Genomics
23 Transcripts
Other
17 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:F26H11.2a | F26H11.2a |
6594
 |
II: 14390720-14391012 |
| CDS:F26H11.2b | F26H11.2b |
4866
|
II: 14390720-14391012 |
| CDS:F26H11.2i | F26H11.2i |
4860
|
II: 14390720-14391012 |
| CDS:F26H11.2s | F26H11.2s |
6600
|
II: 14390720-14391012 |
| CDS:F26H11.2n | F26H11.2n |
6591
|
II: 14390720-14391012 |
| CDS:F26H11.2m | F26H11.2m |
6222
|
II: 14391754-14392340 |
| CDS:F26H11.2r | F26H11.2r |
702
|
II: 14400082-14400531 |
| CDS:F26H11.2p | F26H11.2p |
1359
|
II: 14403527-14403698 |
| CDS:F26H11.2e | F26H11.2e |
1218
|
II: 14404654-14404684 |
| CDS:F26H11.2f | F26H11.2f |
1533
|
II: 14405545-14405890 |
| CDS:F26H11.2c | F26H11.2c |
6585
|
II: 14390720-14391012 |
| CDS:F26H11.2d | F26H11.2d |
2427
|
II: 14400082-14400531 |
| CDS:F26H11.2j | F26H11.2j |
435
|
II: 14407276-14407351 |
| CDS:F26H11.2k | F26H11.2k |
4866
|
II: 14390720-14391012 |
| CDS:F26H11.2l | F26H11.2l |
6228
|
II: 14391754-14392340 |
| CDS:F26H11.2o | F26H11.2o |
1707
|
II: 14401682-14401783 |
| CDS:F26H11.2q | F26H11.2q |
708
|
II: 14400082-14400531 |
37 RNAi Result
487 Allele
| Public Name |
|---|
| gk963801 |
| gk963053 |
| WBVar01320047 |
| WBVar01320051 |
| WBVar01320052 |
| WBVar01320055 |
| WBVar01320056 |
| WBVar01320057 |
| WBVar01320058 |
| WBVar01320067 |
| WBVar01320068 |
| WBVar01320069 |
| WBVar01320073 |
| WBVar01320076 |
| WBVar01320078 |
| WBVar01320080 |
| WBVar01320091 |
| WBVar01320092 |
| WBVar01320096 |
| gk962684 |
| gk487481 |
| WBVar02040996 |
| gk847682 |
| WBVar00556821 |
| cxTi8305 |
| WBVar02068480 |
| WBVar02068484 |
| WBVar02068483 |
| WBVar02068482 |
| WBVar02068481 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00009180 | 14390713 | 14407911 | 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_14407912..14408611 | 700 | II: 14407912-14408611 | Caenorhabditis elegans |
211 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Coexpression clique No. 256, pek-1_22220-pek-1_33, on the genome-wide coexpression clique map for the nematode GPL200 platform. | All available microarray datasets for the GPL200 platform (Affymetrix C. elegans Genome Array) were obtained from the GEO repository. This included 2243 individual microarray experiments. These were normalized against each other with the software RMAexpress (Bolstad, 2014). Based on these normalized values, Pearsons correlation coefficients were obtained for each probe-probe pair of the 22,620 probes represented on this array type. The resulting list of correlation coefficients was then ranked to generate the ranked coexpression database with information on each probe represented on the GPL200 platform. | WBPaper00061527:pek-1_22220-pek-1_33 | |
| 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 | |
| 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 |
| mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis. | Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05. | WBPaper00045420:fertilization_downregulated_transcript | |
| Genes that were downregulated 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)_downregulated | |
| Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin and 250uM Allantoin from day 1 to day 3 adult hermaphradite. | DESeq2(v1.14.1), fold change > 2, p-value < 0.05 | WBPaper00055354:Rifampicin-Allantoin_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 that showed significantly increased expression after animals were treated with 100uM Psora and 250uM Allantoin from day 1 to day 3 adult hermaphradite. | DESeq2(v1.14.1), fold change > 2, p-value < 0.05 | WBPaper00055354:Psora-Allantoin_upregulated | |
| Transcripts that showed significantly increased expression after animals were treated with 100uM Rapamycin and 50mM Metformin from day 1 to day 3 adult hermaphradite. | DESeq2(v1.14.1), fold change > 2, p-value < 0.05 | WBPaper00055354:Rapamycin-Metformin_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 | |
| Genes significantly enriched in NSM neurons (isolated by FACS) versus the reference, according to RNAseq analysis towards total RNA. | Gene expression quantification and differential expression was analyzed using cufflinks v2.2.1. Enriched contains only genes significantly enriched (differentially expressed >= 2.4 fold in total RNA or >= 3.2 fold in DSN treated total RNA) in the NSM neurons versus the reference. | WBPaper00045974:NSM_enriched_totalRNA_RNAseq | |
| 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 | |
| Heat shock: 35C for 1 hour. | Transcripts that showed significantly increased expression immediately after 1-day post L4 adult hermaphrodite endu-2(tm4977) animals were exposed to 35C for 1 hour. | The DESeq2 (GalaxyVersion 2.11.40.6 + galaxy1) was used to determine differentiallyexpressed features from count tables of differential transcript abundances. log2FC > 1, FDR < 0.01. | WBPaper00065749:Heat-Shock_upregulated_endu-2(tm4977) |
| 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 | |
| Heat shock: 35C for 1 hour. | Transcripts that showed significantly increased expression immediately after 1-day post L4 adult hermaphrodite N2 animals were exposed to 35C for 1 hour. | The DESeq2 (GalaxyVersion 2.11.40.6 + galaxy1) was used to determine differentiallyexpressed features from count tables of differential transcript abundances. log2FC > 1, FDR < 0.01. | WBPaper00065749:Heat-Shock_upregulated_N2 |
