Genomics
1 Transcripts
WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
---|---|---|---|
Transcript:C08F8.8.1 | C08F8.8.1 |
1586
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IV: 11169748-11174791 |
Other
1 CDSs
WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
---|---|---|---|
CDS:C08F8.8 | C08F8.8 |
1251
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IV: 11169834-11169870 |
48 RNAi Result
78 Allele
Public Name |
---|
gk964278 |
gk964078 |
gk964500 |
gk962765 |
gk212181 |
gk881980 |
gk907560 |
gk666620 |
ok631 |
WBVar00243124 |
WBVar01542870 |
gk440306 |
WBVar02037155 |
gk915811 |
gk869046 |
gk623746 |
WBVar01846960 |
gk731651 |
tm2217 |
gk552838 |
WBVar02114972 |
ot407 |
ot136 |
gk692511 |
WBVar01857866 |
gk581400 |
gk838837 |
gk445145 |
gk511843 |
WBVar01857862 |
1 Chromosome Location
Feature . Primary Identifier |
Start | End | Strand |
---|---|---|---|
WBGene00003657 | 11169748 | 11174791 | 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_chrIV_11174792..11176099 | 1308 | IV: 11174792-11176099 | Caenorhabditis elegans |
160 Expression Clusters
Regulated By Treatment | Description | Algorithm | Primary Identifier |
---|---|---|---|
Transcripts that showed significantly increased expression in L1 neural cells comparing to in adult neural cells. | DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction. | WBPaper00060811:L1_vs_adult_upregulated_neural | |
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 |
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 | |
Genome-wide analysis of developmental and sex-regulated gene expression profile. | self-organizing map | cgc4489_group_18 | |
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 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 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 | |
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 increased expression in sin-3(tm1276) comparing to in N2. | DESeq2, fold change > 2, p-value < 0.01. | WBPaper00061203:sin-3(tm1276)_upregulated | |
Transcripts that showed significantly increased expression in mrg-1(qa6200) comparing to in control animals in primordial germ cells (PGCs) at L1 larva stage. | DESeq2(v1.32.0), FDR < 0.05. | WBPaper00064315:mrg-1(qa6200)_upregulated_PGCs | |
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 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 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 | |
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 | |
Bacteria infection: Pseudomonas aeruginosa PA14. 4 hours at 25C. | Transcripts that showed significantly decreased expression after N2 L4 animals were infected by P. aeruginosa (PA14) bacteria for 24 hours at 25C. | DESeq R package (1.18.0), FDR < 0.05 and fold change > 2. | WBPaper00062184:PA14_downregulated |
Transcripts that showed significantly increased expression in srbc-48(ac23);kyIs262;fer-1(b232ts) comparing to in kyIs262;fer-1(b232ts), 24h after infection with P.aeruginosa. | DESeq2, FDR <0.05, fold change > 2. | WBPaper00059664:srbc-48(ac23)_upregulated | |
Transcripts that showed significantly decreased expression in eat-2(ad1116) comparing to in N2 at 3-days post L4 adult hermaphrodite animals. | DESeq2(v1.14.1), fold change > 2, p-value < 0.05 | WBPaper00055354:eat-2(ad1116)_downregulated | |
Transcripts that showed significantly altered expression in rnp-6(dh1127) animals comparing to in N2 when fed with heat killed E. coli OP50. | Differentially expressed genes (DEGs) (q-value <0.05) between different samples were identified using the stringtie version 1.3.0, followed by Cufflinks version 2.2. | WBPaper00059824:rnp-6(dh1127)_regulated_OP50 | |
Fungi infection: Haptoglossa zoospora. | Transcripts that showed significantly altered expression after L4 N2 animals were exposed to omycete Haptoglossa zoospora for 6 hours. | Kalisto abundance files were converted and analysed using Sleuth in a R pipeline. Standard Sleuth protocols were used to calculate differential expression. P value < 0.01 and FDR < 0.01. | WBPaper00062354:H.zoospora_6h_regulated |
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 | |
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_downregulated | |
Transcripts that showed significantly increased 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)_upregulated | |
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 | |
Transcripts that showed significantly increased expression in animals fed with JM103 bacteria producing Cry5B, comparing to control animals fed with JM103. | ANOVA, p-value < 0.05. | WBPaper00056167:Cry5B_upregulated | |
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 | |
