Genomics
1 Transcripts
WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
---|---|---|---|
Transcript:W10C8.2.1 | W10C8.2.1 | 2560 | I: 2822243-2830311 |
Other
1 CDSs
WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
---|---|---|---|
CDS:W10C8.2 | W10C8.2 | 1317 | I: 2823468-2823937 |
249 RNAi Result
168 Allele
Public Name |
---|
gk963902 |
gk964159 |
gk962616 |
q624 |
q645 |
q772 |
WBVar01691722 |
WBVar01691721 |
WBVar01691723 |
WBVar01931778 |
WBVar01931777 |
WBVar01762027 |
WBVar01500435 |
WBVar01500434 |
gk106055 |
WBVar02001699 |
gk106056 |
WBVar02001700 |
WBVar00535379 |
gk106057 |
WBVar01981988 |
WBVar02001698 |
gk106058 |
WBVar01981987 |
gk106051 |
gk106052 |
WBVar00535375 |
gk106053 |
gk106054 |
gk106063 |
1 Chromosome Location
Feature . Primary Identifier |
Start | End | Strand |
---|---|---|---|
WBGene00004077 | 2822243 | 2830311 | -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_2822135..2822242 | 108 | I: 2822135-2822242 | Caenorhabditis elegans |
121 Expression Clusters
Regulated By Treatment | Description | Algorithm | Primary Identifier |
---|---|---|---|
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 | |
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 hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:hypodermis_expressed | |
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 |
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 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 |
Significantly differentially expressed genes as determined by microarray analysis of wild-type and cde-1 mutant germlines. | RNAs that changed at least 2-fold with a probability of p < 0.05 were considered differentially regulated between wildtype and cde-1. | WBPaper00035269:cde-1_regulated | |
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 detected in body muscle nuclei according to a nuclear FACS-based strategy. | Cufflinks | WBPaper00065120:body-muscle-transcriptome | |
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 | |
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 increased expression in pry-1(mu38) animals comparing to in N2 at L1 larva stage. | DESeq, FDR < 0.05 | WBPaper00055626:pry-1(mu38)_upregulated | |
Transcripts detected in germline isolated from day-1 adult hermaphrodite animals. | All three experiments have CPM >= 1. | WBPaper00067147:germline_expressed | |
Transcripts that showed significantly decreased expression in the neurons of bcat-1(RNAi) animals at 5-days post L4 adult hermaphrodite stage, comparing to animals injected with empty vector. | DESeq2. FDR < 0.05. | WBPaper00060459:bcat-1(RNAi)_downregulated | |
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 | |
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours. | Transcripts that showed significantly decreased expression in hpx-2(dg047) after animals were exposed to E. faecalis OG1RF for 16 hours comparing to exposure to E. Coli OP50. | Cuffcompare and Cuffdiff | WBPaper00056090:E.faecalis_downregulated_hpx-2(dg047) |
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:coelomocytes_L1-larva_expressed | |
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:hypodermis_L1-larva_expressed | |
Transcripts of coding genes that showed significantly increased 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_enriched_coding-RNA | |
Genes expressed in N2. | Expressed transcripts were identified on the basis of a Present call in 3 out of 4 N2 experiments as determined by Affymetrix MAS 5.0. | WBPaper00025141:N2_Expressed_Genes | |
Embryonic class (E): genes that significantly increase in abundance at some point during embryogenesis. | 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_E | |
WT-Pico Pan-neural Depleted Genes, with genes found multiple times in a single dataset removed (without dups). | To identify differentially expressed transcripts, normalized intensity values from the pan-neural data sets were compared to a reference (from all larval cells) using Significance Analysis of Microarray software (SAM). A two class unpaired analysis of the data was performed to identify neuron-enriched genes. Pan-neural enriched transcripts in the IVT and WT-Pico-derived data set were defined as 1.5X elevated vs the reference at a False Discovery Rate (FDR) = 3%. | WBPaper00031532:Larva_Pan_Neuronal_Depleted | |
Strictly embryonic class (SE): genes that are the subset of embryonic genes that are not also classified as maternal. | 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_SE | |
Genes that showed significantly altered expression between N2 and npr-1(ur89) strains exposed to either the nematocidal B. thuringiensis B-18247, the pathogenic P. aeruginosa PA14, or the control E. coli OP50 for 12 or 24 hours. | Estimation of transcript abundance and significantly differentially expressed genes were identified by Cuffdiff using the quartile normalization method. Transcripts with a significant change between different conditions (adjusted p-value < 0.01 by the false discovery rate, FDR) were treated as signature for each comparison. | WBPaper00049498:npr-1(ur89)_regulated_3 | |
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 |
15 Expression Patterns
Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
---|---|---|---|---|
Expr1031966 | Tiling arrays expression graphs | |||
Expr1019247 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