| 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 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 expressed in vulva. | FPKM >= 1. | WBPaper00064122:vulva_transcriptome | |
| 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 |
| 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 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 | |
| Bacteria infection: Staphylococcus aureus MW2. 4 hours of exposure. | Transcripts that showed significantly increased expression after N2 animals had 4 hours of infection by Staphylococcus aureus (MW2). | DEseq 1.18.0, adjusted p-value < 0.05. | WBPaper00056471:S.aureus-4h_upregulated_N2 |
| 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 |
12 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr9824 | Very broad GFP expression was seen from early embryogenesis to the mature adult. Many cells expressed GFP in the head, including nerve cells, cells in the pharynx and the hypodermis. Many neurons in the tail also showed GFP expression. Body wall expression of GFP was observed throughout the length of the body, in the hypodermis and possibly muscle cells. GFP could also be seen in the intestine and reproductive system. The level of GFP and the number of cells with detectable levels of GFP was reduced in the adult. | |||
| Expr9826 | Very broad GFP expression was seen from early embryogenesis to the mature adult. Many cells expressed GFP in the head, including nerve cells, cells in the pharynx and the hypodermis. Many neurons in the tail also showed GFP expression. Body wall expression of GFP was observed throughout the length of the body, in the hypodermis and possibly muscle cells. GFP could also be seen in the intestine and reproductive system. The level of GFP and the number of cells with detectable levels of GFP was reduced in the adult. | |||
| Expr9827 | Very broad GFP expression was seen from early embryogenesis to the mature adult. Many cells expressed GFP in the head, including nerve cells, cells in the pharynx and the hypodermis. Many neurons in the tail also showed GFP expression. Body wall expression of GFP was observed throughout the length of the body, in the hypodermis and possibly muscle cells. GFP could also be seen in the intestine and reproductive system. The level of GFP and the number of cells with detectable levels of GFP was reduced in the adult. | |||
| Expr1034005 | Tiling arrays expression graphs | |||
| Clone: pUL#JRH/AG10 | Expr7522 | Expression is seen in 3 cells in the terminal bulb of the pharynx and in the junction between the pharynx and intestine, late embryo onwards, weakening through the larval stages. There is also expression in the developing gonad, possibly the spermathecae. However, all the expression is quite weak. | ||
| Expr9842 | Non-nuclear-localized GFP was observed from early embryogenesis GFP was seen in the body wall in the head and tail. Particularly high levels of GFP were seen in the rectal cells, in some unidentified cells in the head and in the adult vulva. Two other independently generated strains, transgenic for the same reporter gene fusion construction, gave similar GFP expression patterns but the transmission of the transgenic array was very low and these strains were not retained. | |||
| Expr9828 | No GFP expression was seen in two independent transgenic strains. | |||
| Expr2014533 | 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). | |||
| Expr2041710 | Translational efficiency and RNA abundance/Ribosome occupancy across early embryonic stages (1-cell to 8-cell). For each developmental stage, translational efficiency was calculated as the ratio between ribosome footprint reads and mRNA abundance after normalization. A detailed description of the experimental methods and analysis can be found in: Shukla Y, Ghatpande V, Hu CF, Dickinson DJ, Cenik C. Landscape and regulation of mRNA translation in the early C. elegans embryo. Cell Rep. 2025 June 24;44(6):115778. doi: 10.1016/j.celrep.2025.115778. PMID: 40450690 | |||
| Expr2032772 | 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). | |||
| Expr1017951 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr1149612 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 |
11 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| involved_in | |
| enables | |
| enables | |
| enables | |
| part_of | |
| part_of | |
| located_in | |
| located_in | |
| has_input(WB:WBGene00002015),happens_during(GO:0001666) | involved_in |
| involved_in | |
| involved_in |
4 Homologues
| Type |
|---|
| least diverged orthologue |
| least diverged orthologue |
| least diverged orthologue |
| least diverged orthologue |
11 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| involved_in | |
| enables | |
| enables | |
| enables | |
| part_of | |
| part_of | |
| located_in | |
| located_in | |
| has_input(WB:WBGene00002015),happens_during(GO:0001666) | involved_in |
| involved_in | |
| involved_in |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrII_14390079..14390712 | 634 | II: 14390079-14390712 | Caenorhabditis elegans |
