Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:C14B9.4.1 | C14B9.4.1 |
2289
 |
III: 8101348-8104069 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:C14B9.4 | C14B9.4 |
1947
|
III: 8101348-8101593 |
32 RNAi Result
38 Allele
| Public Name |
|---|
| gk964518 |
| gk963887 |
| h13738 |
| lt18 |
| gk179536 |
| gk179535 |
| gk179532 |
| gk179534 |
| gk179533 |
| gk729490 |
| lt106 |
| gk446366 |
| gk681565 |
| WBVar00064974 |
| it17 |
| gk379295 |
| WBVar01408942 |
| gk691830 |
| gk778613 |
| WBVar00067553 |
| gk312386 |
| gk799796 |
| gk510204 |
| gk676271 |
| gk337630 |
| gk320360 |
| gk884453 |
| WBVar01628906 |
| gk824830 |
| WBVar01628907 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00004042 | 8101348 | 8104069 | 1 |
4 Data Sets
| Name | URL |
|---|---|
| WormBaseAcedbConverter | |
| GO Annotation data set | |
| C. elegans genomic annotations (GFF3 Gene) | |
| Panther orthologue and paralogue predictions |
1 Downstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrIII_8104070..8106651 | 2582 | III: 8104070-8106651 | Caenorhabditis elegans |
205 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| oocyte proteins identified by two or more unique peptides during proteomics study. | In the pooled data set, 1453 C. elegans proteins were identified with a probability >= 0.9 according to ProteinProphet, of which 1165 proteins were identified by more than one unique peptide. | WBPaper00038289:oocyte_protein | |
| 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 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 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 | |
| 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 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 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 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) | |
| 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 |
| 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 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 |
17 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr1031942 | Tiling arrays expression graphs | |||
| Picture: Figure 2A to F. | Expr7873 | With this antibody, authors observed, in addition to the previously reported localization patterns, strong cytoplasmic staining in newly fertilized embryos following the completion of meiosis. This cytoplasmic staining was asymmetric along the AP axis, with the highest levels at the anteriormost portion of the embryo. After the first mitotic division, anti PLK-1 cytoplasmic staining was higher in the somatic cell AB than in the germline blastomere P. This asymmetric pattern, that is, asymmetric cytoplasmic localization before division and enrichment in the somatic cell after division, reiterated at the three subsequent germline blastomere divisions. The level of cytoplasmic staining was dynamic throughout the cell cycle, decreasing during mitosis when a high level of staining was observed on centrosomes and chromosomes. | ||
| Expr7876 | Only a small proportion of GFP fluorescence was associated with centrosomes and chromosomes. In only a small percentage of embryos (~5%, n>200), the cytoplasmic GFP is slightly higher in the somatic cell compared with the germline blastomere. | |||
| Picture: Fig. 2G to L. | [plk-1::gfp-PBD (amino acids 340 to 648)] translational fusion. | Expr7875 | Expression pattern recapitulated the anti-PLK-1 staining pattern, including centrosomal, chromosomal and asymmetric cytoplasmic stainings. See Expr7873. | |
| Picture: Fig. 1 D. | Expr8237 | PLK-1 is enriched in the anterior cytoplasm of the one-cell embryo. PLK-1 distribution is uniform at meiosis (n = 8) and then becomes asymmetric by pronuclear migration (n = 6). From metaphase of P0 to the end of the two-cell stage, all embryos continue to show anterior enrichment of PLK-1 (n = 56). As previously shown, authors also observed PLK-1 localization to centrosomes and metaphase chromosomes. | ||
| Authors found an analogous distribution using antibodies directed against GFP in transgenic animals expressing GFP-PLK-1, although the asymmetry is somewhat less pronounced in this case. Picture: Figure 1. The signals detected by these antibodies in wild-type embryos are absent from embryos depleted of PLK-1 by RNAi, demonstrating specificity. | Expr8180 | PLK-1 is distributed in a uniform manner in the cytoplasm just after meiotic exit. PLK-1 distribution becomes asymmetric shortly thereafter, with more protein present on the anterior side of the embryo. This asymmetry persists throughout the one-cell stage and until the end of the two-cell stage. Line scans quantifying pixel intensities confirm these observation. These antibodies also label centrosomes, the midbody and kinetochores. | ||
| Expr9850 | Immunolocalization of PLK-1 revealed association with centrosomes and kinetochores in mitotic cells of the proliferating region of the germline. | |||
| Expr9848 | PLK-1 colocalizes with PLK-2 to the nuclear periphery in some NE-associated patches but is undetectable in others. | |||
| Expr13565 | In the interphase of two-cell stage embryos, PLK-1::sGFP was exclusively cytoplasmic and enriched in the AB blastomere, as reported previously using PLK-1 antibodies (Budirahardja and Gonczy, 2008; Rivers et al., 2008). Concomitantly with chromosomes condensation, PLK-1::sGFP started to accumulate on chromosomes but could also be detected at the NE. The PLK-1::sGFP signal at the NE became detectable 2.5-3 min prior to NEBD. PLK-1::sGFP was similarly detected at the NE in oocytes with condensed chromosomes. | |||
| This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope). | Expr711 | First detected at centrosomes after pronuclear meeting in post-meiotic 1-cell embryos. PLK-1 remains associated with centrosomes as the embryo enters prophase of mitosis and this localization persists through late anaphase. PLK-1 also detected in chromosome-specific localization of PLK-1 diminishes during anaphase and is not observed during telophase. PLK-1 detected at the region of spindle overlap during telophase (coincident with alpha-tubulin staining). At the time this appears as two discrete points suggesting it was part of a ring-like structure. PLK-1 is detected in newly fertilized embryos. PLK-1 staining in mature, unfertilized oocytes is diffuse and cytoplasmic. In new fertilized embryos, PLK-1 staining is coincident with six maternal bivalent pre-metaphase chromosome before their segregation. As fertilized embryos progressed through anaphase of meiosis, PLK-1 was again coincident with the dividing chromatin but has also redistributed and was found in the areas between the dividing chromatin. | located at centrosomes after pronuclear meeting in post-meiotic 1-cell embryos. PLK-1 remains associated with centrosomes as the embryo enters prophase of mitosis and this localization persists through late anaphase. PLK-1 staining in mature, unfertilized oocytes is diffuse and cytoplasmic. | |
| Expr13566 | Using PLK-1 antibodies, we confirmed the localization of endogenous PLK-1 to the Nuclear Envelope in wild-type oocytes and in early embryos. | |||
| Expr1144571 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr1010511 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr2014958 | 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). | |||
| Expr13696 | PLK-1::sGFP is intensely concentrated on centrosomes and on metaphase chromosomes in the zygote. In addition, we see relatively weak PLK-1::sGFP signal on chromosomes and the nuclear envelope beginning during pronuclear centration. | |||
| Expr2033193 | 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). | |||
| Expr14833 | In wild-type gonads, PLK-1 signal was detected in premeiotic germ cell nuclei, exhibiting chromosome adjacent and/or nucleoplasmic localization, and it became largely undetectable (except for an occasional patch at the nuclear periphery) as nuclei transitioned into meiotic prophase. |
44 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| enables | |
| located_in | |
| located_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in |
44 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| enables | |
| located_in | |
| located_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in |