Genomics
9 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:F58B6.3a.1 | F58B6.3a.1 |
2182
 |
III: 1081395-1095082 |
| Transcript:F58B6.3b.1 | F58B6.3b.1 |
1946
|
III: 1081401-1094990 |
| Transcript:F58B6.3d.1 | F58B6.3d.1 |
1753
|
III: 1081402-1094801 |
| Transcript:F58B6.3e.1 | F58B6.3e.1 |
2098
|
III: 1081402-1095005 |
| Transcript:F58B6.3e.2 | F58B6.3e.2 |
2056
|
III: 1081623-1095071 |
| Transcript:F58B6.3e.3 | F58B6.3e.3 |
1992
|
III: 1082974-1095081 |
| Transcript:F58B6.3e.4 | F58B6.3e.4 |
1634
|
III: 1087783-1095076 |
| Transcript:F58B6.3e.5 | F58B6.3e.5 |
2374
|
III: 1090035-1095077 |
| Transcript:F58B6.3c.1 | F58B6.3c.1 |
228
|
III: 1094240-1094801 |
Other
5 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:F58B6.3e | F58B6.3e |
486
|
III: 1091647-1091697 |
| CDS:F58B6.3c | F58B6.3c |
228
|
III: 1094240-1094374 |
| CDS:F58B6.3a | F58B6.3a |
1887
|
III: 1081409-1081519 |
| CDS:F58B6.3b | F58B6.3b |
1749
|
III: 1081409-1081519 |
| CDS:F58B6.3d | F58B6.3d |
1746
|
III: 1081409-1081519 |
96 RNAi Result
332 Allele
| Public Name |
|---|
| gk963623 |
| gk962532 |
| gk964281 |
| WBVar02120666 |
| WBVar02124686 |
| WBVar01323560 |
| WBVar01323562 |
| WBVar01323564 |
| WBVar01323563 |
| WBVar01323566 |
| WBVar01323565 |
| WBVar01323571 |
| WBVar01323570 |
| WBVar01323578 |
| WBVar01606599 |
| gk854831 |
| gk413321 |
| gk881820 |
| gk827357 |
| gk855406 |
| gk332527 |
| gk494588 |
| gk715190 |
| gk857401 |
| gk513647 |
| gk452841 |
| gk753811 |
| gk905394 |
| gk636159 |
| gk713113 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00003917 | 1081395 | 1095082 | 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_1095083..1099648 | 4566 | III: 1095083-1099648 | Caenorhabditis elegans |
109 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 |
| Transcripts that showed significantly decreased expression in AGP22 [nhr-49(nr2041)I;glp-1(e2141)III] comparing to in CF1903 [glp-1(e2144)III] at Day 2 adults. | Fold change > 2, p Value of < 0.05 and a false discovery rate (FDR) of < 0.05. | WBPaper00061530:nhr-49(e2144)_downregulated | |
| 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 | |
| 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 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 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) | |
| Strictly maternal class (SM): genes that are the subset of maternal genes that are not also classified as embryonic. | 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_SM | |
| 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 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 | |
| Gamma irradiation 100 mGY per hour for 72 hours since L1 larva. | Transcripts that showed significantly increased expression after exposure to 100mGy per hour gamma irradiation from L1 to day 1 adult hermaphrodite stage. | DESeq2, FDR <= 0.05, log2 fold change >= 0.3 or <= -0.3. | WBPaper00058958:100mGy-irradiation-72h_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 | |
| Proteins that showed significantly decreased expression in 1-day-old sek-1(km4) adults comparing to in wild type animals, both with 6 hours of cisplatin treatment. | The differential expression analysis was performed in R. Differentially expressed proteins were identified by using a two-sided t-test on log-transformed data. | WBPaper00065373:sek-1(km4)_downregulated_cisplatin | |
| 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 in pfd-6(gk493446); daf-2(e1370) comparing to in daf-2(e1370). | Limma version 3.24.15. Fold change < 0.67 (p < 0.05). | WBPaper00055827:pfd-6(gk493446)_downregulated | |
| 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 | |
| Transcripts that showed decreased expression in hlh-11(ko1) knockout strain comparing to in wild type background. | DESeq2, FDR < 0.05 | WBPaper00060683:hlh-11(ko1)_downregulated | |
| Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours. | Transcripts that showed significantly decreased expression in hpx-2(dg047) 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_hpx-2(dg047) |
11 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr1031850 | Tiling arrays expression graphs | |||
| Antibodies against the amino and carboxy termini gave the same results. early embryo(author) = blastula + gastrulating embryo(curator). | Expr579 | PAR-1 is found in the cortex of germ line cells in the whole adult gonad. In early embryos, cortical PAR-2 expression continues in P0, P1, P2, P3 and P4 (the cells of germline lineage), fades in Z2 and Z3. In all but P4, PAR-1 exhibits an asymmetric distribution. | In the distal gonad, PAR-2 staining is strongest at septa between nuclei. In the proximal gonad, PAR-2 is found uniformly in the periphery. PAR-2 is associated with the cortical cytoskeleton. PAR-2 becomes localized to the posterior cortex in P0 through P3. During the symmetrical division of P4, PAR-2 is uniformly distributed at the cortex so that both Z2 and Z3 initially show PAR-2. | |
