Genomics
8 Transcripts
| Class | WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|---|
| MRNA | Transcript:F08B1.1e.1 | F08B1.1e.1 |
1986
 |
II: 5323276-5340247 |
| MRNA | Transcript:F08B1.1a.2 | F08B1.1a.2 |
2169
|
II: 5331486-5340663 |
| MRNA | Transcript:F08B1.1a.1 | F08B1.1a.1 |
2559
|
II: 5331486-5340829 |
| MRNA | Transcript:F08B1.1d.1 | F08B1.1d.1 |
1761
|
II: 5334558-5340247 |
| MRNA | Transcript:F08B1.1b.1 | F08B1.1b.1 |
2611
|
II: 5336097-5340827 |
| MRNA | Transcript:F08B1.1f.1 | F08B1.1f.1 |
1509
|
II: 5338228-5340247 |
| NcPrimaryTranscript | Transcript:F08B1.1c | F08B1.1c |
1577
|
II: 5338228-5340247 |
| MRNA | Transcript:F08B1.1g.1 | F08B1.1g.1 |
1347
|
II: 5338773-5340247 |
Other
6 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:F08B1.1e | F08B1.1e |
1986
|
II: 5323276-5323284 |
| CDS:F08B1.1d | F08B1.1d |
1761
|
II: 5334558-5334649 |
| CDS:F08B1.1f | F08B1.1f |
1509
|
II: 5338228-5338356 |
| CDS:F08B1.1g | F08B1.1g |
1347
|
II: 5338773-5339014 |
| CDS:F08B1.1a | F08B1.1a |
1974
|
II: 5331489-5331671 |
| CDS:F08B1.1b | F08B1.1b |
1821
|
II: 5336307-5336562 |
97 RNAi Result
213 Allele
| Public Name |
|---|
| gk963801 |
| gk963053 |
| gk963388 |
| h8905 |
| sa366 |
| WBVar01695510 |
| WBVar01603844 |
| WBVar01437754 |
| WBVar01437755 |
| WBVar01437758 |
| WBVar01437759 |
| WBVar01437756 |
| WBVar01783368 |
| gk377357 |
| gk743386 |
| gk801289 |
| gk339621 |
| gk795816 |
| gk313183 |
| gk472560 |
| gk621785 |
| WBVar01249195 |
| gk565639 |
| gk142685 |
| WBVar01719714 |
| gk142672 |
| gk142671 |
| gk142674 |
| gk142673 |
| gk142668 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00006923 | 5323276 | 5340829 | 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_chrII_5340830..5342665 | 1836 | II: 5340830-5342665 | Caenorhabditis elegans |
280 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons. | DESeq. False discovry rate (FDR) < 0.1. | WBPaper00048988:neuron_expressed | |
| Transcripts that showed significantly increased expression glp-1(e2141); TU3401 animals comparing to in TU3401 animals. | Fold change > 2, FDR < 0.01. | WBPaper00065993:glp-1(e2141)_upregulated | |
| 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 |
| Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology. | DESEQ2, fold change > 2 and FDR < 0.01. | WBPaper00062103:neuron_enriched | |
| Genes that were upregulated 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)_upregulated | |
| Bacteria infection: Enterococcus faecalis | Genes with increased expression after 24 hours of infection by E.faecalis Fold changes shown are pathogen vs OP50. | For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated. | WBPaper00038438:E.faecalis_24hr_upregulated_TilingArray |
| 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 that showed significantly increased expression in pri-1(RNAi) animals comparing to in N2 animals fed with empty vector. | Differential expression analysis was performed quasi-likelihood F-test with the generalized linear model (GLM) approach in edgeR ver 3.32.1. FDR < 0.05, fold change > 2. | WBPaper00066418:pri-1(RNAi)_upregulated | |
| Transcripts that showed significantly increased expression in eft-2(RNAi) animals at N2 background. | DESeq2, fold change > 2 and p-value < 0.01. | WBPaper00067953:eft-2(RNAi)_upregulated_N2 | |
| Transcripts that showed significantly increased expression in eft-2(RNAi) animals at zip-2(tm4248) background. | DESeq2, fold change > 2 and p-value < 0.01. | WBPaper00067953:eft-2(RNAi)_upregulated_zip-2(tm4248) | |
| Transcripts that showed significantly increased expression in eif-2alpha(RNAi) animals at N2 background. | DESeq2, fold change > 2 and p-value < 0.01. | WBPaper00067953:eif-2alpha(RNAi)_upregulated_N2 | |
| Transcripts that showed significantly increased expression in eif-2alpha(RNAi) animals at zip-2(tm4248) background. | DESeq2, fold change > 2 and p-value < 0.01. | WBPaper00067953:eif-2alpha(RNAi)_upregulated_zip-2(tm4248) | |
| 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 | |
| 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 sin-3(tm1276) comparing to in N2. | DESeq2, fold change > 2, p-value < 0.01. | WBPaper00061203:sin-3(tm1276)_upregulated | |
