Genomics
20 Transcripts
Other
19 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:Y105E8B.1k | Y105E8B.1k |
771
 |
I: 14621514-14621596 |
| CDS:Y105E8B.1o | Y105E8B.1o |
855
|
I: 14621514-14621596 |
| CDS:Y105E8B.1p | Y105E8B.1p |
855
|
I: 14621514-14621596 |
| CDS:Y105E8B.1s | Y105E8B.1s |
855
|
I: 14621514-14621596 |
| CDS:Y105E8B.1c | Y105E8B.1c |
771
|
I: 14622429-14622511 |
| CDS:Y105E8B.1t | Y105E8B.1t |
771
|
I: 14622429-14622511 |
| CDS:Y105E8B.1j | Y105E8B.1j |
468
|
I: 14622429-14622511 |
| CDS:Y105E8B.1e | Y105E8B.1e |
771
|
I: 14622661-14622743 |
| CDS:Y105E8B.1a | Y105E8B.1a |
855
|
I: 14621514-14621596 |
| CDS:Y105E8B.1b | Y105E8B.1b |
582
|
I: 14622429-14622511 |
| CDS:Y105E8B.1d | Y105E8B.1d |
855
|
I: 14622429-14622511 |
| CDS:Y105E8B.1f | Y105E8B.1f |
456
|
I: 14623660-14623709 |
| CDS:Y105E8B.1g | Y105E8B.1g |
855
|
I: 14622429-14622511 |
| CDS:Y105E8B.1i | Y105E8B.1i |
582
|
I: 14622429-14622511 |
| CDS:Y105E8B.1l | Y105E8B.1l |
771
|
I: 14621514-14621596 |
| CDS:Y105E8B.1m | Y105E8B.1m |
582
|
I: 14621514-14621596 |
| CDS:Y105E8B.1n | Y105E8B.1n |
468
|
I: 14621514-14621596 |
| CDS:Y105E8B.1q | Y105E8B.1q |
855
|
I: 14621514-14621596 |
| CDS:Y105E8B.1r | Y105E8B.1r |
855
|
I: 14621514-14621596 |
31 RNAi Result
206 Allele
| Public Name |
|---|
| gk963849 |
| gk964175 |
| gk962681 |
| h13551 |
| h13552 |
| h9501 |
| gk963947 |
| gk963269 |
| rg1 |
| s2031 |
| WBVar00248312 |
| WBVar00248313 |
| st536 |
| st557 |
| st566 |
| gk963731 |
| tm10757 |
| gk129643 |
| gk129642 |
| gk129645 |
| gk129644 |
| gk129639 |
| gk129638 |
| gk129641 |
| gk129640 |
| gk129646 |
| gk129648 |
| gk129647 |
| gk129654 |
| gk129653 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00002978 | 14621169 | 14631094 | -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_chrI_14620638..14621168 | 531 | I: 14620638-14621168 | Caenorhabditis elegans |
307 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| oocyte proteins identified by two or more unique peptides during proteomics study. | In the pooled data set, 1453 C. elegans proteins were identified with a probability >= 0.9 according to ProteinProphet, of which 1165 proteins were identified by more than one unique peptide. | WBPaper00038289:oocyte_protein | |
| 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 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 |
| Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr reference). | A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes. | WBPaper00037950:bodywall-muscle_L1-larva_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 | |
| Coexpression clique No. 60, 176662_at-Y53F4B.16, 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. | WBPaper00061527:176662_at-Y53F4B.16 | |
| Proteins interacting with NHR-49-GFP according to co-IP and LC-MS. | N.A. | WBPaper00064071:NHR-49_interacting | |
| 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 decreased expression at 5-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites. | DESeq2, fold change > 2, FDR < 0.05 | WBPaper00065835:Day5_vs_Day1_downregulated | |
| 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 that showed significantly decreased expression at 11-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites. | DESeq2, fold change > 2, FDR < 0.05 | WBPaper00065835:Day11_vs_Day1_downregulated | |
| 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 | |
| Genes up regulated in alg-1(gk214) comparing to in N2. | Differential expression was assessed using an empirical Bayes statistics using the eBayes function. | WBPaper00040823:alg-1(gk214)_upregulated | |
| 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 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_regulated_aging | |
| 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 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) | |
| 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 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 infection: Bacillus thuringiensis | mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 12h), according to RNAseq. | Cuffdiff, ajusted p-value < 0.01. | WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h |
| 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 | |
| Bacteria infection: Bacillus thuringiensis | mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 12h), according to RNAseq. | Cuffdiff, ajusted p-value < 0.01. | WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h |
