Genomics
2 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:C47C12.3b.1 | C47C12.3b.1 |
948
 |
X: 7744239-7749430 |
| Transcript:C47C12.3a.1 | C47C12.3a.1 |
1500
|
X: 7745815-7750013 |
Other
2 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:C47C12.3b | C47C12.3b |
948
|
X: 7744239-7744269 |
| CDS:C47C12.3a | C47C12.3a |
909
|
X: 7745823-7745907 |
96 Allele
| Public Name |
|---|
| gk964260 |
| gk964193 |
| gk964194 |
| gk963896 |
| gk963732 |
| gk964088 |
| gk964087 |
| tm589 |
| WBVar01820317 |
| WBVar01820318 |
| WBVar01820319 |
| WBVar01820320 |
| WBVar02027222 |
| WBVar01849260 |
| WBVar01883761 |
| WBVar01849259 |
| ot762 |
| WBVar01849261 |
| gk285922 |
| mu218 |
| gk285921 |
| gk285920 |
| gk285919 |
| gk285918 |
| gk285930 |
| gk285929 |
| gk285928 |
| gk285927 |
| gk285926 |
| gk285925 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00004335 | 7744239 | 7750013 | 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_7750014..7753069 | 3056 | X: 7750014-7753069 | Caenorhabditis elegans |
156 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 | |
| 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 |
| Osmotic stress | Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when food was present | DESeq(version 1.10.1), FDR < 0.05. | WBPaper00050726:OsmoticStress_regulated_Food |
| Transcripts that showed significantly increased expression in csr-1a(tor159) comparing to in N2 at 25C. | DESeq2, fold change > 2, p-value < 0.05. | WBPaper00061753:csr-1(tor159)_upregulated_25C | |
| 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 that showed significantly decreased expression in atfs-1(cmh15) (null allele) animals comparing to in N2 animals at L4 larva stage. | edgeR, fold change > 2, FDR < 0.05 | WBPaper00060909:atfs-1(cmh15)_downregulated | |
| Transcripts that showed significantly decreased expression in lipl-4 overexpression transgenic lines comparing to wild type control animals. | DESeq2 fold change > 2, FDR < 0.05. | WBPaper00064156:lipl-4(overexpress)_downregulated | |
| 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 |
| 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 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 | |
| 25C vs. 20C | Transcripts that showed significantly increased expression in 1-day post L4 adult hermaphrodite N2 grown at 25C, comparing to in N2 animals grown at 20C. | CuffDiff, fold change > 2. | WBPaper00065096:25C_vs_20C_upregulated |
| Transcripts that showed significantly increased expression in 10-days post L4 adult hermaphrodite N2 grown at 20C, comparing to in 1-day post L4 adult hermaphrodite N2 animals grown at 20C. | CuffDiff, fold change > 2. | WBPaper00065096:Day10_vs_Day1_upregulated | |
| Transcripts that showed significantly increased expression in wdr-5(ok1417);skn-1(lax188) comparing to in skn-1(lax188) at day 2 adult stage. | fold change > 2 | WBPaper00058711:wdr-5(ok1417)_upregulated | |
| Transcripts that showed significantly decreased expression in 10-days post L4 adult hermaphrodite npr-8(ok1439) animals grown at 20C, comparing to in N2 animals. | CuffDiff, fold change > 2. | WBPaper00065096:npr-8(ok1439)_downregulated_Day10_20C | |
| Transcripts that showed significantly decreased expression in tetraploid N2 comparing to diploid N2 animals at L4 larva stage. | DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05. | WBPaper00066110:tetraploid_vs_diploid_downregulated | |
| Genes which expression is changed in isp-1;ctb-1 mutant and is not affected by developmental klf-1 RNAi, but is brought to wild type levels by klf-1 RNAi in adulthood. | N.A. | WBPaper00059194:klf-1(RNAi)_regulated | |
| Genes that showed expression levels higher than the corresponding reference sample (L2 all cell 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:coelomocytes_L2-larva_expressed | |
| Transcripts that showed significantly increased expression in hda-1(ne4752[3xFLAG-Degron-HDA-1]) in gonads dissected from 1-day old adult animals. | Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R. | WBPaper00061479:hda-1(ne4752)_upregulated | |
| Genes that showed expression levels higher than the corresponding reference sample (L3/L4 all cell 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:dopaminergic-neurons_L3-L4-larva_expressed | |
| Genes that showed expression levels higher than the corresponding reference sample (embryonic 0hr 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:germline-precursors_blastula-embryo_expressed | |
| 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 | |
| Starvation | Transcripts that showed significantly altered expression by starvation with 100 mM salt (NaCl) | DESeq(version 1.10.1), FDR < 0.05. | WBPaper00050726:starvation_regulated_LowSalt |
| 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 | |
| Genes found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014. | N.A. | WBPaper00026929:sir-2.1_overexpression_regulated |