| Expr2885 | Decreased levels of expression in the glp-4(bn2) mutant compared to the mixed stage N2, embryo, and T6 samples (adults). | |||
| Previous data: analysis of the PAR proteins has focused primarily on their anterior-posterior localization at the 1-cell stage and their roles in subsequent anterior-posterior polarity. After cell division begins, however, this anterior-posterior asymmetry is reiterated only in the lineage of cells that form the germline. In contrast, some somatic (non-germline) cells show an apical-basal polarity in PAR localization. | Expr1820 | The apical-basal polarity of the PAR protein persists through early gastrulation, although the level of PAR-2 diminishes. Later changes in PAR distribution were not analyzed further. | By the 4-cell stage, the posterior PAR protein PAR-2 is localized to basolateral surfaces, and is not detected on the apical surfaces of somatic cells. | |
| Picture: Figure 1a, Supplementary Movie 1. | Marker5 | GFPPAR-2 labels the posterior cortex. | ||
| Expr1152702 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr2014727 | 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). | |||
| Expr10542 | At the onset of cytokinesis, as the furrow has formed, cortical anterior PAR-6-mCherry fluorescence intensity decreases while it increases at the cleavage furrow. The anterior levels of PAR-6- mCherry then steadily decrease at beginning of furrow closure. In the posterior cortex of the single-cell embryo, PAR- 2-GFP fluorescence intensity decreases at furrow initiation to furrow closure, yet increases in intensity at the cleavage furrow. The posterior cortex fluorescence of PAR-2- GFP continues to decrease after furrow closure. After 4-min postclosure, posterior PAR-2-GFP fluorescence starts to increase until 16-min postclosure resulting in an 18% increase in cortical fluorescence intensity. The increase in the cortical posterior fluorescence correlates with the clearance of PAR-2-GFP at the cleavage furrow. In wild-type embryos, PAR-6-mCherry and PAR-2-GFP localize to the anterior and posterior poles prior to cleavage furrow initiation. As the furrow starts to ingress (2.7 min), both anterior and posterior PAR proteins appear along the furrow membrane, but only PAR-6-mCherry is found at the leading edge of the furrow membrane. As the furrow continues to ingress (4.7 min), this localization pattern is maintained. At 12.5 min after the initiation of furrow ingression, the flanking membrane along the furrow is predominately labeled with PAR-6- mCherry. The midbody region is the only place where PAR-2-GFP co-localizes with PAR-6-mCherry. As the embryo continues to divide to become a four-celled embryo, the localization of the anterior and posterior PAR proteins segregate to the membrane boundaries on opposite sides of the embryo. Here, PAR-6 is found predominantly along the membrane boundaries between the ABa, Abp, and EMS blastomeres. Anterior and posterior PAR protein localization at the furrow is observed until 8-min postcleavage furrow closure. Between 8- and 16-min postcleavage furrow closure, PAR-2-GFP localization becomes restricted to the membrane region in vicinity of the midbody (8-16-min postclosure). PAR-6-mCherry localizes along the entire furrow membrane during cytokinesis, whereas, PAR-2 is temporally and spatially restricted along the furrow. | |||
| Expr1017548 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr2032961 | 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). | |||
| Expr2462 | Before pronuclear formation, GFP:PAR-2 and GFP:PAR-6 were distributed uniformly throughout the embryo. | Both GFP:PAR-2 and GFP:PAR-6 could be detected readily in the cytoplasm, and were also visibly enriched at the cortex. The first asymmetry was seen after the appearance of pronuclei when ruffling ceased abruptly near the paternal pronucleus. At that time, GFP:PAR-2 began to increase and GFP:PAR-6 began to decrease on the cortex in the smooth region. For the next 10 minutes, as the smooth region expanded towards the anterior, the GFP:PAR-2 domain expanded along with it, whereas GFP:PAR-6 receded, becoming more prominent in the area where ruffling is maintained. By pseudocleavage, the fusions reached their final configurations on the cortex, with GFP:PAR-2 enriched in the posterior and GFP:PAR-6 enriched in the anterior. GFP:PAR-2 was also detected on centrosomes during pronuclear rotation and GFP:PAR-6 was detected in both pronuclei just before pronuclear fusion. The latter localizations have not been reported previously for the endogenous proteins. |
22 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| enables | |
| enables | |
| enables | |
| located_in | |
| located_in | |
| located_in | |
| involved_in | |
| located_in | |
| involved_in | |
| involved_in |
4 Homologues
| Type |
|---|
| least diverged orthologue |
| least diverged orthologue |
| least diverged orthologue |
| least diverged orthologue |