Genomics
29 Transcripts
| Class | WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|---|
| MRNA | Transcript:C23F12.1a.1 | C23F12.1a.1 |
11450
 |
X: 9397701-9427246 |
| MRNA | Transcript:C23F12.1r.1 | C23F12.1r.1 |
9774
|
X: 9397752-9426683 |
| MRNA | Transcript:C23F12.1s.1 | C23F12.1s.1 |
10743
|
X: 9397752-9426683 |
| MRNA | Transcript:C23F12.1t.1 | C23F12.1t.1 |
10752
|
X: 9397752-9426683 |
| MRNA | Transcript:C23F12.1u.1 | C23F12.1u.1 |
9690
|
X: 9397752-9426683 |
| MRNA | Transcript:C23F12.1v.1 | C23F12.1v.1 |
10659
|
X: 9397752-9426683 |
| MRNA | Transcript:C23F12.1w.1 | C23F12.1w.1 |
9597
|
X: 9397752-9426683 |
| NcPrimaryTranscript | Transcript:C23F12.1b | C23F12.1b |
11340
|
X: 9397752-9426683 |
| MRNA | Transcript:C23F12.1e.1 | C23F12.1e.1 |
10241
|
X: 9397752-9427243 |
| MRNA | Transcript:C23F12.1g.1 | C23F12.1g.1 |
8815
|
X: 9404056-9427247 |
| MRNA | Transcript:C23F12.1g.2 | C23F12.1g.2 |
8723
|
X: 9405289-9427247 |
| MRNA | Transcript:C23F12.1h.1 | C23F12.1h.1 |
9120
|
X: 9405390-9426683 |
| MRNA | Transcript:C23F12.1i.1 | C23F12.1i.1 |
7965
|
X: 9405390-9426683 |
| MRNA | Transcript:C23F12.1j.1 | C23F12.1j.1 |
8595
|
X: 9407289-9426683 |
| MRNA | Transcript:C23F12.1k.1 | C23F12.1k.1 |
7440
|
X: 9407289-9426683 |
| MRNA | Transcript:C23F12.1g.3 | C23F12.1g.3 |
7863
|
X: 9409784-9427247 |
| MRNA | Transcript:C23F12.1g.4 | C23F12.1g.4 |
7743
|
X: 9409787-9427223 |
| MRNA | Transcript:C23F12.1c.1 | C23F12.1c.1 |
8331
|
X: 9409814-9426683 |
| MRNA | Transcript:C23F12.1d.1 | C23F12.1d.1 |
7739
|
X: 9409814-9427246 |
| MRNA | Transcript:C23F12.1g.5 | C23F12.1g.5 |
7711
|
X: 9412245-9427253 |
| MRNA | Transcript:C23F12.1l.1 | C23F12.1l.1 |
8163
|
X: 9412285-9426683 |
| MRNA | Transcript:C23F12.1m.1 | C23F12.1m.1 |
7008
|
X: 9412285-9426683 |
| MRNA | Transcript:C23F12.1n.1 | C23F12.1n.1 |
7971
|
X: 9413133-9426683 |
| MRNA | Transcript:C23F12.1o.1 | C23F12.1o.1 |
6816
|
X: 9413133-9426683 |
| MRNA | Transcript:C23F12.1g.7 | C23F12.1g.7 |
7335
|
X: 9414104-9427236 |
| MRNA | Transcript:C23F12.1g.6 | C23F12.1g.6 |
7445
|
X: 9414104-9427253 |
| MRNA | Transcript:C23F12.1p.1 | C23F12.1p.1 |
7248
|
X: 9415567-9426683 |
| MRNA | Transcript:C23F12.1q.1 | C23F12.1q.1 |
6093
|
X: 9415567-9426683 |
| MRNA | Transcript:C23F12.1f.1 | C23F12.1f.1 |
6732
|
X: 9417087-9426683 |
Other
22 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:C23F12.1a | C23F12.1a |
10836
|
X: 9397752-9397832 |
| CDS:C23F12.1r | C23F12.1r |
9774
|
X: 9397752-9397832 |
| CDS:C23F12.1u | C23F12.1u |
9690
|
X: 9397752-9397832 |
| CDS:C23F12.1v | C23F12.1v |
10659
|
X: 9397752-9397832 |
| CDS:C23F12.1w | C23F12.1w |
9597
|
X: 9397752-9397832 |
| CDS:C23F12.1j | C23F12.1j |
8595
|
X: 9407289-9407301 |
| CDS:C23F12.1k | C23F12.1k |
7440
|
X: 9407289-9407301 |
| CDS:C23F12.1d | C23F12.1d |
7176
|
X: 9409814-9409943 |
| CDS:C23F12.1m | C23F12.1m |
7008
|
X: 9412285-9412365 |
| CDS:C23F12.1o | C23F12.1o |
6816
|
X: 9413133-9413403 |
| CDS:C23F12.1g | C23F12.1g |
5670
|
X: 9417087-9418554 |
| CDS:C23F12.1f | C23F12.1f |
6732
|
X: 9417087-9418554 |
| CDS:C23F12.1c | C23F12.1c |
8331
|
X: 9409814-9409943 |
| CDS:C23F12.1e | C23F12.1e |
9681
|
X: 9397752-9397832 |
| CDS:C23F12.1h | C23F12.1h |
9120
|
X: 9405390-9405479 |
| CDS:C23F12.1i | C23F12.1i |
7965
|
X: 9405390-9405479 |
| CDS:C23F12.1l | C23F12.1l |
8163
|
X: 9412285-9412365 |
| CDS:C23F12.1n | C23F12.1n |
7971
|
X: 9413133-9413403 |
| CDS:C23F12.1p | C23F12.1p |
7248
|
X: 9415567-9415626 |
| CDS:C23F12.1q | C23F12.1q |
