Genomics
4 Transcripts
| Class | WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|---|
| MRNA | Transcript:H30A04.1a.2 | H30A04.1a.2 |
3313
 |
X: 15510011-15524029 |
| MRNA | Transcript:H30A04.1b.1 | H30A04.1b.1 |
3272
|
X: 15516653-15524030 |
| MRNA | Transcript:H30A04.1a.1 | H30A04.1a.1 |
3261
|
X: 15516655-15524027 |
| NcPrimaryTranscript | Transcript:H30A04.1c | H30A04.1c |
2439
|
X: 15516757-15523295 |
Other
2 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:H30A04.1a | H30A04.1a |
2427
|
X: 15516757-15516790 |
| CDS:H30A04.1b | H30A04.1b |
2433
|
X: 15516757-15516790 |
302 Allele
| Public Name |
|---|
| gk964260 |
| gk962707 |
| gk963810 |
| gk963581 |
| gk963194 |
| WBVar01929016 |
| WBVar01929018 |
| WBVar01929017 |
| WBVar01942403 |
| WBVar02083521 |
| WBVar01955413 |
| gk481296 |
| gk692758 |
| WBVar02001195 |
| gk388009 |
| gk320575 |
| gk716673 |
| gk303580 |
| gk532012 |
| gk342668 |
| gk720136 |
| gk432131 |
| gk930211 |
| gk381663 |
| WBVar01942404 |
| gk677543 |
| gk523124 |
| gk723154 |
| WBVar01760756 |
| nc4 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00001148 | 15510011 | 15524030 | 1 |
3 Data Sets
| Name | URL |
|---|---|
| WormBaseAcedbConverter | |
| GO Annotation data set | |
| C. elegans genomic annotations (GFF3 Gene) |
1 Downstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrX_15524031..15526827 | 2797 | X: 15524031-15526827 | Caenorhabditis elegans |
138 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| 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 |
| 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 | |
| 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 |
| 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 | |
| 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 | |
| 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 |
| 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 6h), according to RNAseq. | Cuffdiff, ajusted p-value < 0.01. | WBPaper00046497:B.thuringiensis_0.5mix_downregulated_6h |
| 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 |
| 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 increased expression after exposure to 75uM paraquat(PQ) from L1 to day 2 adult stage in skn-1(lax188) animals | fold change > 2 | WBPaper00058711:paraquat_upregulated | |
| Gamma irradiation 100 mGY per hour for 72 hours since L1 larva. | Transcripts that showed significantly increased expression after exposure to 100mGy per hour gamma irradiation from L1 to day 1 adult hermaphrodite stage. | DESeq2, FDR <= 0.05, log2 fold change >= 0.3 or <= -0.3. | WBPaper00058958:100mGy-irradiation-72h_upregulated |
| Genes that showed oscillating mRNA expression level throughout the 16 hour time courses from L3 larva to young adult. | The following three lines of R code were used to perform the classification: increasing <-2*amplitude-PC1 < -1.7; oscillating <-!increasing & (amplitude > 0.55); flat <-!increasing & !oscillating; Note that the amplitude of a sinusoidal wave corresponds to only half the fold change between trough and peak. | WBPaper00044736:oscillating_dev_expression | |
| Transcripts that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage. | DESeq2, fold change > 2, FDR < 0.05. | WBPaper00066594:ilc-17.1(syb5296)_upregulated | |
| Transcripts that showed significantly decreased expression in set-2(tm1630) animals at embryo stage, comparing to in N2 animals. | DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction. | WBPaper00060014:set-2(tm1630)_downregulated | |
| Transcripts detected in germline isolated from day-1 adult hermaphrodite animals. | All three experiments have CPM >= 1. | WBPaper00067147:germline_expressed | |
| Bacteria: B.thuringiensis | Transcripts in elt-2(RNAi) animals that were significantly differentially expressed at least for one time point and one pathogenic strain Bt247 and Bt679 compared to the non pathogenic strain Bt407. | Cuffdiff | WBPaper00060358:B.thuringiensis_pathogen_regulated_elt-2(RNAi) |
| Bacteria: B.thuringiensis | Transcripts in N2 animals that were significantly differentially expressed at least for one time point and one pathogenic strain Bt247 and Bt679 compared to the non pathogenic strain Bt407. | Cuffdiff | WBPaper00060358:B.thuringiensis_pathogen_regulated_N2 |
| Transcripts that showed significantly decreased expression in nhl-2(ok818) comparing to in N2 at 25C. | EdgeR, FDR < 0.05, fold change < 0.5. | WBPaper00055971:nhl-2(ok818)_25C_upregulated | |
| Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(+), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage. | DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2. | WBPaper00050859:upregulated_P-granule(-)GFP(+)_vs_control_day2-adult | |
| 20C vs 25C | Transcripts that showed differential expression in 20C vs 25C in mir-34(OverExpression) animals at adult stage. | N.A. | WBPaper00050488:20C_vs_25C_regulated_mir-34(OverExpression)_adult |
| Transcripts that showed significantly decreased expression after animals grew in 500 uM glycine from hatch till 1-day post L4 adult, comparing to untreated animals. | Differential expression was assessed using a nempirical Bayes moderated t-test within limmas linear model framework including the precision weights estimated by voom.Resulting p-values were corrected for multiple testing using the Benjamini-Hochberg false discovery rate. Curator applied threshold: fold change > 2, adjusted p-value < 0.01. | WBPaper00056330:glycine_downregulated | |
| Transcripts that showed significantly decreased 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)_downregulated | |
| Transcripts that showed significantly increased expression in lin-22(ot269) comparing to in N2 at L3 larva. | Differences in gene expression were then calculated using the negative binomial test in the DESeq package (FDR = 0.1). | WBPaper00053295:lin-22(ot269)_upregulated | |
| Genes with significantly decreased expression in eat-2(ad465) comparing to N2. | The criteria for differential gene regulation included a greater than 1.5-fold change in expression compared to wild-type, a false discovery rate less than 0.05, and greater than 10 reads when normalized to the base mean. Statistical analysis and drawing of plots was performed in R using the bioconductor package Deseq (Anders, Huber 2010) and R function gplots. | WBPaper00044037:eat-2_downregulated | |
| Transcripts that showed significantly increased expression in jmjd-3.1p::jmjd-3.1 comparing to in N2. | DESeq2 Benjamini-Hochberg adjusted p-value < 0.05. | WBPaper00049545:jmjd-3.1(+)_upregulated | |
| Transcripts that showed significantly increased expression in rgef-1p::jmjd-1.2 comparing to in N2. | DESeq2 Benjamini-Hochberg adjusted p-value < 0.05. | WBPaper00049545:rgef-1p-jmjd-1.2(+)_upregulated | |
| Transcripts with significantly increased expression in isp-1(qm150) vs. N2, and in isp-1(qm150) ced-4(n1162) vs. ced-4(n1162). | Comparisons of each genotype were compared to the wild-type using the Empirical Base (Wright & Simon) algorithm and fold changes were represented on a log2 scale. A threshold of p < 0.05 and a fold change of 1.3 (log2) was set to determine differentially expressed targets. | WBPaper00045263:isp-1(qm150)_upregulated |
9 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr1030729 | Tiling arrays expression graphs | |||
| Reporter gene fusion type not specified. The antibody staining showed EAT-20 expression in the seam cells and hypodermal cells, which is inconsistent with the absence of GFP expression in those cells in the promoter trap lines, suggesting that p5E5 may not contain all the cis-regulatory elements necessary for the expression of the eat-20 gene. | GFP expression was analyzed in ncIs1 hermaphrodites carrying p5E5 as a stable integrated transgenic array. Though p5E5 contains a 2-kb genomic fragment derived from LGV at the 5' side in addition to the fragment corresponding to the eat-20 gene, it is confirmed that an extrachromosomal array of p5E5 and that of p5E5del, in which the 2-kb fragment was deleted, gave the same GFP expression pattern. Thus, the fragment at the 5' part of the insert had no effects on the expression of GFP. Neurons expressing GFP were first identified in L1 larvae. | Expr976 | In embryos, GFP expression was first detected at the 2-fold stage. Sometimes eight cells in the anterior half of the body expressed GFP. At the 3-fold stage, several cells around the pharynx expressed GFP in most embryos. About half of the embryos also expressed GFP weakly in the pharynx. At L1, GFP was detected in a subset of neurons. About half of the larvae also expressed GFP in the pharynx; expression in the terminal bulb was the most intense. At the adult stage, GFP was detected in the pharyngeal muscles, m3, m4, and m6. In addition, GFP was detected in a subset of neurons: IL1, OLQ, BAG, and ALN, several circumpharyngeal cells, and coelomocytes. Very faint GFP fluorescence was detected in the pharyngeal neurons including I4 and I5 in L1 larvae. | |
