Genomics
11 Transcripts
| Class | WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|---|
| MRNA | Transcript:F54F2.2a.2 | F54F2.2a.2 |
5270
 |
III: 8791535-8806289 |
| MRNA | Transcript:F54F2.2a.3 | F54F2.2a.3 |
4764
|
III: 8791545-8806289 |
| MRNA | Transcript:F54F2.2a.4 | F54F2.2a.4 |
5211
|
III: 8791545-8806289 |
| MRNA | Transcript:F54F2.2b.1 | F54F2.2b.1 |
1668
|
III: 8791827-8794319 |
| MRNA | Transcript:F54F2.2a.5 | F54F2.2a.5 |
4312
|
III: 8792486-8806289 |
| NcPrimaryTranscript | Transcript:F54F2.2d | F54F2.2d |
3894
|
III: 8792847-8806274 |
| MRNA | Transcript:F54F2.2a.6 | F54F2.2a.6 |
3470
|
III: 8794031-8806289 |
| MRNA | Transcript:F54F2.2a.7 | F54F2.2a.7 |
3773
|
III: 8794409-8806289 |
| MRNA | Transcript:F54F2.2a.1 | F54F2.2a.1 |
3373
|
III: 8798398-8806305 |
| MRNA | Transcript:F54F2.2c.1 | F54F2.2c.1 |
2812
|
III: 8799533-8806287 |
| MRNA | Transcript:F54F2.2c.2 | F54F2.2c.2 |
2706
|
III: 8802819-8806288 |
Other
3 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:F54F2.2c | F54F2.2c |
1908
|
III: 8802954-8803421 |
| CDS:F54F2.2a | F54F2.2a |
2604
|
III: 8798555-8798663 |
| CDS:F54F2.2b | F54F2.2b |
636
|
III: 8792847-8792947 |
49 RNAi Result
222 Allele
| Public Name |
|---|
| gk964518 |
| gk963887 |
| gk471755 |
| gk507356 |
| gk879107 |
| gk888202 |
| gk381488 |
| gk317148 |
| gk367516 |
| gk466648 |
| gk471235 |
| gk335503 |
| gk394016 |
| gk894017 |
| gk355277 |
| gk570867 |
| gk930400 |
| gk469795 |
| gk595056 |
| gk522280 |
| gk674526 |
| gk568333 |
| gk816160 |
| gk479372 |
| gk404729 |
| gk713178 |
| gk518877 |
| gk587367 |
| gk456719 |
| gk559630 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00006975 | 8791535 | 8806305 | 1 |
4 Data Sets
| Name | URL |
|---|---|
| WormBaseAcedbConverter | |
| GO Annotation data set | |
| C. elegans genomic annotations (GFF3 Gene) | |
| Panther orthologue and paralogue predictions |
135 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 | |
| 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 | |
| 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 |
| 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 |
| Proteins interacting with NHR-49-GFP according to co-IP and LC-MS. | N.A. | WBPaper00064071:NHR-49_interacting | |
| Transcripts expressed in the epithelial tissues surrounding the pharynx that includes the arcade and intestinal valve (AIV) cells, according to PAT-Seq analysis using Pbath-15-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:arcade_intestinal-valve_expressed | |
| 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 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 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 | |
| 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 | |
| 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 | |
| Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:pharynx_expressed | |
| 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 expressed in vulva. | FPKM >= 1. | WBPaper00064122:vulva_transcriptome | |
| 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 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 | |
| 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 | |
| Proteins that showed significantly decreased expression after 1-day-old wild type adults were exposed to cisplatin (300ug per mL) for 6 hours. | The differential expression analysis was performed in R. Differentially expressed proteins were identified by using a two-sided t-test on log-transformed data. | WBPaper00065373:Cisplatin_downregulated_WT | |
| 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 | |
| Transcripts that showed significantly altered expression in rnp-6(dh1127) animals comparing to in N2 when fed with live S. aureus. | 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_S.aureus | |
| Transcripts that showed significantly decreased 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)_downregulated | |
| Proteins interacting with HA-PPM-1.D. | N.A. | WBPaper00062498:PPM-1.D_interacting | |
| Bacteria: B.thuringiensis | Transcripts in elt-2(RNAi) animals that were significantly differentially expressed at least for one time point and one pathogenic strain Bt247 and Bt679 compared to the non pathogenic strain Bt407. | Cuffdiff | WBPaper00060358:B.thuringiensis_pathogen_regulated_elt-2(RNAi) |