6093
|
X: 9415567-9415626 |
| CDS:C23F12.1s | C23F12.1s |
10743
|
X: 9397752-9397832 |
| CDS:C23F12.1t | C23F12.1t |
10752
|
X: 9397752-9397832 |
466 Allele
| Public Name |
|---|
| gk964260 |
| gk962707 |
| gk963732 |
| WBVar01927946 |
| WBVar01927947 |
| WBVar01927948 |
| WBVar01927949 |
| WBVar01927950 |
| WBVar01927951 |
| gk964126 |
| WBVar01758896 |
| WBVar01758897 |
| WBVar01887259 |
| WBVar01887260 |
| ttTi18237 |
| WBVar01887261 |
| WBVar01619729 |
| gk817748 |
| WBVar01987468 |
| gk428708 |
| gk486061 |
| WBVar01527484 |
| otn11684 |
| WBVar00243325 |
| gk915424 |
| WBVar01887242 |
| gk670185 |
| gk736202 |
| WBVar01527475 |
| WBVar01527474 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00016006 | 9397701 | 9427253 | 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_9427254..9428430 | 1177 | X: 9427254-9428430 | Caenorhabditis elegans |
253 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 | |
| Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons. | DESeq. False discovry rate (FDR) < 0.1. | WBPaper00048988:neuron_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:all-neurons_L1-larva_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 |
| 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 | |
| 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:AVE-neuron_L1-larva_expressed | |
| 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 |
| 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:bodywall-muscle_L1-larva_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 | |
| Genes that were downregulated in lin-15B(n744). | For each gene in each microarray hybridization experiment, the ratio of RNA levels from the two samples was transformed into a log2 value and the mean log2 ratio was calculated. The log2 ratios were normalized by print-tip Loess normalization (Dudoit and Yang, 2002). All genes with a false discovery rate of <= 5% (q <= 0.05) (Storey and Tibshirani, 2003) and a mean fold-change ratio of >= 1.5 were selected for further analysis. | WBPaper00038168:lin-15B(n744)_downregulated | |
| 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 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 higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc). | DESeq2, fold change >= 2, FDR <= 0.01. | WBPaper00056826:SGP_biased | |
| Genome-wide analysis of developmental and sex-regulated gene expression profile. | self-organizing map | cgc4489_group_18 | |
| Coexpression clique No. 60, 176662_at-Y53F4B.16, on the genome-wide coexpression clique map for the nematode GPL200 platform. | All available microarray datasets for the GPL200 platform (Affymetrix C. elegans Genome Array) were obtained from the GEO repository. This included 2243 individual microarray experiments. These were normalized against each other with the software RMAexpress (Bolstad, 2014). Based on these normalized values, Pearsons correlation coefficients were obtained for each probe-probe pair of the 22,620 probes represented on this array type. The resulting list of correlation coefficients was then ranked to generate the ranked coexpression database with information on each probe represented on the GPL200 platform. | WBPaper00061527:176662_at-Y53F4B.16 | |
| 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 that showed significantly decreased expression at 5-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites. | DESeq2, fold change > 2, FDR < 0.05 | WBPaper00065835:Day5_vs_Day1_downregulated | |
