Genomics
6 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:F29G9.4a.1 | F29G9.4a.1 |
1584
 |
V: 6003601-6016059 |
| Transcript:F29G9.4a.2 | F29G9.4a.2 |
2298
|
V: 6008068-6016087 |
| Transcript:F29G9.4b.1 | F29G9.4b.1 |
1404
|
V: 6008566-6015691 |
| Transcript:F29G9.4a.3 | F29G9.4a.3 |
3580
|
V: 6009063-6016087 |
| Transcript:F29G9.4a.4 | F29G9.4a.4 |
1722
|
V: 6010808-6016087 |
| Transcript:F29G9.4a.5 | F29G9.4a.5 |
1477
|
V: 6011211-6016087 |
Other
2 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:F29G9.4a | F29G9.4a |
996
|
V: 6011296-6011352 |
| CDS:F29G9.4b | F29G9.4b |
1404
|
V: 6008566-6008823 |
43 RNAi Result
184 Allele
| Public Name |
|---|
| gk963301 |
| WBVar02060208 |
| gk963591 |
| gk963553 |
| gk963042 |
| gk963041 |
| gk964259 |
| gk964351 |
| gk963850 |
| otn12393 |
| WBVar01862500 |
| WBVar01862502 |
| WBVar01862501 |
| WBVar01862504 |
| WBVar01862503 |
| WBVar01588351 |
| WBVar01588352 |
| WBVar01588353 |
| WBVar01588354 |
| tm1757 |
| gk395593 |
| WBVar01973703 |
| WBVar01973702 |
| WBVar01973701 |
| WBVar01973700 |
| WBVar01973697 |
| WBVar01973699 |
| WBVar01973698 |
| gk760749 |
| gk236386 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00001345 | 6003601 | 6016087 | 1 |
4 Data Sets
| Name | URL |
|---|---|
| WormBaseAcedbConverter | |
| GO Annotation data set | |
| C. elegans genomic annotations (GFF3 Gene) | |
| Panther orthologue and paralogue predictions |
173 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 that showed significantly increased expression in L1 neural cells comparing to in adult neural cells. | DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction. | WBPaper00060811:L1_vs_adult_upregulated_neural | |
| 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 |
| 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 |
| 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 |
| 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 higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc). | DESeq2, fold change >= 2, FDR <= 0.01. | WBPaper00056826:SGP_biased | |
| 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 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 that showed significantly increased expression in hsf-1(sy441) vs. in N2 day 1 adults without heat shock. | edgeR, fold change > 2, FDR < 0.05 | WBPaper00066900:hsf-1(sy441)_upregulated | |
| 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 | |
| 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 | |
| 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 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 |
13 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr1030820 | Tiling arrays expression graphs | |||
| Expr1200089 | Data from the TransgeneOme project | |||
| Clone: pUL#IAH8H3 | Expr7530 | Weak, infrequent, unconvincing expression seen in nerve cells in the head, nerve cord and tail from L1 to adult in 2 of 5 lines generated. Also see probably background expression in very anterior head body wall muscle cells. | ||
| Expr2011872 | 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). | |||
| Expr3686 | Transgenic animals containing the fos-1a::YFP-TX and -TL reporters showed the same expression pattern at all times examined, and fos-1a::YFP-TL protein localized to the nucleus. fos-1a::YFP-TL also rescued the AC-invasion defect when expressed in fos-1(ar105) mutants. fos-1a was expressed at the highest level in the AC and at lower levels in neighboring somatic gonad cells during AC invasion. No expression of fos-1a was detected in vulval cells. In contrast, both the fos-1b::CFP-TX and -TL reporters directed expression in vulval cells and the AC. fos-1b::CFP-TL also drove expression in neighboring uterine cells, whereas fos-1b::CFP-TX did not, suggesting the presence of a downstream uterine enhancer element in fos-1b::CFP-TL. Unlike fos-1a expression, levels of fos-1b::CFP-TL protein were not greater in the AC compared to neighboring cells. Moreover, whereas the fos-1a reporters drove expression almost exclusively in the somatic gonad cells, the fos-1b reporters directed expression in nearly all cells at the L3 stage. | fos-1a::YFP-TL protein localized to the nucleus | ||
| Expr1020029 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr1200246 | Data from the TransgeneOme project | |||
| Expr2030110 | 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). | |||
| Expr11182 | fos-1b::cfp is expressed in a subset of vulval progeny. During the mid-L4 stage, CFP fluorescence is brighter in presumptive vulD cells compared with vulE and vulF cells. This pattern is dynamic, such that by late-L4 stage, the presumptive vulE and vulF cells were much brighter compared with the presumptive vulD cells. | |||
| Expr11183 | fos-1a::yfp was undetectable in vulval cells during the L3 and L4 stages. | |||
| Expr11184 | The authors observed that a fos-1a translational fusion is expressed throughout the VU intermediate prescursor cells, including pi cells. | |||
| Expr1149842 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr11185 | plastFOS-1c::YFP showed expression primarily in the early dorsal and ventral uterus during L3 and L4 stages. Importantly, expression was observed in all VU intermediate precursors including pi cells. Furthermore, the authors confirmed that plastFOS-1c::YFP co-localized with cells expressing an egl-13 pi marker from the late L3 induction stage through generation of pi descendants. |
34 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| involved_in | |
| has_input(WB:WBGene00006987)|has_input(WB:WBGene00000395)|has_input(WB:WBGene00001863) | involved_in |
| involved_in | |
| happens_during(WBls:0000041),happens_during(GO:0042594) | involved_in |
| involved_in | |
| involved_in | |
| has_input(WB:WBGene00018725) | involved_in |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| happens_during(WBls:0000041) | involved_in |
| involved_in | |
| involved_in | |
| involved_in | |
| located_in | |
| part_of | |
| located_in | |
| located_in | |
| involved_in | |
| located_in | |
| enables | |
| enables | |
| has_input(WB:WBGene00018725) | enables |
| enables | |
| enables | |
| enables | |
| enables | |
| enables |
39 Homologues
| Type |
|---|
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
34 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| involved_in | |
| has_input(WB:WBGene00006987)|has_input(WB:WBGene00000395)|has_input(WB:WBGene00001863) | involved_in |
| involved_in | |
| happens_during(WBls:0000041),happens_during(GO:0042594) | involved_in |
| involved_in | |
| involved_in | |
| has_input(WB:WBGene00018725) | involved_in |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| happens_during(WBls:0000041) | involved_in |
| involved_in | |
| involved_in | |
| involved_in | |
| located_in | |
| part_of | |
| located_in | |
| located_in | |
| involved_in | |
| located_in | |
| enables | |
| enables | |
| has_input(WB:WBGene00018725) | enables |
| enables | |
| enables | |
| enables | |
| enables | |
| enables |