| Transcripts detected in germline isolated from day-1 adult hermaphrodite animals. | All three experiments have CPM >= 1. | WBPaper00067147:germline_expressed | |
| Transcripts that showed significantly increased expression in mrg-1(qa6200) comparing to in control animals in primordial germ cells (PGCs) at L1 larva stage. | DESeq2(v1.32.0), FDR < 0.05. | WBPaper00064315:mrg-1(qa6200)_upregulated_PGCs | |
| Transcripts that showed significantly increased expression in exos-8(RNAi) animals. | fold change > 2, FDR < 0.05 | WBPaper00068292:exos-8(RNAi)_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 | |
| Transcripts that showed significantly increased expression in nhr-114(gk849) comparing to wild type animals at L4 larva. | DESeq2 1.26.0, fold change > 2, FDR < 0.05. | WBPaper00064539:nhr-114(gk849)_upregulated | |
| Transcripts that showed significantly decreased expression in N2 animals exposed to 0.1mM Paraquat from hatching to reaching adult stage. | DESeq2 version 1.22.2, p < 0.05 | WBPaper00064716:paraquat_downregulated | |
| 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 | |
| Transcripts that showed significantly increased expression in daf-2(e1370) 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:daf-2(e1370)_upregulated | |
| Transcripts that showed significantly increased expression in nuo-6(qm200) 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:nuo-6(qm200)_upregulated |
6 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2941 | Transgenic C. elegans bearing the vhp-1gfp fusion showed that VHP-1GFP is expressed throughout development in the pharynx, intestine, neurons, and vulval hypodermal cells. | |||
| Expr2036133 | 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). | |||
| Expr1032940 | Tiling arrays expression graphs | |||
| Expr2017997 | 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). | |||
| Expr1027552 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr1147932 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 |
40 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| enables | |
| enables | |
| enables | |
| enables | |
| has_input(WB:WBGene00004393),happens_during(GO:0006979) | acts_upstream_of_negative_effect |
| happens_during(WBls:0000109),has_input(WB:WBGene00004055)|happens_during(WBls:0000041),has_input(WB:WBGene00004055) | involved_in |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| has_input(WB:WBGene00002187) | enables |
| enables | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| happens_during(WBls:0000041) | involved_in |
| happens_during(WBls:0000041) | involved_in |
| involved_in | |
| involved_in | |
| happens_during(WBls:0000109),has_input(WB:WBGene00000912),occurs_in(WBbt:0003672) | involved_in |
| happens_during(WBls:0000041),has_input(WB:WBGene00000912),occurs_in(WBbt:0003672) | involved_in |
| happens_during(WBls:0000109),occurs_in(WBbt:0005190) | involved_in |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in |
11 Homologues
| Type |
|---|
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| least diverged orthologue |
| least diverged orthologue |
| least diverged orthologue |
| orthologue |
| least diverged orthologue |
| orthologue |
| orthologue |
40 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| enables | |
| enables | |
| enables | |
| enables | |
| has_input(WB:WBGene00004393),happens_during(GO:0006979) | acts_upstream_of_negative_effect |
| happens_during(WBls:0000109),has_input(WB:WBGene00004055)|happens_during(WBls:0000041),has_input(WB:WBGene00004055) | involved_in |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| has_input(WB:WBGene00002187) | enables |
| enables | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| happens_during(WBls:0000041) | involved_in |
| happens_during(WBls:0000041) | involved_in |
| involved_in | |
| involved_in | |
| happens_during(WBls:0000109),has_input(WB:WBGene00000912),occurs_in(WBbt:0003672) | involved_in |
| happens_during(WBls:0000041),has_input(WB:WBGene00000912),occurs_in(WBbt:0003672) | involved_in |
| happens_during(WBls:0000109),occurs_in(WBbt:0005190) | involved_in |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrII_5319618..5323275 | 3658 | II: 5319618-5323275 | Caenorhabditis elegans |
