Genomics
16 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:K11C4.5a.1 | K11C4.5a.1 |
16030
 |
V: 6901681-6929038 |
| Transcript:K11C4.5d.1 | K11C4.5d.1 |
15550
|
V: 6901682-6928949 |
| Transcript:K11C4.5c.1 | K11C4.5c.1 |
15896
|
V: 6901684-6928949 |
| Transcript:K11C4.5g.1 | K11C4.5g.1 |
15895
|
V: 6901688-6928949 |
| Transcript:K11C4.5e.1 | K11C4.5e.1 |
15936
|
V: 6901689-6928949 |
| Transcript:K11C4.5i.1 | K11C4.5i.1 |
15600
|
V: 6902016-6924961 |
| Transcript:K11C4.5j.1 | K11C4.5j.1 |
15252
|
V: 6902016-6924961 |
| Transcript:K11C4.5k.1 | K11C4.5k.1 |
15558
|
V: 6902016-6924961 |
| Transcript:K11C4.5l.1 | K11C4.5l.1 |
15210
|
V: 6902016-6924961 |
| Transcript:K11C4.5m.1 | K11C4.5m.1 |
15603
|
V: 6902016-6924961 |
| Transcript:K11C4.5n.1 | K11C4.5n.1 |
15255
|
V: 6902016-6924961 |
| Transcript:K11C4.5o.1 | K11C4.5o.1 |
15561
|
V: 6902016-6924961 |
| Transcript:K11C4.5p.1 | K11C4.5p.1 |
15213
|
V: 6902016-6924961 |
| Transcript:K11C4.5b.1 | K11C4.5b.1 |
15258
|
V: 6902016-6928949 |
| Transcript:K11C4.5f.1 | K11C4.5f.1 |
15261
|
V: 6902016-6928949 |
| Transcript:K11C4.5h.1 | K11C4.5h.1 |
15219
|
V: 6902016-6928949 |
Other
16 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:K11C4.5a | K11C4.5a |
15606
|
V: 6902016-6902169 |
| CDS:K11C4.5g | K11C4.5g |
15567
|
V: 6902016-6902169 |
| CDS:K11C4.5i | K11C4.5i |
15600
|
V: 6902016-6902169 |
| CDS:K11C4.5k | K11C4.5k |
15558
|
V: 6902016-6902169 |
| CDS:K11C4.5m | K11C4.5m |
15603
|
V: 6902016-6902169 |
| CDS:K11C4.5p | K11C4.5p |
15213
|
V: 6902016-6902169 |
| CDS:K11C4.5f | K11C4.5f |
15261
|
V: 6902016-6902169 |
| CDS:K11C4.5h | K11C4.5h |
15219
|
V: 6902016-6902169 |
| CDS:K11C4.5b | K11C4.5b |
15258
|
V: 6902016-6902169 |
| CDS:K11C4.5c | K11C4.5c |
15564
|
V: 6902016-6902169 |
| CDS:K11C4.5d | K11C4.5d |
15216
|
V: 6902016-6902169 |
| CDS:K11C4.5e | K11C4.5e |
15609
|
V: 6902016-6902169 |
| CDS:K11C4.5j | K11C4.5j |
15252
|
V: 6902016-6902169 |
| CDS:K11C4.5l | K11C4.5l |
15210
|
V: 6902016-6902169 |
| CDS:K11C4.5n | K11C4.5n |
15255
|
V: 6902016-6902169 |
| CDS:K11C4.5o | K11C4.5o |
15561
|
V: 6902016-6902169 |
20 RNAi Result
351 Allele
| Public Name |
|---|
| gk963301 |
| WBVar02060217 |
| gk963553 |
| gk964259 |
| gk964351 |
| gk963850 |
| gk964527 |
| gk962860 |
| gk964528 |
| r1158 |
| r1162 |
| r1161 |
| r1221 |
| s92 |
| WBVar02124239 |
| WBVar02121266 |
| gk506145 |
| WBVar01588536 |
| WBVar01588539 |
| WBVar01588537 |
| WBVar01588538 |
| WBVar01588540 |
| WBVar01973961 |
| WBVar01973962 |
| gk238240 |
| gk238239 |
| gk238238 |
| gk238246 |
| gk238245 |
| gk238244 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00006801 | 6901681 | 6929038 | -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_chrV_6901286..6901680 | 395 | V: 6901286-6901680 | Caenorhabditis elegans |
214 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 | |
| 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 |
| TGF- Dauer pathway adult transcriptional targets. Results obtained by comparing the microarray results of the dauer-constitutive mutants daf-7(e1372), daf-7(m62), and daf-1(m40) with dauer-defective mutants daf-3(mgDf90), daf-5(e1386), and daf-7(e1372);daf-3(mgDf90) double mutants at the permissive temperature, 20C, on the first day of adulthood. | SAM | WBPaper00031040:TGF-beta_adult_upregulated | |
| Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology. | DESEQ2, fold change > 2 and FDR < 0.01. | WBPaper00062103:neuron_enriched | |
| 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 | |
| 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 | |
| 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 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 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 | |
| Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:seam_expressed | |
| 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) | |
| Transcripts expressed in vulva. | FPKM >= 1. | WBPaper00064122:vulva_transcriptome | |
| Bacteria infection: Bacillus thuringiensis | Transcripts that showed significantly increased expression in N2 animals infected by bacteria BMB171/Cry5Ba, an acrystalliferous Bt mutant BMB171 transformed with toxin gene cry5Ba on the shuttle vector pHT304, comparing to N2 animals infected by BMB171/pHT304. | N.A. | WBPaper00064229:B.thuringiensis-Cry5Ba_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 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 after four-day-old young adult worms were placed on NGM plates seeded with OP50 in the presence 5% Agaro-oligosaccharides(AGO) for 24 h, comparing to animals grown in the absence of AGO. | Fold change > 2. | WBPaper00064306:Agaro-oligosaccharides_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 6h), according to RNAseq. | Cuffdiff, ajusted p-value < 0.01. | WBPaper00046497:B.thuringiensis_0.5mix_downregulated_6h |
| 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 |
| Maternal class (M): genes that are called present in at least one of the three PC6 replicates. | A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing. | [cgc5767]:expression_class_M |
