Genomics
3 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:M88.6b.1 | M88.6b.1 |
2197
 |
III: 4562738-4566276 |
| Transcript:M88.6a.1 | M88.6a.1 |
1262
|
III: 4564293-4566283 |
| Transcript:M88.6c.1 | M88.6c.1 |
279
|
III: 4565544-4565879 |
Other
3 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:M88.6a | M88.6a |
858
|
III: 4564293-4564446 |
| CDS:M88.6b | M88.6b |
1785
|
III: 4562753-4562872 |
| CDS:M88.6c | M88.6c |
279
|
III: 4565544-4565669 |
36 RNAi Result
32 Allele
| Public Name |
|---|
| WBVar01263124 |
| WBVar01263125 |
| WBVar01263126 |
| WBVar01607013 |
| WBVar01837469 |
| gk172999 |
| gk819283 |
| gk172996 |
| gk489624 |
| gk172995 |
| gk794101 |
| gk172998 |
| gk172997 |
| WBVar01893268 |
| gk541620 |
| gk934228 |
| gk712688 |
| gk916355 |
| gk607040 |
| gk142 |
| gk398252 |
| gk632670 |
| gk828419 |
| gk1856 |
| gk583660 |
| gk800663 |
| gk530637 |
| gk550455 |
| gk329061 |
| gk329062 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00003915 | 4562738 | 4566283 | 1 |
4 Data Sets
| Name | URL |
|---|---|
| WormBaseAcedbConverter | |
| GO Annotation data set | |
| C. elegans genomic annotations (GFF3 Gene) | |
| Panther orthologue and paralogue predictions |
200 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 expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons. | DESeq. False discovry rate (FDR) < 0.1. | WBPaper00048988:neuron_expressed | |
| Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr 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:all-neurons_L1-larva_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 |
| 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 showed increased expression in wdr-5(ok1417) comparing with in N2. | Statistical analysis for misexpression was performed using a moderated t test from the package limma. All genes with a false discovery rate (FDR) of <= 5% (p <= 0.05) were selected as differentially regulated. | WBPaper00045861:wdr-5(ok1417)_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 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 that showed significantly decreased expression in atfs-1(cmh15) (null allele) animals comparing to in N2 animals at L4 larva stage. | edgeR, fold change > 2, FDR < 0.05 | WBPaper00060909:atfs-1(cmh15)_downregulated | |
| 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 | |
| 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 | |
| Genes with expression level regulated by genotype (N2 vs CB4856) and age at L3 larva and Late reproduction stage (96 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_developing | |
| Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:seam_expressed | |
| Genes with expression level regulated by genotype (N2 vs CB4856) at L3 larva and Late reproduction stage (96 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_regulated_developing | |
| 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) | |
| Genes with expression level regulated by genotype (N2 vs CB4856) at Late reproduction stage (96 hours at 24 centigrade). | Authors permuted transcript values and used a genome-wide threshold of log10 P-value = 2, which resembles a false discovery rate (FDR) of 0.0118. | WBPaper00040858:eQTL_regulated_reproductive | |
| 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 sin-3(tm1276) comparing to in N2. | DESeq2, fold change > 2, p-value < 0.01. | WBPaper00061203:sin-3(tm1276)_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 | |
| Significantly upregulated genes from clk-1(qm30) microarrays using SAM algorithm with an FDR < 0.1 from adult-only chips. | SAM algorithm with an FDR < 0.1. | WBPaper00033065:clk-1(qm30)_upregulated | |
| Transcripts that showed significantly changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals. | Sleuth | WBPaper00051558:aging_regulated | |
| Transcripts that showed significantly decreased expression in sin-3(tm1276) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult. | DESeq2, fold change > 2, adjusted p-value < 0.01 | WBPaper00058598:sin-3(tm1276)_downregulated |
12 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr1031848 | Tiling arrays expression graphs | |||
