00066982
• WBRNAi00066989
• WBRNAi00067027
• WBRNAi00067260
• WBRNAi00067280
• WBRNAi00067394
• WBRNAi00067401
• WBRNAi00085622
• WBRNAi00094178
• WBRNAi00077036
• WBRNAi00077037
• WBRNAi00094618
• WBRNAi00022947
• WBRNAi00025884
• WBRNAi00003938
• WBRNAi00065362
• WBRNAi00113421
• WBRNAi00065366
• WBRNAi00022985
• WBRNAi00065363
• WBRNAi00050031
• WBRNAi00034008
• WBRNAi00095365
• WBRNAi00116660
• WBRNAi00085307
• WBRNAi00022984
• WBRNAi00025885
• WBRNAi00086042

44 Allele

• gk962858
• gk962706
• gk963902
• rr31
• rr36
• WBVar01431892
• WBVar01431891
• otn1167
• otn2552
• nr2036
• WBVar02039687
• gk714493
• ok1888
• ij48
• gk308720
• gk595454
• gk363396
• gk113074
• otn6141
• gk603895
• gk113079
• gk712041
• WBVar01900335
• gk882816
• gk620879
• gk939892
• gk113075
• gk446936
• gk113076
• gk471033

1 Chromosome

• WormBase ID: I
• Organism: Caenorhabditis elegans
• Length (nt): 15072434

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000386
• Start: 6469386
• End: 6471922
• Strand: -1

4 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)
• Panther orthologue and paralogue predictions

0 Downstream Intergenic Region

179 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
	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
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly decreased expression in N2 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_N2
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_expressed
	Genes with expression level regulated by genotype (N2 vs CB4856) and age at old adults stage (214 hours at 24 centigrade).	For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR).	WBPaper00040858:eQTL_age_regulated_aging
	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: 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
	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
	Significantly differentially expressed genes as determined by microarray analysis of wild-type and cde-1 mutant germlines.	RNAs that changed at least 2-fold with a probability of p < 0.05 were considered differentially regulated between wildtype and cde-1.	WBPaper00035269:cde-1_regulated
Heat Shock: 35C 4 hours at L4 larva stage.	Transcripts that showed significantly decreased expression after L4 larva N2 animals were heat stressed at 35C for 4 hours	DESeq2	WBPaper00057154:HeatShock_downregulated_mRNA
	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
Bacteria infection: Pseudomonas aeruginosa PA14. 24 hours of exposure at 25C.	Transcripts that showed significantly increased 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_upregulated
Temprature shift to 28C for 24 hours.	Transcripts that showed significantly decreased expression after animals were exposed to 28C temperature for 24 hours.	Differentially expressed genes wereidentified using DESeq (v.1.18.0) by normalizing readsbased on the negative binomial distribution method andcomparing each HS timepoint to the 0-h control.	WBPaper00061341:28C_24h_downregulated
	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:dopaminergic-neurons_L3-L4-larva_expressed
	Transcripts that showed significantly altered expression at URX, AQR, and PQR neurons in camt-1(ok515) animals comparing to in wild type AX1888-1 strain.	RNA-seq data were mapped using PRAGUI - a Python 3-based pipeline for RNA-seq data analysis.	WBPaper00061902:camt-1(ok515)_regulated_URX-AQR-PQR
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 0hr 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:germline-precursors_blastula-embryo_expressed
	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
	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:PVD-OLL-neurons_L3-L4-larva_expressed

13 Expression Patterns

• Primary Identifier: Expr2009779
• 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: Expr1030210
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr8236
• Remark: Picture: Fig. 1 B.
• Subcellular Localization: Soon after CDC-25.1 is detectable in AB and P1 nuclei, there is an asymmetric distribution. In early two-cell embryos, where DNA condensation has yet to occur, authors observed enrichment of CDC-25.1 in AB nuclei in 10/12 embryos. This asymmetric nuclear enrichment persists until NEBD in AB and is apparent in all two cell embryos where DNA condensation has begun (n = 18).

• Primary Identifier: Expr12834
• Pattern: CDC-25.1 in the germline shows a very obvious gradient of abundance being at very low levels in the distal region, becoming obvious in young developing oocytes (toward the top left of the gonad shown) and increasing significantly in more mature oocytes (those toward the top right of the gonad shown). Also, although CDC-25.1 is abundant within the cytoplasm of the oocytes, it is slightly more concentrated within their nuclei. CDC-25.1 is much less abundant within the distal arm of the gonad, but extended exposures at high magnification suggest that it is present being located both outside and within the nuclei, but absent from the periphery of nuclei.

• Primary Identifier: Expr16198
• 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: Expr1838
• Pattern: Previous report: Expressed in the developing germline, oocytes, and in all embryonic blastomeres. In early embryo, the protein is detected in non-dividing nuclei and in a cell membrane-associated localization; it is not present in dividing nuclei. See Expr600. Result consistent with previous report with exception that protein is detected in most or all nuclei later in embryonic development than previously reported. However, its abundance clearly declines as the number of embryonic cells increases.
• Subcellular Localization: Expressed in nuclei and cell membrane.

• Primary Identifier: Expr12794
• Pattern: cdc-25.1 is expressed predominantly, if not exclusively, in the germ line during postembryonic stages.

• Primary Identifier: Expr1153726
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr11876
• Pattern: The antibody did not detect any embryonic protein after the 28-cell stage, suggesting that zygotic CDC-25.1 is not present or is below detection levels in older embryos. CDC-25.1 expression was next detected after the embryo had hatched. In particular, the antibody stained only the germline precursor cells Z2 and Z3 (n 66) during the L1 larval stage.

• Primary Identifier: Expr2028019
• 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: Expr1016989
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr599
• Remark: This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope). aka cdc-25.1. See Expr600 for the expression pattern for the same locus.
• Pattern: ~2.3 kb band detected at low levels during all stages of development and at elevated levels in animals with proliferating germ lines.

• Primary Identifier: Expr600
• Remark: This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope). aka cdc-25.1. See Expr599 for the expression pattern for the same locus.
• Pattern: Detected in nuclei of oocytes and the nuclei and cell cortex of early embryos. Diffuse in pachytene nuclei of distal gonad but more apparent in diakinetic nuclei of oocytes in proximal gonad arm. Cytoplasmic staining in older oocytes but lost once fertilized. After fertilization and completion of meiosis, staining observed in both oocyte and sperm pronuclei. Nuclear staining seen during pronuclear migration and meeting. Diffuse cytoplasmic labeling observed during the first mitotic cleavage. Staining seen in nuclei of 2 and 4-cell embryo. Staining persists until 24-28 cell stage, only in embryonic nuclei during interphase and prophase, diffuse cytoplasmic staining seen when nuclear envelop breakdown occurs after entry into M phase. The antibody localized specifically to cortical membrane between neighbouring blastomeres during all phases of cell cycle.

19 GO Annotation

12 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000386
• Start: 6469386
• End: 6471922
• Strand: -1

19 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 2537

1 Sequence Ontology Term

• Name: gene

5 Strains

• WBStrain00026690
• WBStrain00036562
• WBStrain00040724
• WBStrain00000065
• WBStrain00008606

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrI_6471923..6473206
• Length (nt): 1284
• Chromosome Location: I: 6471923-6473206
• Organism: Caenorhabditis elegans