| 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 | |
| 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 | |
| Bacteria infection: Photorhabdus luminescens | Genes down-regulated in animals infected with Photorhabdus luminescens compared to the E. coli OP50 control after 24h of infection. | MAANOVA and BRB-Array-Tools. | WBPaper00030985:Photorhabdus_luminescens_downregulated |
| Transcripts that showed significantly increased expression in rrf-3(pk1426) comparing to in N2 at embryo stage. | DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01. | WBPaper00056169:rrf-3(pk1426)_upregulated_embryo | |
| Transcripts detected in germline isolated from day-1 adult hermaphrodite animals. | All three experiments have CPM >= 1. | WBPaper00067147:germline_expressed | |
| 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 after four-day-old young adult worms were placed on NGM plates seeded with OP50 in the presence 5% Agaro-oligosaccharides(AGO) for 24 h, comparing to animals grown in the absence of AGO. | Fold change > 2. | WBPaper00064306:Agaro-oligosaccharides_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 6h), according to RNAseq. | Cuffdiff, ajusted p-value < 0.01. | WBPaper00046497:B.thuringiensis_0.5mix_downregulated_6h |
8 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr9642 | Based on RNA-seq expression data from modENCODE it seems likely that fln-2a and b are only expressed during embryogenesis, while fln-2c and d are expressed throughout the life stages. Analysis of a series of GFP reporter constructs suggests the various isoforms of fln- 2 are expressed broadly, with strong expression in the hypodermis, pharynx, intestine, anal depressor muscle and distal tip cell. The modENCODE data suggests that the FLN-2C isoform might be the most strongly expressed version of FLN-2. | FLN-2C::GFP localizes in small puncta at the cell membranes of vulval and hypodermal cells and to the intestinal lumen. | ||
| Expr16312 | FLN-2 is expressed in the hypodermis including the main body syncytium hyp7 and the smaller head and tail hypodermal cells. In hyp7, FLN-2::GFP shows both vesicular and parallel stripe-like patterns. FLN-2::GFP co-localizes with VHA-5::RFP on the vesicular structures. The parallel stripe- like pattern of FLN-2 overlaps with VAB-10A, a component of the epidermal attachment structures called fibrous organelles (FOs), which suggests that FLN-2 also localizes to the FOs (Zhang and Labouesse, 2010). FLN-2 is also expressed in the kidney-like excretory canal cell, which is important for osmoregulation (Liegeois et al., 2006; Sundaram and Buechner, 2016). In the excretory canal, FLN-2::GFP is aligned at the apical side of VHA-5::RFP. | |||
| Expr2011820 | 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). | |||
| Expr1036836 | Tiling arrays expression graphs | |||
| Expr1025198 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr1145045 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr16559 | spGFP11::FLN-2c localized diffusely throughout the cytoplasm and was slightly enriched in the nucleoplasm. This diffuse pattern of FLN-2 localization was quite distinct from the localization pattern of actin observed in these cells, suggesting that the bulk of FLN-2does not co-localize to actin networks in P cells. | |||
| Expr2030058 | 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). |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrX_9395282..9397700 | 2419 | X: 9395282-9397700 | Caenorhabditis elegans |