| Expr11020 | Examination of transgenic animals bearing the transcriptional fusion revealed that pan- 1prom::GFP is expressed in most somatic tissues. Expression was observed in all developmental stages from embryos undergoing morphogenesis to gravid adults. pan- 1prom::GFP exhibited strong expression in body wall muscle, vulva, somatic gonad and pharynx. Expression was also observed in the nerve ring, hypodermis, and rectal epithelia. Expression in the intestine was typically not observed or very weak. With respect to spatial expression, the pattern of pan-1FL::GFP was the same as pan-1prom::GFP with some notable exceptions. First, PAN- 1FL::GFP exhibited differences in expression intensity depending on the developmental point within the intermolt period. PAN-1FL::GFP was substantially qualitatively brighter at the mid to late intervals of the intermolt. Early in the intermolt bright expression of PAN- 1FL::GFP was typically only observed in the pharynx. Expression was also weak in the adult with the pharynx being the predominant expressing tissue. The other difference with respect to expression is that PAN-1FL::GFP was observed in the intestine, especially when expression was bright towards the end of the molt. | PAN-1FL::GFP exhibited a punctate localization in expressing cells. In the vulva and somatic gonad epithelia (spermatheca and uterus), these punctae were concentrated on the apical (luminal) surface of these cells. During embryonic pharyngeal development, PAN-1FL::GFP was found in the apical pharyngeal epithelium, as indicated by co-staining with the monoclonal antibody MH27 which recognizes the adherens junctions of epithelial cells. The localization in apical regions of epithelial cells is consistent with membrane association of the PAN-1B isoform. Additionally, immunolocalization data for PAN-1 indicate membrane association in intestinal cells. Cytoplasmic expression of GFP is also observed (likely corresponding to PAN-1A or PAN-1C); especially in the pharynx but also in other cell types. However, apparent cytoplasmic expression was not consistently observed indicating that some cell types may only express cytoplasmic isoforms of PAN-1 at certain developmental times. | ||
| Expr9903 | Expressed in hypodermis, pharynx, and head muscles. | |||
| Expr9980 | PAN-1 is a P granule component that co-localizes with GLH-1 in the germline from the first larval stage throughout germline development; it is present in P granules surrounding the germ cell nuclei throughout oogenesis, until oocytes mature and P granules disperse in the oocyte cytoplasm, and throughout spermatogenesis, except in mature sperm. In addition, PAN-1 is found in the pharynx and intestine, the somatic tissues associated with molting. | At the L1 stage, PAN-1 is seen in the pharynx and on the membranes of intestinal cells; PAN-1 also localizes to punctate granules that surround the nuclei of Z2 and Z3, the two germline precursor cells. This perinuclear localization to the germline precursor cells is characteristic of P granules and PAN-1 persists at this location as the wild type larvae mature. As wild type larvae mature, PAN-1 remains localized around the developing germ cell nuclei. Immuno-reactivity of older larvae to PAN-1 antibody revealed a strong, uniform cytoplasmic distribution in somatic tissue, as well as a distinct peri-nuclear pattern for PAN-1 around the germ cell nuclei, confirmed as localizing with P granules by confocal images that show the co-localization of PAN-1 with the P-granule proteins GLH-1 and PGL-1 as also seen for PGL-1 in the L3 larva. During embryogenesis, PAN-1 protein is uniformly distributed throughout the cytoplasm of the germline and somatic blastomeres, as seen for pan-1 mRNA, with no obvious concentration of PAN-1 in the P granules. PAN-1 was not seen in P granules at any stage of embryogenesis. In the adult worm PAN-1 is most obvious in the germline P granules shown here in a single gonad arm of an adult hermaphrodite. In confocal images, PAN-1 co-localizes with GLH-1 and PGL-1 throughout the germline, beginning with the distal mitotic region through to the proximal region, which contains maturing oocytes. After oocyte maturation, the nuclear membrane breaks down and PAN-1, as is the case for other P-granule proteins, disperses into the cytoplasm. The perinuclear localization of PAN-1 is most obvious in the meiotic, pachytene region of the germline, as also seen with PGL-1. In the adult male testis, PAN-1 is also present in P granules co-localizing with GLH-1 throughout spermatogenesis. However, PAN-1 is not present in mature sperm. Along with its germline location, PAN-1 is also concentrated in the somatic tissue of the pharynx in adult hermaphrodites, males, and larvae, a presence that is less obvious in the L1 stage and is very obvious in the adult, while PAN-1 reacts at decreased levels in the adult gut. PAN-1 protein was detected throughout the cytoplasm of both somatic and germline tissues in adult hermaphrodite worms, while the pre-immune sera were negative. | ||