Expr886 | The levels of POP-1 were higher in the anterior T cell daughter in wild-type animals(28/28). In lin-17 animals, which display a loss of T cell polarity, the level of POP-1 was high in both T cell daughters in 71% of divisions, higher in the posterior T cell daughter in 8% of divisions and higher in the anterior T cell daughter in 17% of divisions (n=65). | |||
Clone: pUL#JS9A1 | Expr7703 | Expression is seen in many tissues including pharynx, nerves of the head and tail and the ventral nerve cord, intestine, and developing gonad. Expression is seen from early embryo onwards. | ||
No detailed description on cellular expression pattern at later stages. | Expr1444 | Between the 2-cell and 28-cell stages of embryogenesis, equal levels of POP-1 staining were detected in sister cells born from transverse cleavages. However, different levels of POP-1 stained in almost all pairs of sister cells resulting from an a/p cleavage. For example, in the AB lineage there are no POP-1 differences after the first two divisions, which are transverse, but there are differences after the third division, which is a/p. After the first a/p division in the AB lineage, as well as after a/p divisions in other lineages, authors invariably see higher levels of staining in the nucleus of the anterior sister than in the nucleus of its posterior sister. POP-1 asymmetry appears in interphase nuclei, then POP-1 staining diminishes and is not observed in prophase nuclei. The only anterior cell in which authors fail to detect POP-1 is the P4 blastomere. Heterogeneity in POP-1 staining is observed between many neighboring nuclei in embryos after the 28-cell stage. The descendants of the E lineage can be identified readily in fixed embryos at all stages; POP-1 asymmetry was found after the first, third, and fourth divisions of the E lineage, which are a/p. The second division of the E lineage is transverse (left/right), and symmetrical levels of POP-1 were found in both pairs of sister blastomeres. In late-stage embryos, POP-1 is prominent in the developing nervous system but absent from some other tissues like the hypodermis. In larvae during postembryonic development, POP-1 is present in the row of hypodermal cells, called seam cells, along the lateral surfaces of the body. POP-1 asymmetry is observed after the seam cells divide a/p; in each pair of sisters, POP-1 appears at higher levels in the anterior sister than in the posterior sister. In addition, POP-1 is detected in migratory cells called the Q neuroblasts and in the developing gonad and vulva. | nucleus | |
Two GFP::POP transgenes under control of a promoter that drives expression at the same apparent level in many cells, including Z1, Z4, and their descendants. One transgene, GFP::POP(del1-5), has GFP-coding sequences fused in frame to the sixth codon of pop-1 cDNA, while the other, GFP::POP(FL), fuses GFP to the full-length pop-1 cDNA. Both transgenes displayed similar expression levels and response to Wnt/MAPK signaling. In addition, both transgenes exhibited similar POP-1 asymmetry in the Z1/Z4 daughters. GFP::POP(del1-5) had dominant negative activity and was not viable in certain mutant backgrounds; by contrast, GFP::POP(FL) had only marginal dominant negative effects and rescued a pop-1 mutant. [jmp#1::pop-1-gfp] translational fusion constructs. Two GFP::POP-1 constructs, GFP::POP-1(del1-5) and GFP::POP-1(FL), were made with GFP fused at the N terminus of the pop-1 cDNA. These reporters were placed under control of a promoter expressed in Z1 and Z4 as well as many other tissues, called jmp#1. GFP::POP-1(del1-5) was made by first amplifying GFP with primers containing SacI sites at the 5 ends. This GFP fragment was cloned in frame into the SacI site of pJK706, which inserts GFP upstream of amino acid 6 of the POP-1 protein. GFP::POP-1(del1-5) was subcloned into pPD49.26 to add the unc-54 3'-UTR and then cloned into pDPMM0166 to add the unc-119 gene for use as a selective marker when producing transgenics. The resulting plasmid is named pJK789. The second construct, POP-1::GFP(FL), differs from the first only in that GFP is fused in frame upstream of the first methionine of the pop-1 cDNA. This construct is called pJK908. | Expr2852 | The developing hypodermis and the early gonad was observed using the GFP::POP reporters. As seen in previous studies, GFP was more abundant in anterior than in posterior daughters in hypodermal lineages. Expression in the early gonad departed from this anterior-posterior asymmetry: the nucleus of Z1.p was brighter than that of Z1.a, and the nucleus of Z4.a was brighter than that of Z4.p. Proximal daughters was noted contained nuclear GFP puncta similar to those described in the anterior daughters of asymmetric divisions in the embryo. | ||
Genetic analysis indicate that POP-1 staining before 28 cell stage is maternal, while expression after 28 cell stage is zygotic. No detailed description on expression patter at later stages. | Expr1556 | POP-1 protein was first detected in the nuclei of maturing oocytes in the gonad. After fertilization, POP-1 was detected in nuclei of most early embryonic cells. The antibody does not stain cells during mitosis. After 360 cell stage, POP-1 is detected in only a subset of tissues. | nuclei | |
Expr3998 | In wild type, the sisters generated by the division of P7.p (P7.pa and P7.pp) most often localized POP-1 in a low/high pattern (21 of 25 specimens). | |||
