WormMine: Gene WBGene00000868

• WormBase Gene ID: WBGene00000868
• Gene Name: cyb-3
• Sequence Name: T06E6.2
• Brief Description: cyb-3 encodes one of four C. elegans cyclin B family members that is most closely related to the B3-type cyclins; cyb-3 is required for a number of dynein-related mitotic processes and specifically for initiation of anaphase chromosome segregation; cyb-3 is also required for completion of meiosis II and proper pronuclear migration, centrosome maturation, and pronuclear condensation in the fertilized oocyte; cyb-3 is also essential for embryonic viability.
• Organism: Caenorhabditis elegans
• Automated Description: Enables cyclin-dependent protein serine/threonine kinase regulator activity. Involved in several processes, including chromosome organization; regulation of cell cycle; and sexual reproduction. Acts upstream of or within nematode male tail tip morphogenesis. Located in cytoplasm and nucleus. Expressed in several structures, including EMS; Psub2; germ cell; germ line; and male gonad. Is an ortholog of human CCNB3 (cyclin B3).
• Biotype: SO:0001217
• Genetic Position: V :7.97972 ±0.013538
• Length (nt): 1658

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000868

Genomics

3 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T06E6.2b.1	T06E6.2b.1	1456	V: 15395696-15397351
Transcript:T06E6.2a.1	T06E6.2a.1	1456	V: 15395696-15397348
Transcript:T06E6.2a.2	T06E6.2a.2	1452	V: 15395705-15397353

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T06E6.2b	T06E6.2b	1155	V: 15395713-15395758
CDS:T06E6.2a	T06E6.2a	1158	V: 15395713-15395758

35 RNAi Result

• WBRNAi00027641
• WBRNAi00099941
• WBRNAi00100463
• WBRNAi00085668
• WBRNAi00078816
• WBRNAi00052666
• WBRNAi00052667
• WBRNAi00100837
• WBRNAi00101225
• WBRNAi00101282
• WBRNAi00099335
• WBRNAi00099537
• WBRNAi00099739
• WBRNAi00101244
• WBRNAi00101263
• WBRNAi00101129
• WBRNAi00106165
• WBRNAi00000203
• WBRNAi00007566
• WBRNAi00009133
• WBRNAi00026216
• WBRNAi00078936
• WBRNAi00097998
• WBRNAi00098021
• WBRNAi00098024
• WBRNAi00100089
• WBRNAi00100276
• WBRNAi00100650
• WBRNAi00101300
• WBRNAi00106166

48 Allele

• gk963271
• gk963301
• gk964458
• gk964459
• gk964389
• WBVar02124624
• WBVar02122678
• WBVar01745259
• gk195
• WBVar01809220
• WBVar02124725
• WBVar02050001
• gk255703
• gk255702
• gk255701
• WBVar01896970
• gk255700
• gk949348
• gk949349
• gk949346
• WBVar00020820
• gk949347
• gk949345
• gk641080
• gk447079
• WBVar01590644
• WBVar01590643
• WBVar01590642
• gk892962
• gk743700

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000868
• Start: 15395696
• End: 15397353
• 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_15397354..15397384
• Length (nt): 31
• Chromosome Location: V: 15397354-15397384
• Organism: Caenorhabditis elegans

236 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
	Genes that were downregulated in lin-15B(n744).	For each gene in each microarray hybridization experiment, the ratio of RNA levels from the two samples was transformed into a log2 value and the mean log2 ratio was calculated. The log2 ratios were normalized by print-tip Loess normalization (Dudoit and Yang, 2002). All genes with a false discovery rate of <= 5% (q <= 0.05) (Storey and Tibshirani, 2003) and a mean fold-change ratio of >= 1.5 were selected for further analysis.	WBPaper00038168:lin-15B(n744)_downregulated
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
	Transcripts expressed in the epithelial tissues surrounding the pharynx that includes the arcade and intestinal valve (AIV) cells, according to PAT-Seq analysis using Pbath-15-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:arcade_intestinal-valve_expressed
	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
	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 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 expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
	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
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
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
	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
	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
Transgeneration hypoxia treatment.	Transcripts that are significantly upregulated in F1 animals after P0 parents were exposed to 0.1% oxygen for 16 hours at L4 larva stage.	For calling the significant differentially expressed genes (DEGs),the false discovery rate (FDR) after multiple testing correction was set as 0.05 and analyzed in edgeR.	WBPaper00064871:hypoxia_upregulated_F1
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