| Bacteria: B.thuringiensis | Transcripts in N2 animals that were significantly differentially expressed at least for one time point and one pathogenic strain Bt247 and Bt679 compared to the non pathogenic strain Bt407. | Cuffdiff | WBPaper00060358:B.thuringiensis_pathogen_regulated_N2 |
| Transcripts that showed decreased expression in hlh-11(ko1) knockout strain comparing to in wild type background. | DESeq2, FDR < 0.05 | WBPaper00060683:hlh-11(ko1)_downregulated |
9 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Another strain generated with this plasmid, UL191, shows similar expression to UL256, though the component involving the seam cell expression is weaker and expression of the intestinal nuclei is stronger. Legacy Data: "Bauer PK" "Hope IA"Date 1998-01. | Expr107 | In adults nuclear-localised expression is observed in the hypodermal seam cells running from the head to the tail and in additional cells of the tail that could be the phasmids. There is some expression in other sites which may be artefactual. Weak and non-localised expression is also occasionally seen in late embryos and young larvae. Young larvae may exhibit strong non-localised staining of the pharynx which may persist to later stages. Expression has also been seen in the posterior intestinal nuclei or non-localised throughout the intestine. Such expression has been attributed to use of incomplete promoters but the upstream region in pUL#PB27 is 2.7kb, which is quite large and includes all but 1kb of the intergenic region. | ||
| Expr2036265 | 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). | |||
| Expr1032980 | Tiling arrays expression graphs | |||
| Expr10609 | ZFP-1::GFP was expressed in somatic cells at all developmental stages of C. elegans. High expression in oocytes and lower expression in the distal germline was observed.Immunostaining showed high expression in maturing oocyte nuclei and lower expression in the rest of the germline. The long isoform of the protein is expressed in the germline, while the short isoform is not. The immunostaining results are consistent with the expression patterns of the short and long isoforms of ZFP-1 determined by western, where the long isoform is predominantly expressed in embryos and in adult worms with developed germline tissue and the short isoform more abundant at the larval stages. The authors conclude that only the long ZFP-1 isoform is expressed in the germline and localizes to chromosomes there. | Consistent with immunostaining, ZFP-1::GFP localization is seen at the condensed chromosomes in oocytes; the ZFP-1::GFP protein binds to all six condensed chromosomes. The authors conclude that only the long ZFP-1 isoform is expressed in the germline and localizes to chromosomes there. | ||
| Expr13643 | The zfp-1(2c) promoter drove GFP expression uniformly in the worm. | |||
| Expr1152158 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr1012254 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr2018128 | 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). | |||
| Expr13644 | The zfp-1(2a) promoter-driven expression was noticeably absent from the pharynx, germline and the tail regions. |
18 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| part_of | |
| located_in | |
| located_in | |
| located_in | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables |
7 Homologues
| Type |
|---|
| orthologue |
| orthologue |
| orthologue |
| least diverged orthologue |
| least diverged orthologue |
| least diverged orthologue |
| least diverged orthologue |
18 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| part_of | |
| located_in | |
| located_in | |
| located_in | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables |
2 Regulates Expr Cluster
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Genes with expression level down in zfp-1 mutant background. | Sets of probesets with up- or down-regulated expression in the mutants relative to WT were determined via t test (two-tailed, homoscedastic) with a P value cutoff of 0.01, requiring in addition an average expression difference of 1.5 or greater on the natural scale. | WBPaper00032425:down_in_zfp-1 | |
| Genes with expression level up in zfp-1 mutant background. | Sets of probesets with up- or down-regulated expression in the mutants relative to WT were determined via t test (two-tailed, homoscedastic) with a P value cutoff of 0.01, requiring in addition an average expression difference of 1.5 or greater on the natural scale. | WBPaper00032425:up_in_zfp-1 |