Genomics
11 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:T07H8.4a.1 | T07H8.4a.1 |
6150
 |
V: 6956537-6966425 |
| Transcript:T07H8.4d.1 | T07H8.4d.1 |
6090
|
V: 6956537-6966401 |
| Transcript:T07H8.4d.2 | T07H8.4d.2 |
5989
|
V: 6956637-6966352 |
| Transcript:T07H8.4j.1 | T07H8.4j.1 |
768
|
V: 6956638-6957968 |
| Transcript:T07H8.4i.1 | T07H8.4i.1 |
2865
|
V: 6956638-6960653 |
| Transcript:T07H8.4c.1 | T07H8.4c.1 |
3504
|
V: 6956638-6961338 |
| Transcript:T07H8.4b.1 | T07H8.4b.1 |
5280
|
V: 6956638-6965058 |
| Transcript:T07H8.4h.1 | T07H8.4h.1 |
6021
|
V: 6956638-6966352 |
| Transcript:T07H8.4f.1 | T07H8.4f.1 |
5945
|
V: 6956736-6966352 |
| Transcript:T07H8.4e.1 | T07H8.4e.1 |
5865
|
V: 6957078-6966352 |
| Transcript:T07H8.4g.1 | T07H8.4g.1 |
4815
|
V: 6958798-6966352 |
Other
10 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:T07H8.4a | T07H8.4a |
6024
|
V: 6956638-6956778 |
| CDS:T07H8.4b | T07H8.4b |
5058
|
V: 6956638-6956778 |
| CDS:T07H8.4g | T07H8.4g |
4815
|
V: 6958798-6959517 |
| CDS:T07H8.4c | T07H8.4c |
3504
|
V: 6956638-6956778 |
| CDS:T07H8.4d | T07H8.4d |
5988
|
V: 6956638-6956778 |
| CDS:T07H8.4e | T07H8.4e |
5865
|
V: 6957078-6957398 |
| CDS:T07H8.4f | T07H8.4f |
5457
|
V: 6957565-6957601 |
| CDS:T07H8.4h | T07H8.4h |
6021
|
V: 6956638-6956778 |
| CDS:T07H8.4i | T07H8.4i |
2865
|
V: 6956638-6956778 |
| CDS:T07H8.4j | T07H8.4j |
768
|
V: 6956638-6956778 |
160 Allele
| Public Name |
|---|
| gk963301 |
| gk963553 |
| gk964259 |
| gk964351 |
| gk963850 |
| gk964527 |
| gk962860 |
| gk964528 |
| WBVar01973969 |
| gk633957 |
| gk238337 |
| gk238336 |
| WBVar01973970 |
| gk238358 |
| gk238357 |
| gk238361 |
| gk238360 |
| gk238359 |
| gk238339 |
| gk238338 |
| gk238346 |
| gk238345 |
| gk238344 |
| gk238343 |
| gk238342 |
| gk238341 |
| gk238340 |
| gk238350 |
| gk238349 |
| gk238348 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00003165 | 6956537 | 6966425 | 1 |
4 Data Sets
| Name | URL |
|---|---|
| WormBaseAcedbConverter | |
| GO Annotation data set | |
| C. elegans genomic annotations (GFF3 Gene) | |
| Panther orthologue and paralogue predictions |
179 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 expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons. | DESeq. False discovry rate (FDR) < 0.1. | WBPaper00048988:neuron_expressed | |
| 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 | |
| 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 |
| 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 | |
| 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 | |
| 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 decreased expression in eat-2(ad465) comparing to in N2. | DESeq2 1.30.1, fold change > 2, FDR < 0.05. | WBPaper00066890:eat-2(ad465)_downregulated | |
| Transcripts that showed significantly increased expression in eft-2(RNAi) animals at N2 background. | DESeq2, fold change > 2 and p-value < 0.01. | WBPaper00067953:eft-2(RNAi)_upregulated_N2 | |
| Transcripts that showed significantly increased expression in eif-2alpha(RNAi) animals at N2 background. | DESeq2, fold change > 2 and p-value < 0.01. | WBPaper00067953:eif-2alpha(RNAi)_upregulated_N2 | |
| Transcripts that showed significantly increased expression in eif-2alpha(RNAi) animals at zip-2(tm4248) background. | DESeq2, fold change > 2 and p-value < 0.01. | WBPaper00067953:eif-2alpha(RNAi)_upregulated_zip-2(tm4248) | |
| Genes that are significantly up regulated in tdp-1(ok803) poly(A) RNA-seq verses in N2. | DESeq v1.14, with cut-off p-value < 0.05 and FDR < 0.1. | WBPaper00046012:tdp-1(ok803)_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 | |
| 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 | |
| Genes with expression level regulated by genotype (N2 vs CB4856) 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_regulated_aging | |
| 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) | |
| 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) | |
| Bacteria: Pseudomonas donghuensis HYS | Transcripts that showed significantly increased expression after 24 hours of infection by Pseudomonas donghuensis HYS with deletion of ferric uptake regulator (FUR), comparing to control animals exposed to OP50. | DESeq2, fold change > 2, FDR < 0.05. | WBPaper00068216:FUR_vs_OP50_upregulated |
| 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 hrde-1(tm1200) animals, comparing to in N2, after growing at 25C for five generations (late generation). | CuffDiff2 | WBPaper00051265:F4_hrde-1(tm1200)_upregulated | |
| Transcripts that showed significantly increased expression in exos-8(RNAi) animals. | fold change > 2, FDR < 0.05 | WBPaper00068292:exos-8(RNAi)_upregulated | |
| 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 | |