| 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 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 |
15 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Picture: Figure 5. | Expr4808 | Detailed immunolocalization studies revealed a preferential localization of UNC-87 to the center of the I-band region, whereas it was found to be absent from the distal edges of the thin filaments. Double staining of UNC-87 and actin showed a similar striated localization patterns for both proteins with no detectable signal at the dense bodies in the center of the striations. However, the band of UNC-87 was slightly narrower than that of actin, indicating that UNC-87 is absent from the distal portions of the thin filaments (near the pointed ends of the actin filaments). By contrast, CeTM has been shown previously to localize to the distal portion of the thin filaments, and, double staining of CeTM and UNC-87 indeed identified CeTM at the istal portion and UNC-87 at the central portion of the actin bands, albeit with some overlap. UNC-60B localized to the center of the actin bands between dense bodies, together with UNC-87. However, with the exception of this partial overlap, UNC-87 and UNC-60B mostly localized to different regions of the thin filaments. | ||
| Expr1031378 | Tiling arrays expression graphs | |||
| This Expr_pattern is about CeTMIV, an isoform of tmy-1 transcription. To confirm the CeTMIV isoform expression pattern, corresponding tmy-1::gfp vectors were assayed. Similar GFP expressions induced in pharynx and intestines respectively. These results show that the CeTMIV isoform was expressed in the pharyngeal muscles and intestinal cells and establish that the primary promoter region was located within 853 bp upstream of the initial ATG. pretzel stage (author) = fully-elongated embryo (wjc). | Expr1679 | The constructs pTMZIV4349 and pTMZIV1957 induced beta-galactosidase expressions in both the pharyngeal muscles and intestinal cells with similar intensities. Specifically, pharyngeal expressions were observed in all the eight muscle cells (m1-m8), one marginal cell (mc), one epithelial cell (e1) and the four cells of the pharyngo-intestinal valve (PIV). The 20 intestinal cells, some of which are binucleated and localized alongside the intestine, posterior of pharynx and anterior of anus were all stained with intense staining occurring at the most posterior end. Intestinal staining was limited only to intestinal cells, although there were slight variations in position of nuclei and staining intensity. Expression was also detected in embryos between gastrulation and the comma stage. At this stage of development, the exact nuclei are difficult to identify, but the positions and topology suggest pharynx and intestines. By the pretzel stage, identification of the different pharyngeal muscles showing expression becomes possible. A similar expression was also observed in the pharynx of males, although the intestinal staining was more restricted to the posterior region. No expression was induced by the further deletion construct pTMZIV1219. In all cases, the most uniform and intense expression patterns were observed between L1 and L2 worms, and were completed by L2. From L3 to adult, there was a reduction in expression intensity. Both pharyngeal and intestinal expressions were evident within six hours after staining. | ||
| Expr1864 | Expressed in muscle. | Both UNC-60B and CeTM became detectable in muscle cells at a very early stage of muscle development (~290 min), nearly at the same time. At the comma stage (290350 min), both UNC-60B and CeTM are diffusely localized in the cytoplasm and positions of nuclei are devoid of staining. After the 1.5-fold stage (~430 min), CeTM was gradually localized to a narrow region which represented myo-fibrils as determined by double staining with anti-actin antibody, whereas UNC-60B remained in the diffuse cytoplasm. This differential localization of UNC-60B and CeTM was maintained throughout the later embryonic development. In adult body wall muscle, CeTM and UNC-60B were also localized to different regions of thin filaments. Interestingly, the staining patterns of CeTM and actin were different. CeTM was localized in linear patterns, whereas actin was localized in ladder-like patterns in which the regions of dense bodies were devoid of staining. UNC-60B was stained as dotted lines between two lines of CeTM with little overlapping zones. Double staining of actin and UNC-60B showed that UNC-60B was localized to the central areas of the actin ladders between dense bodies. Double staining of vinculin, as a marker for dense bodies, and UNC-60B revealed that UNC-60B filled the gaps between dense bodies but was not colocalized with them. The shape of the UNC-60Bpositive dots was irregular, suggesting that association of UNC-60B with myofibrils is unstable and dynamic. | ||