Transcripts that showed significantly increased expression in spr-1(ok2144) comparing to in N2. | DESeq2, fold change > 2, p-value < 0.01. | WBPaper00061203:spr-1(ok2144)_upregulated |
18 Expression Patterns
Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
---|---|---|---|---|
Expr4643 | A 4.5-kb reporter construct that spans from the fourth intron to the 3' noncoding region is sufficient to drive expression in the same tissues as seen with the 8-kb fragment (see Expr4642). No expression is seen in the vulC, vulD, vulE, and vulF cells during the L4 stage unless nhr-67 or cog-1 activity is eliminated. | |||
Expr4644 | An nhr-67 transcriptional reporter driven by 1 kb of its native promoter and containing regulatory sequences downstream of the fourth exon in their normal context. The nhr-67 transcriptional construct containing the endogenous promoter recapitulated the vulval and embryonic expression pattern observed with the nhr-67::[Delta]pes-10 constructs. See Expr4642 and Expr4643. | |||
Expr4645 | In the presence of the 6-kb promoter region, the vulval expression is identical to that of the 8-kb nhr-67::[Delta]pes-10 constructs (see Expr4642). Besides the previously reported expression in head neurons, expression was also observed in the anchor cell (AC) (during mid to late L3 stage) in hermaphrodites and the linker cell in males. | |||
Expr4642 | Expression was observed in the vulva, the hyp7 epidermal syncytium, late stage embryos, and the male tail. This nhr-67 construct exhibits a dynamic expression pattern in the vulval cells. During the late L4 stage, nhr-67 is first observed in vulA cells (and occasionally in vulB1), and this expression is maintained throughout adulthood. Expression in vulC is only seen upon entry into L4 lethargus and persists in adults. Strong vulB1 and vulB2 expression (and occasional vulD expression) is observed only in young adults. | |||
Expr2871 | The mRNAs for lin-42, nhr-23, and nhr-41a exhibit a low-high (peak)-low profile during the L1 intermolt that is precisely reiterated at later stages. The mRNAs for nhr-25a, nhr-25b, and nhr-41b have a high-low-high (peak) expression profile during the L1 stage (and into early L2) that is also reiterated. nhr-25a and nhr-41b also show a downward trend in baseline expression as development proceeds. For all six mRNAs, there are peaks of expression that occur at precise intervals relative to the molt at all larval stages: nhr-25b and nhr-41b peak at the beginning of the intermolt; nhr-23 peaks at mid-intermolt, slightly preceding the intermolt peak in lin-42 expression; and nhr-25a and nhr-41a peak at the time the larval molts occur. Two mRNAs, nhr-6 and nhr-85a, show a more irregular expression pattern with respect to the molt; however, it should be noted that nhr-6 mRNA has consistent relatively lower expression values at the times the molt takes place. nhr-67 also does not display a reiterated, oscillating expression pattern, although two early peaks are observed at the end of the L1 stage and at the beginning of L2. | |||
Expr1031698 | Tiling arrays expression graphs | |||
Clone: pUL#JRH/AA2 | Expr7425 | Strong expression is seen in approximately 6 head nerve cells from late embryogenesis onwards, although expression by the adult stage is weaker. Also expression is seen in a single cell in the mid body of mid larval stages and onwards that may be the utse cell from its shape. Some weak posterior intestinal expression (probably background artefact) is seen in the adult. | ||
Picture: Fig 6. | Expr8786 | Apart from cells in the neuroblast lineage that generate ASE, nhr-67::mCherry was expressed in multiple other neuroblast lineages in the developing embryo. Expression was usually observed in the grandmother or mother of a neuron, but not earlier. Within the ASEL and ASER-generating lineage branches, nhr-67 was expressed in neuroblasts that generate closely or distantly related cousins of ASEL and ASER. For example, the sister neuroblast of the ASE-generating neuroblast creates the AUA and ASJ neurons and it expressed nhr-67. The cousin of the ASE-mother cell generates the AWB and ADF sensory neurons. nhr-67 was expressed in these cells. In late stage embryos, a few other, postmitotic neurons started to express nhr-67. Embryonic nhr-67 expression was not restricted to the nervous system, but was observed in a small subset of mesodermal and hypodermal cells. No expression was detected in endodermal cells or the germ line. nhr-67 was expressed in the excretory canal cell. Postembryonically, nhr-67 expression persisted only in a few neurons in the head ganglia until the first larval stage and faded shortly thereafter in most, but not all, of these neurons, with