| Expr1801 | Expressed in pharynx. | |||
| Expr2251 | The signal was first detected in a few cells at the midline of the 1.5-fold stage embryo. At the twofold stage and thereafter, the signal was detected in the presumptive pharynx. At the L1 stage, the entire pharynx stained. In the older larvae and adults the entire pharynx stained in some animals though the staining was rather inconsistent. Cells around the metacorpus and the procorpus sometimes stained. | |||
| Expr977 | Neither immunoblotting nor immunostaining analysis with the anti-EAT-20 polyclonal antibody detected any signal in eat-20 mutants. At the 16-cell stage, patches of staining on the entire surface of embryos were first detected. From the comma stage on, staining was detected in coelomocytes, the nervous tissues, hypodermal cells, and the pharynx. At the comma stage, the apical surface of the alimentary canal was stained intensely and the basal surface of presumptive pharynx was moderately stained. The staining in the presumptive pharynx gradually weakened thereafter and disappeared completely at the late 3-fold stage. The staining of the apical surface of the pharynx and pharyngeal intestinal valve remained intense throughout the rest of the embryogenesis stage. Granular staining in the region surrounding the pharyngeal lumen was observed from the L2 stage on and spread to the external surface. Staining of the entire surface of the pharyngeal muscle was observed in the late L3 or L4 stage. The inner linings of the intestine and anus were intensely stained until the 2-fold stage, and then the staining became weak and disappeared completely at the 3-fold stage. The anterior-most intestinal cell became stained from the L3 stage. Staining was also observed in the nervous tissues. At the rostral end of the head, staining that seemed to correspond to the distal segments of labial process bundles was seen from the comma stage up to the adult stage. In larvae, the staining sometimes extended posteriorly to the level of the isthmus. A pair of cells, which might be support cells of sensory neurons posterior to the distal structures, were stained from the L1 stage up to the adult stage. The motor neurons in the ventral cord, which sometimes expressed GFP in the promoter trap line, were stained at the early L1 stage. This staining disappeared at the late L1 stage and, in the later stages, was replaced by segmental staining of the ventral nerve cord. The nerve ring and the nerve bundles that connect the nerve ring and the ventral nerve cord had dots of very faint staining. On the lateral body wall at the base of the tail spike, staining was detected from the L2 stage up to the adult stage, which may correspond to the axon of ALN neuron that expressed reporter GFP in the promoter trap lines. In the adult male tail, sensory rays were intensely stained. There was also extensive hypodermal staining. Weak staining of the seam cells began at the 3-fold stage and the staining became intense from the L3 stage up to the adult stage. Thin longitudinal bands were stained along the dorsal and ventral midline from the rostral end of the body to the base of the tail spike, which corresponds to the position of the dorsal and ventral hypodermal ridges. The hypodermal staining co-localizing with the position of the ventral nerve cord was the most intense. The hypodermal cells at the opening and inside of the vulva were stained from the L4 stage up to the adult stage. The hypodermis around the anus was stained from the L2 stage up to the adult stage. The coelomocytes were continuously stained from the comma stage up to the adult stage. | |||
| Expr1153240 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr2011155 | 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). | |||
| Expr1020145 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr2029391 | 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). |
5 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| enables | |
| located_in | |
| located_in | |
| located_in | |
| located_in |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrX_15508644..15510010 | 1367 | X: 15508644-15510010 | Caenorhabditis elegans |