| Reporter gene fusion type not specified. This Expr_pattern is about CeTMIII, an isoform of tmy-1 transcription. | Expr1680 | The constructs pTMZIII4135 and pTMZIII1743 permanently induced beta-galactosidase expression in pharyngeal muscles and intestinal cells of the worm from L4 stage. Pharyngeal expression was observed in m1, m3, m4, m5 and m7 muscle cells. Between the L2 and L3 stages, both constructs induced expression in tissues corresponding to germ-line tissue of the gonadal primordium: one anterior and one posterior. At this stage, intestinal expression was restricted to the most posterior part of the worm. The expression in the germ-line tissue was eliminated by L4 stage. The beta-galactosidase expression of CeTMIII isoform was stage specific. In about 95 % of L1 worms, expression was observed in the pharynx only; between L2 and L3 stages, the expression extended further to germ-line tissue and intestinal cells. Permanent expressions in pharynx and intestines were evident from L4 stage and continued to adulthood. The pharyngeal staining was much stronger than those of germ-line tissue and intestines. Unlike CeTMIV isoform, embryonic expression of CeTMIII isoform was absent and the expression intensity of intestinal cells did not decrease with stage. | ||
| This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope). | Expr723 | PTMIZ2328: this fusion gene was specifically expressed in the body wall muscles, the anal muscles, the vulva muscles and the male sex muscles except the pharyngeal muscles. pTMIIIZ3256: this fusion gene expressed only in the pharyngeal muscles. | ||
| This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope). | Expr724 | Staining of body wall muscles with anti CeTMI, pharyngeal muscle with anti CeTMIII. | ||
| Expr14598 | When these minigenes were ubiquitously expressed, only a small number of body wall muscle cells at the head predominantly expressed E7a-mCherry, whereas the other tissues expressed E7b-EGFP. To determine the E7a/E7b selections more clearly in the body wall muscle cells, these minigenes were expressed under the control of the myo-3 promoter, which is active in all body wall muscle cells (Okkema et al., 1993). These muscle-specific reporters showed that the two most anterior muscle cells in each muscle quadrant strongly expressed E7a-mCherry but only weakly expressed E7b-EGFP. The rest of the body wall muscle cells and vulval muscle cells predominantly expressed E7b-EGFP. These cells also weakly expressed E7a-mCherry. | |||
| Expr12871 | C. elegans tropomyosin (CeTM ) colocalized with actin filaments in the myoepithelial sheath of the ovary. CeTM was expressed in both myoepithelial sheath and spermatheca and localized to the actin filaments in a nonstriated pattern. | |||
| Expr1023698 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr2013084 | 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). | |||
| Expr1158775 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr14599 | In the wild type, the LEV-11 proteins colocalized with actin in sarcomeres in the body wall muscle cells of both the head and main-body regions. | |||
| Original chronogram file: chronogram.2253.xml | [Y105E8B.1:gfp] transcriptional fusion. | Chronogram1131 | ||
| Expr2031316 | 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). |
18 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| involved_in | |
| involved_in | |
| enables | |
| involved_in | |
| enables | |
| enables | |
| located_in | |
| located_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in |
23 Homologues
| Type |
|---|
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| least diverged orthologue |
| least diverged orthologue |
| orthologue |
| orthologue |
| least diverged orthologue |
| orthologue |
| least diverged orthologue |
| least diverged orthologue |