12 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr13672 | The ryr-1 gene generates transcripts from two promoters. Reporter constructs demonstrated that the upstream promoter is expressed in muscle, whereas the downstream promoter is expressed in neurons. | |||
| Expr13673 | The ryr-1 gene generates transcripts from two promoters. Reporter constructs demonstrated that the upstream promoter is expressed in muscle, whereas the downstream promoter is expressed in neurons. | |||
| Expr1620 | ryr-1 is expressed in body-wall and pharyngeal muscles and in non-muscle cells. Beta-galactosidase activity detected in body-wall and pharyngeal muscle cells. Deletion of 3.3 kb of 5H-upstream sequence resulted in expression in non-muscle cells such as neuron and intestine (pRRZ462). Non-muscle expression was observed in constructs containing a short (less than 1470 bp) 5H-upstream sequence. Two regions appear to be required for body-wall muscle expression. Expression in younger animals was much higher than that in adults. | |||
| Expr2036034 | 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). | |||
| Expr1032869 | Tiling arrays expression graphs | |||
| Reporter gene fusion type not specified. | Expr1255 | GFP fluorescence is observed in several muscle cell types of the transformants, including body-wall muscle cells, terminal bulb muscles of the pharynx, vulval and uterine muscle, diagonal muscles of the male tail, the anal sphincter muscle, and anal depressor muscles. GFP expression is variably observed in unidentified neurons in the head. GFP expression first observed in body-wall and pharyngeal muscle cells in 1.5-fold embryos, approximately the time when twitching of embryonic body wall muscles begins. The corpus muscles of the pharynx did not express GFP. | ||
| The tissue-specific expression of unc-68 protein suggested by antibody staining was confirmed by a gfp-fusion construct. The results of unc-68::gfp expression and immunostaining experiments strongly suggest that CeRyR is present only in muscles. See Expr2281 for GFP result. | Expr2280 | The R16 antibody stained muscle cells of wild-type from the comma stage to the 3-fold stage, but not those of x14 animals. The R16 antibody staining appeared at the later comma stage and became strong at the 1.5-fold stage, when the muscle starts twitching, and continued to the adult stage. Although background staining from the early embryo to pre-comma stages was also observed in the cytoplasm of whole cells, this staining was not different between wild-type and x14 animals. The R16 antibody stained the body wall, pharyngeal, vulval and the anal muscles of adult hermaphrodites and male tail muscles in wild-type, but not in unc-68(x14) animals. The identity of these muscle tissues was confirmed by double-staining with rhodaminephalloidin. Among the anal muscles, the R16 antibody stained the depressor muscle but did not stain the sphincter muscle. The R16 antibody also stained pharyngeal muscles, especially those in the terminal bulb and isthmus. The staining pattern in body wall muscle was observed to be of a series of small dots. Because the antiserum stained in the intestines of both wild-type and unc-68(x14) animals, the intestinal staining is likely to represent the cross-reaction of the R16 antibody with unknown proteins. | ||
| The tissue-specific expression of unc-68 protein suggested by antibody staining was confirmed by a gfp-fusion construct. The results of unc-68::gfp expression and immunostaining experiments strongly suggest that CeRyR is present only in muscles. See Expr2280 for antibody staining results. | Expr2281 | The unc-68::gfp transgene was expressed in most muscles, but not in intestine and neurons. GFP was expressed in most muscle cells, including those of the pharynx, where expression was clearly seen in the terminal bulb and isthmus. However, GFP expression was not detected in the anal sphincter muscle. This may be due to the length of upstream sequence used in the transgenes. The additional 2.2 kb of 5' upstream sequence included in the transgene may contain a regulatory element important for proper unc-68 expression. | ||
| Expr1154288 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr1025192 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr2017898 | 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). | |||
| Expr2282 | The R16 antibody stained the region along the liner filament of body wall muscles as seen at high magnification. The R16 antibody stained actin-localizing areas in thin filaments (I-bands), but not in paramyosin-contain-ing areas in thick filaments. |
24 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| located_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| enables | |
| enables | |
| enables | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| enables | |
| enables |
24 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| located_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| enables | |
| enables | |
| enables | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| enables | |
| enables |
21 Strains
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrV_6929039..6929531 | 493 | V: 6929039-6929531 | Caenorhabditis elegans |