15 Expression Patterns

• Primary Identifier: Expr1030535
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr13285
• Subcellular Localization: CYB-3 was expressed strongly in a few mitotic germ cells in the distal region of the germline, where it localized to the nucleus. CYB-3 was expressed more widely in the distal half of male gonads and localized to the cytoplasm. Nonetheless, CYB-3 was not expressed in the proximal region of male gonads, in which spermatogenesis takes place.

• Primary Identifier: Expr13386
• Pattern: GFP::3xFLAG::CYB-3 is expressed in all germline nuclei in adults.

• Primary Identifier: Expr4124
• Remark: Curated by authors based on online in-situ hybridization database (Y. Kohara, personal communication; http://nematode.lab.nig.ac.jp).
• Pattern: Expressed in medial germline.

• Primary Identifier: Expr15888
• Subcellular Localization: CYB-1 and CYB-3 were detected in the nuclei of the mitotic proliferating region of the gonad.

• Primary Identifier: Expr2010649
• 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: Expr13177
• Pattern: Early embryos were fixed and stained with Mab F2F4 (green), shown to recognize CYB-3 (Michael, 2016), and DAPI, to illuminate the DNA (blue). Either wild type or par-4 mutant embryos were examined, after 24-hour incubation at 25C (the non-permissive temperature for the it47 allele of par-4). Anterior is to the left in all images. The data presented here reveals previously not shown data that depicts CYB-3 as asymmetrically distributed at the 4-cell stage. These data further support reported findings in Michael, 2016. There is more CYB-3 in the AB cell relative to its sister P1. In 4-cell embryos there is more CYB-3 in the EMS cell relative to its sister, P2. Thus, during P-lineage divisions, CYB-3 is asymmetrically distributed such that the somatic precursor receives more than its germline precursor sister cell. This asymmetry is abolished in par-4 mutant embryos, where all blastomeres contain equivalent amounts of CYB-3.

• Primary Identifier: Expr1156272
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr15178
• Pattern: CYB-3 is expressed in germ cells.

• Primary Identifier: Expr13284
• Pattern: mRNA levels of both cyb-1 and cyb-3 were high in young-adult and adult N2 hermaphrodites as well as in feminized fem-1(hc17lf) adult hermaphrodites. By contrast, cyb-1 mRNA, but not cyb-3 mRNA, was highly expressed in the L4 stage N2 hermaphrodites, adult N2 males, and masculinized fem-3(q20gf) adult hermaphrodites, in all of which spermatogenesis proceed specifically and robustly. On the other hand, mRNA levels of both cyb-1 and cyb-3 were negligible in germline proliferation-defective glp-1(q224lf) adult hermaphrodites. These results indicate that cyb-1 is the major B-type cyclin robustly expressed during spermatogenesis.

• Primary Identifier: Expr1018981
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr15886
• Pattern: The highest expression of CYB-1 and CYB-3 proteins was detected in embryos. CYB-1 and CYB-3 expression was virtually absent in developmentally arrested first stage and dauer larvae. Upon release from L1 arrest, sets of post-embryonic blast cells successively initiate cell division,37 and CYB-1 and CYB-3 levels were found to increase during this period. CYB-3 protein levels remained low during larval development, as compared to the levels in embryos, while CYB-1 levels were fairly constant in developing animals.

• Primary Identifier: Expr2028889
• 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: Expr15890
• Subcellular Localization: CYB-1 and CYB-3 remained diffusely distributed throughout the cytoplasm of the fertilized egg during meiosis.

• Primary Identifier: Expr2990
• Subcellular Localization: GFP-CYB-3 was present within nuclei of oocytes and embryonic blastomeres throughout the cell cycle, and was released in the cytoplasm at NEBD.

27 GO Annotation

5 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000868
• Start: 15395696
• End: 15397353
• Strand: 1

27 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 1658

1 Sequence Ontology Term