18 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Clone: pUL#JRH/AD10 | Expr7477 | Expression is observed in three types of cells: in P-cells from mid-embryo to L2; in vulval precursors at L2 only; in ventral nerve cord from late embryo to adult. | ||
| Picture: Figure 2A. | Expr8593 | ref-2::venus is detected in a substantial number of dividing cells in the embryo. At the end of gastrulation, the reporter is detected in some neuroblasts on the ventral side of the embryo. These neuroblasts include the left/right symmetric pair of ABpl/rpapaaa neuroblasts, which will give rise to AIY and its sister cell, the SMDD motor neuron, through an asymmetric cell division. During interphase, the REF-2::VENUS protein is detected in the nucleus of the SMDD/AIY mothers, then spreads into the cytoplasm just before cleavage. No expression is observed in AIY during larval and adult stages. Thus ref-2 appears to be expressed only transiently in the AIY lineage during embryogenesis. REF-2::VENUS is also expressed in the excretory system (G1, G2, excretory pore, and excretory gland) in the P cell lineage and in the Y and B cells. | ||
| Expr1921 | REF-2 was first detected weakly in all 12 P cells just before P-cell migration. REF-2 was present in all P cells as migration occurred and remained in both P cell daughters after division in the ventral cord. This is also the point at which anti-REF-2 staining was strongest. REF-2 then disappears in the Pn.a cell lineage. REF-2 also disappears from the Pn.p cells, although it does so at different rates in different Pn.p cells. REF-2 is present for the longest time in the six unfused Pn.p cells P(3-8).p. REF-2 is also present in P1.p and P2.p shortly after those cells fuse with hyp7, although REF-2 decreases to an undetectable level soon after. REF-2 disappears most rapidly in P(9-11).p, with REF-2 being detectable in only some worms around the time of Pn.p cell fusion. In summary, REF-2 protein levels decrease around the time of Pn.p cell fusion, although they do so less quickly in the cells that remain unfused. REF-2 protein was also detected in the nuclei of the B and Y cells in the tail region during L1. | nuclei | ||
| Original chronogram file: chronogram.1091.xml | [C47C12.3:gfp] transcriptional fusion. | Chronogram81 | ||
| Original chronogram file: chronogram.1082.xml | [C47C12.3:gfp] transcriptional fusion. | Chronogram71 | ||
| Expr1032153 | Tiling arrays expression graphs | |||
| Expr9812 | GFP was observed in many nuclei in the embryo before gastrulation but in only 10 to 12 nuclei after gastrulation. GFP expression was observed in the L1, in the 12 P cells, 6 down each side. The transgenic strains may show considerable mosaicism as in many worms the GFP could only be seen in the 6 cells on one side. GFP expression seems to continue during P cell migration but possibly not in all P cells. GFP was also seen in 1 to 3 cells in the tail (which may be rectal muscles as they were located either side of the rectum) and 2 to 4 neurons in the head from L1 through to adulthood (although the strength of fluorescence was reduced in later stages). The GFP expression pattern looked very similar to that for the C-terminal (see strain UL4024) and ref-2b N-terminal (see strain UL4075) reporter fusions assayed for ref-2 using a similar strategy. | |||
| Expr9813 | GFP expression was observed in the L1, in the 12 P cells, 6 down each side. The transgenic strains may show considerable mosaicism as in many worms the GFP could only be seen in the 6 cells on one side. GFP expression seems to continue during P cell migration but possibly not in all P cells. GFP was also seen in 1 to 3 cells in the tail (which may be rectal muscles as they were located either side of the rectum) and 2 to 4 neurons in the head from L1 through to adulthood (although the strength of fluorescence was reduced in later stages). The GFP expression pattern looked very similar to that for N-terminal reporter fusions assayed for ref-2 using a similar strategy (see strains UL4017 and UL4075). | |||
| Expr9829 | GFP expression was observed in the L1, in the 12 P cells, 6 down each side. The transgenic strains may show considerable mosaicism as in many worms the GFP could only be seen in the 6 cells on one side. GFP expression seems to continue during P cell migration but possibly not in all P cells. GFP was also seen in 1 to 3 cells in the tail (which may be rectal muscles as they were located either side of the rectum) and 2 to 4 neurons in the head from L1 through to adulthood (although the strength of fluorescence was reduced in later stages). The GFP expression pattern looked very similar to that for C-terminal (see strain UL4024) and ref-2a N-terminal (see strain UL4017) reporter fusions assayed for ref-2 using a similar strategy. | |||
