Genomics
15 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:F18A1.3b.1 | F18A1.3b.1 |
1127
 |
II: 7672005-7682360 |
| Transcript:F18A1.3c.1 | F18A1.3c.1 |
1252
|
II: 7672008-7682360 |
| Transcript:F18A1.3i.1 | F18A1.3i.1 |
1149
|
II: 7672008-7682360 |
| Transcript:F18A1.3l.1 | F18A1.3l.1 |
1115
|
II: 7672008-7682360 |
| Transcript:F18A1.3a.1 | F18A1.3a.1 |
1200
|
II: 7672010-7682359 |
| Transcript:F18A1.3d.1 | F18A1.3d.1 |
1155
|
II: 7672010-7682359 |
| Transcript:F18A1.3j.1 | F18A1.3j.1 |
1052
|
II: 7681045-7682358 |
| Transcript:F18A1.3m.1 | F18A1.3m.1 |
1021
|
II: 7681045-7682361 |
| Transcript:F18A1.3h.1 | F18A1.3h.1 |
1032
|
II: 7681045-7682363 |
| Transcript:F18A1.3f.1 | F18A1.3f.1 |
1101
|
II: 7681051-7682359 |
| Transcript:F18A1.3e.1 | F18A1.3e.1 |
750
|
II: 7681165-7682201 |
| Transcript:F18A1.3h.2 | F18A1.3h.2 |
771
|
II: 7681462-7682360 |
| Transcript:F18A1.3g.1 | F18A1.3g.1 |
426
|
II: 7681609-7682083 |
| Transcript:F18A1.3k.1 | F18A1.3k.1 |
429
|
II: 7681609-7682140 |
| Transcript:F18A1.3n.1 | F18A1.3n.1 |
456
|
II: 7681609-7682201 |
Other
14 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:F18A1.3a | F18A1.3a |
891
|
II: 7672043-7672108 |
| CDS:F18A1.3d | F18A1.3d |
903
|
II: 7672043-7672108 |
| CDS:F18A1.3l | F18A1.3l |
921
|
II: 7672043-7672108 |
| CDS:F18A1.3f | F18A1.3f |
711
|
II: 7681165-7681326 |
| CDS:F18A1.3g | F18A1.3g |
426
|
II: 7681609-7681895 |
| CDS:F18A1.3k | F18A1.3k |
429
|
II: 7681609-7681895 |
| CDS:F18A1.3b | F18A1.3b |
930
|
II: 7672043-7672108 |
| CDS:F18A1.3c | F18A1.3c |
756
|
II: 7672043-7672108 |
| CDS:F18A1.3e | F18A1.3e |
750
|
II: 7681165-7681326 |
| CDS:F18A1.3h | F18A1.3h |
465
|
II: 7681609-7681895 |
| CDS:F18A1.3i | F18A1.3i |
894
|
II: 7672043-7672108 |
| CDS:F18A1.3j | F18A1.3j |
714
|
II: 7681165-7681326 |
| CDS:F18A1.3m | F18A1.3m |
741
|
II: 7681165-7681326 |
| CDS:F18A1.3n | F18A1.3n |
456
|
II: 7681609-7681895 |
26 RNAi Result
153 Allele
| Public Name |
|---|
| gk963801 |
| gk963053 |
| gk962682 |
| WBVar01241663 |
| WBVar02079553 |
| gk147380 |
| WBVar01695614 |
| WBVar01695613 |
| WBVar01695612 |
| WBVar01695611 |
| WBVar02068153 |
| gk677280 |
| gk868393 |
| WBVar02069265 |
| WBVar01241665 |
| gk743954 |
| WBVar01604186 |
| WBVar01438533 |
| WBVar01438531 |
| gk696117 |
| WBVar01375723 |
| WBVar01375700 |
| h7558 |
| h15851 |
| h16890 |
| gk438810 |
| gk771850 |
| gk634188 |
| gk412020 |
| gk748780 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00003044 | 7672005 | 7682363 | 1 |
3 Data Sets
| Name | URL |
|---|---|
| WormBaseAcedbConverter | |
| GO Annotation data set | |
| C. elegans genomic annotations (GFF3 Gene) |
93 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| 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 |
| Bacteria: E.faecalis strain OG1RF | Transcripts that showed significantly increased expression after infection by E. faecalis OG1RF. | Ballgown was used to calculate differential expression of genes using FPKM data and to generate tables with fold change and P values. Genes were shortlisted with a cutoff of 2-fold change and P values of less than 0.05. | WBPaper00059754:E.faecalis_OG1RF_upregulated |
| 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 | |
| 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 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 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) | |
| 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 |
| 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 | |
| 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 | |
| Transcripts that showed significantly increased expression in animals exposed to 400uM tamoxifen from L1 to L4 larva stage. | DEseq2, fold change > 2 | WBPaper00064505:tamoxifen_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 | |
| Top 300 transcripts enriched in excretory duct, excretory pore according to single cell RNAseq. | Top 300 enriched transcripts were determined by log2.ratio of the tpm in the cell type vs the tpm in the other cells * the log2 of the cell.type tpm. | WBPaper00061340:Excretory_duct_and_pore | |
| Transcripts enriched in AMso according to single cell RNAseq. | Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched. | WBPaper00061651:AMso_enriched | |