expression persisting through adulthood only in the CEPD/V, RMED/V, AVL and RIS neurons. During mid-larval development, nhr-67 was transiently and dynamically expressed in the AC cells of the vulva. Expression was also found in the VU cells and somatic gonad, but not in vulA, vulB or vulC. Within the ASEL/R generating lineages, nhr-67::mCherry was first observed in the grandmother cells of ASEL and ASER. Transgenic animals that co-express a functional nhr-67::mCherry reporter and a functional che-1::yfp reporter revealed that nhr-67 precedes che-1 expression. nhr-67 expression was maintained in the ASEL and ASER neurons until the first larval stage after which it became undetectable, whereas che-1 expression was maintained throughout the life of the animal. In spite of its genetically deduced role in asymmetric gene expression in ASEL and ASER, nhr-67 expression is bilaterally symmetric in ASEL and ASER. | ||
Expr1200133 | Data from the TransgeneOme project | |||
Expr10383 | 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/ | |||
Expr10384 | 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/ | |||
Expr13015 | The nhr-67::mcherry transgene is continuously expressed in the linker cell. | |||
Expr9638 | nhr-67::gfp was expressed at all postembryonic stages in neurons of the head. nhr-67::gfp expression was not observed in uterine or vulval precursor in embryos or L1 larvae. In the L2 stage, nhr-67::gfp expression was observed in the 4 pre-VU precursor cells (Z1.ppa, Z1.ppp, Z4.aaa, Z4.aap) that become the AC and the three VU cells that give rise to the ventral uterus. Expression of nhr-67::gfp in the 4 pre-VU precursor cells appeared at or shortly after their birth. In the mid- to late-L2 stage, expression of nhr-67::gfp in the three VU cells decreased, while remaining at high levels (or possibly increasing) in the AC. During the L3 and early L4 stages, consistent and continual bright nhr-67::gfp expression was observed in the AC and more variable weak levels of expression were found in the six adjacent pi cells. nhr-67::gfp expression was very rarely detected in all 12 pi cells after their dorsal-ventral division. From early L4 through adulthood, weak expression of nhr-67::gfp was observed in all 8 UTSE cells or syncytium, suggesting that expression is turned off in all pi cells after their division and then re-expressed later in UTSE. Expression of nhr-67::gfp was observed in the UTSE before AC fusion. Bright expression of nhr-67::gfp in the AC nucleus was not observed after mid-L4, indicating that it is reduced after fusion of the AC with the UTSE syncytium. | |||
Reporter gene fusion type not specified. | Expr2863 | nhr-67DGFP exhibited a restricted expression pattern. nhr-67DGFP expression was only observed in six or seven head neurons. There was no vulval GFP expression in the nhr-67DGFP reporter line. | ||
Expr1144206 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
Expr1015998 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
Expr2014218 | 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). | |||
Expr2032459 | 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). |
27 GO Annotation
Annotation Extension | Qualifier |
---|---|
has_input(WB:WBGene00000584) | enables |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
involved_in | |
occurs_in(WBbt:0004522) | involved_in |
involved_in | |
involved_in | |
enables | |
involved_in | |
enables | |
enables | |
occurs_in(WBbt:0004522),happens_during(GO:0000080) | involved_in |
located_in | |
involved_in | |
involved_in | |
involved_in | |
involved_in | |
occurs_in(WBbt:0005062) | involved_in |
occurs_in(WBbt:0004522) | involved_in |
located_in | |
part_of(WBbt:0004522) | located_in |
5 Homologues
Type |
---|
least diverged orthologue |
least diverged orthologue |
least diverged orthologue |
least diverged orthologue |
least diverged orthologue |
27 Ontology Annotations
Annotation Extension | Qualifier |
---|---|
has_input(WB:WBGene00000584) | enables |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
enables | |
involved_in | |
occurs_in(WBbt:0004522) | involved_in |
involved_in | |
involved_in | |
enables | |
involved_in | |
enables | |
enables | |
occurs_in(WBbt:0004522),happens_during(GO:0000080) | involved_in |
located_in | |
involved_in | |
involved_in | |
involved_in | |
involved_in | |
occurs_in(WBbt:0005062) | involved_in |
occurs_in(WBbt:0004522) | involved_in |
located_in | |
part_of(WBbt:0004522) | located_in |
1 Upstream Intergenic Region
WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
---|---|---|---|---|---|
intergenic_region_chrIV_11166124..11169747 | 3624 | IV: 11166124-11169747 | Caenorhabditis elegans |