| Genes that showed significantly increased expression in daf-2(e1370);hel-1(gk148684) comparing to in hel-1(gk148684) | To identify DEGs, Students t test and the log2 median ratio test were performed to compute t values and median ratios for all the annotated genes. The adjusted P values from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjusted P values from the individual tests were combined to compute the overall P values using Stouffers method , and genes with overall P < 0.05 and fold change > 1.5 were selected as DEGs. | WBPaper00047131:daf-2(e1370)_upregulated_hel-1(gk148684)-background | |
| Genes that showed significantly increased expression in daf-2(e1370) comparing to in N2. | To identify DEGs, Students t test and the log2 median ratio test were performed to compute t values and median ratios for all the annotated genes. The adjusted P values from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjusted P values from the individual tests were combined to compute the overall P values using Stouffers method , and genes with overall P < 0.05 and fold change > 1.5 were selected as DEGs. | WBPaper00047131:daf-2(e1370)_upregulated_N2-background | |
| Transcripts that showed significantly decreased expression in N2 animals exposed to 0.1mM Paraquat from hatching to reaching adult stage. | DESeq2 version 1.22.2, p < 0.05 | WBPaper00064716:paraquat_downregulated | |
| Transcripts that showed significantly decreased expression in N2 day 4 adults comparing to in N2 day 1 adult animals according to Illumina RNASeq. | DESeq fold change > 2, FDR < 0.05. | WBPaper00067499:Day4_vs_Day1_downregulated_Illumina | |
| Transcripts that showed significantly decreased expression in N2 day 5 adults comparing to in N2 day 1 adult animals according to Illumina RNASeq. | DESeq fold change > 2, FDR < 0.05. | WBPaper00067499:Day5_vs_Day1_downregulated_Illumina | |
| Transcripts that showed significantly decreased expression in N2 day 7 adults comparing to in N2 day 1 adult animals according to Illumina RNASeq. | DESeq fold change > 2, FDR < 0.05. | WBPaper00067499:Day7_vs_Day1_downregulated_Illumina |
6 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr1031500 | Tiling arrays expression graphs | |||
| Because of the expression in non-touch receptor neurons, mec-1 (also tagged with gfp) was tested whether could rescue the Mec phenotype when expressed from the touch receptor neurons-specific mec-18 promoter. Touch receptor expression was sufficient for rescue (three strains produced 90% +/- 5% touch-sensitive animals; N = 70). LacZ expression was used to test protein topology with respect to the plasma membrane, because cytoplasmic, but not extracellular, beta-galactosidase is active . When lacZ was fused directly after the DNA for the predicted signal sequence, no beta-galactosidase activity was found, suggesting that the resulting fusion protein is extracellular. Insertion of an artificial transmembrane domain after the signal sequence restored activity. beta-galactosidase activity was also absent when lacZ was fused at codon 45, directly after sequence for the weakly predicted transmembrane domain. As before, insertion of a sequence encoding an artificial transmembrane domain before lacZ restored activity. These results suggest that MEC-1 does not contain a transmembrane domain between residues 21 and 41. | Expr3463 | The mec-1 promoter expressed GFP in the touch receptor neurons, many lateral neurons (the SDQ, PLN, and ALN neurons and two neurons of the dorsal sublateral cord), the PVT neuron, and the intestinal muscle. | Expression of a full-length MEC-1::GFP protein fusion from the mec-1 promoter rescued the mec-1(e1496) null phenotype and revealed that MEC-1 was processed differently in touch receptor neurons. The fusion protein was visible in the ER of the same non-touch cells seen with the promoter fusion and in some neurons of the ventral cord, but it was not seen along their processes. In contrast, MEC-1::GFP was consistently visible in the ER and along the processes of the touch receptor neurons. In addition, MEC-1::GFP was sometimes seen along the edge of the body wall muscles. Since these cells did not express the promoter fusion, this muscle fluorescence suggests that MEC-1 is a secreted protein. | |
| Expr1156414 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr2013495 | 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). | |||
| Expr1026744 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr2031729 | 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). |
19 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| located_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| enables | |
| enables | |
| enables | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables |
5 Homologues
| Type |
|---|
| least diverged orthologue |
| orthologue |
| orthologue |
| orthologue |
| least diverged orthologue |
19 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| located_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| enables | |
| enables | |
| enables | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrV_6956144..6956536 | 393 | V: 6956144-6956536 | Caenorhabditis elegans |
