Genomics
5 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:F41D9.3a.1 | F41D9.3a.1 |
1836
 |
X: 8387442-8392584 |
| Transcript:F41D9.3f.1 | F41D9.3f.1 |
1869
|
X: 8387444-8392589 |
| Transcript:F41D9.3e.1 | F41D9.3e.1 |
1878
|
X: 8387446-8392582 |
| Transcript:F41D9.3b.1 | F41D9.3b.1 |
1856
|
X: 8387448-8392586 |
| Transcript:F41D9.3c.1 | F41D9.3c.1 |
1535
|
X: 8387467-8392581 |
Other
5 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:F41D9.3a | F41D9.3a |
1311
|
X: 8387964-8388043 |
| CDS:F41D9.3c | F41D9.3c |
1038
|
X: 8387964-8388043 |
| CDS:F41D9.3e | F41D9.3e |
1359
|
X: 8387964-8388043 |
| CDS:F41D9.3f | F41D9.3f |
1341
|
X: 8387964-8388043 |
| CDS:F41D9.3b | F41D9.3b |
1335
|
X: 8387964-8388043 |
104 Allele
| Public Name |
|---|
| gk964260 |
| gk962707 |
| gk964193 |
| gk964194 |
| gk963896 |
| gk963732 |
| WBVar01927646 |
| WBVar01927647 |
| WBVar01927648 |
| gk964126 |
| gk964401 |
| gk964402 |
| gk781935 |
| gk368297 |
| gk695066 |
| gk287334 |
| WBVar01885240 |
| gk907228 |
| gk858926 |
| WBVar02065132 |
| WBVar01885244 |
| WBVar01820469 |
| tm1099 |
| gk468526 |
| WBVar01816208 |
| WBVar00244705 |
| WBVar00244704 |
| WBVar01820468 |
| gk951573 |
| h17035 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00006942 | 8387442 | 8392589 | -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_chrX_8386687..8387441 | 755 | X: 8386687-8387441 | Caenorhabditis elegans |
199 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 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 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 | |
| Proteins interacting with NHR-49-GFP according to co-IP and LC-MS. | N.A. | WBPaper00064071:NHR-49_interacting | |
| 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 | |
| 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 expressed in vulva. | FPKM >= 1. | WBPaper00064122:vulva_transcriptome | |
| 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 sin-3(tm1276) comparing to in N2. | DESeq2, fold change > 2, p-value < 0.01. | WBPaper00061203:sin-3(tm1276)_upregulated | |
| Dietary restriction | Transcripts that showed significantly decreased expression after N2 animals were under dietary restriction (DR, OP50 OD = 0.1) from 3-day post L4 till 6-day post L4 adult hermaphrodite stage, comparing to under ad libtum (AL, OP50 OD = 3) condition. | Bioconductor package edgeR, p < 0.05. | WBPaper00056443:DietaryRestriction_downregulated |
| Transcripts that showed significantly increased expression in hrde-1(tm1200) animals, comparing to in N2, after growing at 25C for five generations (late generation). | CuffDiff2 | WBPaper00051265:F4_hrde-1(tm1200)_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 N2 day 4 adults comparing to in N2 day 1 adult animals according to Illumina RNASeq. | DESeq fold change > 2, FDR < 0.05. | WBPaper00067499:Day4_vs_Day1_downregulated_Illumina | |
| Transcripts that showed significantly decreased expression in N2 day 5 adults comparing to in N2 day 1 adult animals according to Illumina RNASeq. | DESeq fold change > 2, FDR < 0.05. | WBPaper00067499:Day5_vs_Day1_downregulated_Illumina | |
| Transcripts that showed significantly decreased expression in N2 day 5 adults comparing to in N2 day 1 adult animals according to Oxford Nanopore Technologies Direct RNA sequencing (Nanopore DRS). | DESeq fold change > 2, FDR < 0.05. | WBPaper00067499:Day5_vs_Day1_downregulated_Nanopore | |
| Transcripts that showed significantly decreased expression in N2 day 7 adults comparing to in N2 day 1 adult animals according to Illumina RNASeq. | DESeq fold change > 2, FDR < 0.05. | WBPaper00067499:Day7_vs_Day1_downregulated_Illumina | |