Expr12414 | Following asymmetric division of their mother cell, the anterior NBSMDD/AIY neuroblast (ABplpapaaa, ABprpapaaa) displays a high nuclear concentration of POP-1 and low concentration of SYS-1 while the posterior NBSIAD/SIBV neuroblast (ABplpapaap, ABprpapaap) has a low nuclear concentration of POP-1 and high concentration of SYS-1. | |||
Expr3465 | All of the first and second round cell divisions in a vulval secondary lineage usually produced sister cells with different nuclear levels of POP-1. For example, after the division of P5.p, the anterior sister P5.pa most often had a higher level of nuclear POP-1 than the posterior sister P5.pp (23 of 25 specimens). This pattern, in which the anterior sister has the higher level of POP-1, will hereafter be called a high/low pattern; the opposite pattern, in which the anterior sister has the lower level of POP-1, will be called a low/high pattern. POP-1 was also localized in a high/low pattern after the second round of cell division. P5.paa and P5.ppa both had higher nuclear levels of POP-1 than their respective posterior sisters P5.pap and P5.ppp. The first two rounds of cell division in the secondary lineage of P7.p also produced sister cells that displayed different nuclear levels of POP-1. However, in contrast to the P5.p lineage, POP-1 was most often localized in a low/high pattern after these divisions. For example, P7.pa most often had a lower nuclear level of POP-1 than its posterior sister P7.pp (21 of 25 specimens). The first round of cell division in the primary lineage of P6.p produced sisters (P6.pa and P6.pp) that most often had equal and low levels of POP-1 (21 of 24 specimens). At the second round of cell division in the P6.p lineage, the anterior cell P6.pa produced sisters that localized POP-1 in a high/low pattern, while the posterior cell P6.pp produced sisters that localized POP-1 in a low/high pattern. In summary, these studies show that POP-1 is typically localized in a high/low pattern in the anterior half of the vulva and in a low/high pattern in the posterior half of the vulva. As cell lineages in the two halves of the vulva have opposite orientations, these studies show that the orientation of POP-1 localization correlates with the orientation of the vulval lineages. POP-1 expression was examined in strains N2 and CM1006, and similar results were obtained with both strains. CM1006 expresses an AJM-1::GFP fusion protein that localizes to a cell junction complex along the apical border of epithelial cells. The presence of this protein helped reveal the anatomy of vulval cells in immunostained animals. POP-1 was consistently observed in the vulval precursor cells of mid-L2 and older animals and in the progeny cells produced by the first two rounds of cell division in the primary and secondary lineages. The expression of POP-1 at earlier stages was not examined. The levels of POP-1 seen in the vulval precursors at the mid-L2 stage were low compared to the levels observed in the gonad, or after the division of the vulval precursors. Prior to division, all of the vulval precursor cells in an animal typically had equivalent levels of POP-1. However, in animals in which VPCs had started to divide or had divided, cells of primary and secondary lineages displayed moderately higher levels of POP-1 than cells in tertiary lineages. POP-1 was rapidly lost after the third and final round of cell division in primary and secondary lineages. The loss of POP-1 from these cells is in keeping with the observation that the POP-1 protein is not detectable in most postmitotic cell populations. | |||
Expr12127 | In wild-type worms, POP-1::GFP expression was stronger in the nuclei of Z1.p and Z4.a cells than in Z1.a and Z4.p cells | |||
Expr1158615 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
Expr2015000 | 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). | |||
Expr3997 | In qIs74 males, GFP::POP-1 is asymmetrically distributed to the nuclei of the B.a and B.p cells, with the level of GFP::POP-1 being higher in the B.a nucleus than in the B.p nucleus (100%, n = 27). | |||
Expr2033235 | 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). |
92 GO Annotation
Annotation Extension | Qualifier |
---|---|
enables | |
enables | |
has_input(WB:WBGene00001186),occurs_in(WBbt:0005753) | enables |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
occurs_in(GO:0005634) | enables |
has_input(WB:WBGene00001186),occurs_in(WBbt:0005753) | enables |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables |
17 Homologues
Type |
---|
orthologue |
orthologue |
orthologue |
orthologue |
least diverged orthologue |
least diverged orthologue |
least diverged orthologue |
least diverged orthologue |
least diverged orthologue |
least diverged orthologue |
least diverged orthologue |
orthologue |
least diverged orthologue |
orthologue |
orthologue |
orthologue |
least diverged orthologue |
92 Ontology Annotations
Annotation Extension | Qualifier |
---|---|
enables | |
enables | |
has_input(WB:WBGene00001186),occurs_in(WBbt:0005753) | enables |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
occurs_in(GO:0005634) | enables |
has_input(WB:WBGene00001186),occurs_in(WBbt:0005753) | enables |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables |
1 Upstream Intergenic Region
WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
---|---|---|---|---|---|
intergenic_region_chrI_2830312..2830334 | 23 | I: 2830312-2830334 | Caenorhabditis elegans |