| Expr10428 | Inferred Expression. EPIC dataset. http://epic.gs.washington.edu/ Large-scale cellular resolution compendium of gene expression dynamics throughout development. This reporter was inferred to be expressing in this cell or one of its embryonic progenitor cells as described below. To generate a compact description of which cells express a particular reporter irrespective of time, the authors defined a metric "peak expression" for each of the 671 terminal ("leaf") cells born during embryogenesis. For each of these cells, the peak expression is the maximal reporter intensity observed in that cell or any of its ancestors; this has the effect of transposing earlier expression forward in time to the terminal set of cells. This metric allows straightforward comparisons of genes' cellular and lineal expression overlap, even when the expression occurs with different timing and despite differences in the precise time point that curation ended in different movies, at the cost of ignoring the temporal dynamics of expression, a topic that requires separate treatment. For simplicity, the authors use the term "expressing cells" to mean the number of leaf cells (of 671) with peak expression greater than background (2000 intensity units) and at least 10% of the maximum expression in that embryo. Quantitative expression data for all cells are located here: ftp://caltech.wormbase.org/pub/wormbase/datasets-published/murray2012/ | |||
| Expr13555 | During larval and adult stages ref-2 expression in the head is restricted to only six neurons, corresponding to the six IL1 neurons. | |||
| Original chronogram file: chronogram.1142.xml | [C47C12.3:gfp] transcriptional fusion. | Chronogram137 | ||
| Original chronogram file: chronogram.1636.xml | [C47C12.3:gfp] transcriptional fusion. | Chronogram607 | ||
| Expr10427 | Inferred Expression. EPIC dataset. http://epic.gs.washington.edu/ Large-scale cellular resolution compendium of gene expression dynamics throughout development. This reporter was inferred to be expressing in this cell or one of its embryonic progenitor cells as described below. To generate a compact description of which cells express a particular reporter irrespective of time, the authors defined a metric "peak expression" for each of the 671 terminal ("leaf") cells born during embryogenesis. For each of these cells, the peak expression is the maximal reporter intensity observed in that cell or any of its ancestors; this has the effect of transposing earlier expression forward in time to the terminal set of cells. This metric allows straightforward comparisons of genes' cellular and lineal expression overlap, even when the expression occurs with different timing and despite differences in the precise time point that curation ended in different movies, at the cost of ignoring the temporal dynamics of expression, a topic that requires separate treatment. For simplicity, the authors use the term "expressing cells" to mean the number of leaf cells (of 671) with peak expression greater than background (2000 intensity units) and at least 10% of the maximum expression in that embryo. Quantitative expression data for all cells are located here: ftp://caltech.wormbase.org/pub/wormbase/datasets-published/murray2012/ | |||
| Expr2015293 | 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). | |||
| Expr1146646 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr1013698 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr2033527 | 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). |
21 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| located_in | |
| located_in | |
| involved_in | |
| located_in | |
| has_input(WB:WBGene00006654),occurs_in(WBbt:0006679)|has_input(WB:WBGene00006654),occurs_in(WBbt:0006588) | involved_in |
| results_in_specification_of(WBbt:0003961)|results_in_specification_of(WBbt:0003963) | involved_in |
| happens_during(WBls:0000102) | involved_in |
| involved_in | |
| located_in | |
| located_in | |
| located_in | |
| acts_upstream_of_or_within_positive_effect | |
| enables | |
| involved_in | |
| involved_in | |
| enables | |
| involved_in | |
| enables | |
| enables | |
| has_input(WB:WBGene00006654) | enables |
| enables |
21 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| located_in | |
| located_in | |
| involved_in | |
| located_in | |
| has_input(WB:WBGene00006654),occurs_in(WBbt:0006679)|has_input(WB:WBGene00006654),occurs_in(WBbt:0006588) | involved_in |
| results_in_specification_of(WBbt:0003961)|results_in_specification_of(WBbt:0003963) | involved_in |
| happens_during(WBls:0000102) | involved_in |
| involved_in | |
| located_in | |
| located_in | |
| located_in | |
| acts_upstream_of_or_within_positive_effect | |
| enables | |
| involved_in | |
| involved_in | |
| enables | |
| involved_in | |
| enables | |
| enables | |
| has_input(WB:WBGene00006654) | enables |
| enables |