| Transcripts that showed significantly decreased expression in N2 day 7 adults comparing to in N2 day 1 adult animals according to Oxford Nanopore Technologies Direct RNA sequencing (Nanopore DRS). | DESeq fold change > 2, FDR < 0.05. | WBPaper00067499:Day7_vs_Day1_downregulated_Nanopore | |
| Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage. | DESeq | WBPaper00053302:stavudine_24h_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 | |
| Transcripts depleted in purified oocyte P bodies comparing to in whole oocytes. | DESeq2, FDR < 0.05, fold change > 2. | WBPaper00065975:P-body_vs_oocyte_depleted | |
| Transcripts depleted in purified oocyte P bodies comparing to in the whole animal. | DESeq2, FDR < 0.05, fold change > 2. | WBPaper00065975:P-body_vs_WholeAnimal_depleted | |
| Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy. | Cufflinks | WBPaper00065120:body-muscle-transcriptome |
10 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| [wrk-1::TM-gfp] translational fusion. wrk-1 expression was determined by means of a reporter construct (wrk1::TM::gfp), in which 4 kb of sequences upstream of the ATG start codon, all exons, and the first three introns of the wrk-1 locus were fused in frame to gfp. This construct is able to rescue the phenotype of wrk-1 mutant animals. See Transgene otEx2389. [wrk-1::gfp] transcriptional fusion in which 4 kb of sequences upstream of the ATG start codon was fused to GFP. See Transgene otEx203 [wrk-1::gfp] translational fusion. See Transgene otEx2522. | Expr4281 | The wrk-1 gene is expressed in ventral midline cells, namely in the eMNs. Additional expression is observed in a subset of head neurons, including interneurons (AIY class), sensory neurons (ASI class), and head motoneurons (SMDV/D class), and glial-type sheath and socket cells. Outside the nervous system, the most prominent sites of wrk-1 expression include the intestine, excretory gland cell, distal tip cell, and coelomocytes. | ||
| Picture: Figure 3A, 3B, 3C. | Expr7829 | In WT animals, wrk-1 was expressed in several neurons in the C. elegans nerve ring . In the same animals, AIY was specifically labeled using a ttx-3::DsRed2 reporter. The two reporters co-localized, confirming that wrk-1 is expressed in AIY. wrk-1 was expressed in AIY in 100% of WT animals. | ||
| Picture: Fig 3. | Expr8842 | Neuronal Expression: ASI, ASJ, ASK, AWB, PLM?, AVA, AVE, AIB, AIN?, AIY, AUA, RIC, RIG, DVA?, RMD, RME, SMD, URA?, PDA, DA, DB, DD. Non-neuronal Expression: gut, distal tip cell(embryo, early larval stages), coelomocytes, arcade cells. | ||
| Reference: personal communication from Oliver Hobert 2002-12-07. | Expr1761 | Neuronal expression in: less than 10 head neuron classes (includ. ASI, SMDV, SMDD, AIY; sheath&socket cells; 1 class of VNC-MN. Non-neuronal expression in: intestine, coloemocytes. | ||
| Expr1150847 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr2036210 | 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). | |||
| Expr1032956 | Tiling arrays expression graphs | |||
| Expr1012620 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr2018072 | 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). | |||
| Expr13214 | EGFP::WRK-1 that was expressed in BWM cells by the myo-3 promoter (myo-3p::EGFP::WRK-1) was localized to the plasma membrane in wild type . |
7 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| located_in | |
| located_in | |
| located_in |
12 Homologues
| Type |
|---|
| orthologue |
| orthologue |
| orthologue |
| least diverged orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
7 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| located_in | |
| located_in | |
| located_in |
20 Strains
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrX_8392590..8392757 | 168 | X: 8392590-8392757 | Caenorhabditis elegans |