| Expr9979 | pan-1 mRNA is present in all cells of the young embryo, and is highly enriched in the germline in L3 larvae. However, in the adult germline, pan-1 mRNA levels are much reduced and, in the adult soma, they remain at the low levels seen in the L3. | |||
| Expr15836 | PAN-1GFP signal was detected broadly in embryos and early larvae, but decreased substantially in late larvae and adults. Two types of PAN-1GFP subcellular patterns were observed: at the cell membrane and as cytoplasmic puncta. Some prominent PAN-1GFP signal was found in seam cells, a type of epidermal cells that shows stem-cell like division during larval development. These cells were lined up in a single profile at each lateral line and embedded in syncytial epidermis. Between the seam cells and the epidermis, a ring of tight junctions formed on the apical-lateral side of the cells. By colabelling a tight-junction component DLG-1::RFP and PAN-1GFP, we observed that PAN-1 distributed at the lateral basal membrane of seam cells. PAN-1 is also localized on the cell membrane of many ventral cord neurons, including DD neurons at L1 and L2. Therefore, we observed that PAN-1 is localized on the cell membrane. | |||
| Expr15837 | PAN-1GFP signal was detected broadly in embryos and early larvae, but decreased substantially in late larvae and adults. Two types of PAN-1GFP subcellular patterns were observed: at the cell membrane and as cytoplasmic puncta. Some prominent PAN-1GFP signal was found in seam cells, a type of epidermal cells that shows stem-cell like division during larval development. These cells were lined up in a single profile at each lateral line and embedded in syncytial epidermis. Between the seam cells and the epidermis, a ring of tight junctions formed on the apical-lateral side of the cells. By colabelling a tight-junction component DLG-1::RFP and PAN-1GFP, we observed that PAN-1 distributed at the lateral basal membrane of seam cells. PAN-1 is also localized on the cell membrane of many ventral cord neurons, including DD neurons at L1 and L2. Therefore, we observed that PAN-1 is localized on the cell membrane. | |||
| Expr1154777 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr15838 | PAN-1 distributed at the lateral basal membrane of seam cells. | |||
| Expr1010404 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr2032952 | 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). | |||
| Expr2014718 | 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). |
11 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| located_in | |
| located_in | |
| located_in | |
| part_of(WBbt:0005792) | located_in |
| located_in | |
| located_in | |
| involved_in | |
| located_in | |
| involved_in | |
| involved_in | |
| enables |
10 Homologues
| Type |
|---|
| least diverged orthologue |
| least diverged orthologue |
| least diverged orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| least diverged orthologue |
11 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| located_in | |
| located_in | |
| located_in | |
| part_of(WBbt:0005792) | located_in |
| located_in | |
| located_in | |
| involved_in | |
| located_in | |
| involved_in | |
| involved_in | |
| enables |
1 Regulates Expr Cluster
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Proteins interacting with GFP-PAN-1. | The fil-tering criteria were: 1% FDR at both the peptide level and the protein level; precursor mass toler-ance, 20 ppm; fragment mass tolerance, 20 ppm; the peptide length, 6100 aa. To identify high-confidence candidate interacting proteins, The WD-Scores of proteins identified in each IP-MS sam-ple were calculated against the identification results of 71 unrelated IP-MS samples, according tothe formulas from the CompPASS tutorial. | WBPaper00061377:PAN-1_interacting |