| Transcripts enriched in PHso according to single cell RNAseq. | Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched. | WBPaper00061651:PHso_enriched | |
| 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 | |
| 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 | |
| Transcripts that showed significantly increased expression in isp-1(qm150) comparing to in N2. | Differential gene expression analysis was performed using the quasi-likeli-hood framework in edgeR package v. 3.20.1 in R v. 3.4.1. | WBPaper00053810:isp-1(qm150)_upregulated | |
| Transcripts detected in germline isolated from day-1 adult hermaphrodite animals. | All three experiments have CPM >= 1. | WBPaper00067147:germline_expressed | |
| 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 | |
| Genes found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014. | N.A. | WBPaper00026929:sir-2.1_overexpression_regulated | |
| TGF- Dauer pathway adult transcriptional targets. Results obtained by comparing the microarray results of the dauer-constitutive mutants daf-7(e1372), daf-7(m62), and daf-1(m40) with dauer-defective mutants daf-3(mgDf90), daf-5(e1386), and daf-7(e1372);daf-3(mgDf90) double mutants at the permissive temperature, 20C, on the first day of adulthood. | SAM | WBPaper00031040:TGF-beta_adult_downregulated | |
| Genes expressed in N2. | Expressed transcripts were identified on the basis of a Present call in 3 out of 4 N2 experiments as determined by Affymetrix MAS 5.0. | WBPaper00025141:N2_Expressed_Genes | |
| Transcripts with significantly increased expression in isp-1(qm150) vs. N2, and in isp-1(qm150) ced-4(n1162) vs. ced-4(n1162). | Comparisons of each genotype were compared to the wild-type using the Empirical Base (Wright & Simon) algorithm and fold changes were represented on a log2 scale. A threshold of p < 0.05 and a fold change of 1.3 (log2) was set to determine differentially expressed targets. | WBPaper00045263:isp-1(qm150)_upregulated | |
| Transcripts with significantly increased expression in nuo-6(qm200) vs. N2, and in nuo-6(qm200);ced-4(n1162) vs. ced-4(n1162). | Comparisons of each genotype were compared to the wild-type using the Empirical Base (Wright & Simon) algorithm and fold changes were represented on a log2 scale. A threshold of p < 0.05 and a fold change of 1.3 (log2) was set to determine differentially expressed targets. | WBPaper00045263:nuo-6(qm200)_upregulated |
7 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr1031428 | Tiling arrays expression graphs | |||
| Reporter gene fusion type not specified. | Expr1327 | Expression of the lir-1::lacZ construct pML169, which should reflect the expression of all lir-1 isoforms, and of the lir-1::lacZ construct pML165, which should reflect only the expression of lir-1 isoforms starting after the second exon, were first very weakly detected at the 200-cell stage and then clearly detected at the 350-cell stage in major hypodermal cells and at the early comma stage in those same hypodermal cells, as well as in support cells and in all minor hypodermal cells. Starting at the late comma stage, expression of the lir-1::lacZ construct pML169, but not that of pML165, was detected in all cells (i.e., in intestinal, pharyngeal, muscle, neuronal, hypodermal, and support cells). Similarly, during larval development, expression of the lir-1::lacZ pML169 was detected in virtually all cells, including cells of the somatic gonad, but not in intestinal cells after the late L1 stage nor in germ cells. | ||
| Expr1324 | lir-1 transcripts were detected by in situ hybridization in all cells between the 2- and 50-cell stages, disappearing after that stage. They reappeared between the 200- and 350-cell stages, but they were too weak to allow a clear identification of cells. At the comma stage, a signal was detected mostly in the anterior and ventral parts of the head and in the tail. | |||
| Expr1020151 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr2013224 | 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). | |||
| Expr1148878 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr2031455 | 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). |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrII_7671910..7672004 | 95 | II: 7671910-7672004 | Caenorhabditis elegans |
