Genomics
2 Transcripts
WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
---|---|---|---|
Transcript:C14F11.5b.1 | C14F11.5b.1 |
1385
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X: 6233151-6235543 |
Transcript:C14F11.5a.1 | C14F11.5a.1 |
1307
![]() |
X: 6233152-6235541 |
Other
2 CDSs
WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
---|---|---|---|
CDS:C14F11.5a | C14F11.5a |
1107
![]() |
X: 6233327-6233448 |
CDS:C14F11.5b | C14F11.5b |
1182
![]() |
X: 6233327-6233448 |
46 Allele
Public Name |
---|
gk964260 |
WBVar01926926 |
gk460133 |
gk729243 |
gk368630 |
gk336813 |
gk583279 |
gk326449 |
gk808824 |
gk539793 |
gk963921 |
gk801021 |
gk803436 |
gk899701 |
gk551837 |
gk587706 |
gk373398 |
gk630008 |
gk340806 |
gk454579 |
gk551838 |
gk391255 |
gk602382 |
gk721825 |
tm359 |
WBVar00032891 |
WBVar01881061 |
WBVar01469264 |
tm12233 |
WBVar01881057 |
1 Chromosome Location
Feature . Primary Identifier |
Start | End | Strand |
---|---|---|---|
WBGene00002024 | 6233151 | 6235543 | -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_6233049..6233150 | 102 | X: 6233049-6233150 | Caenorhabditis elegans |
263 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 | |
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 | |
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 in pri-1(RNAi) animals comparing to in N2 animals fed with empty vector. | Differential expression analysis was performed quasi-likelihood F-test with the generalized linear model (GLM) approach in edgeR ver 3.32.1. FDR < 0.05, fold change > 2. | WBPaper00066418:pri-1(RNAi)_upregulated | |
Transcripts that showed significantly increased expression in hsf-1(sy441) vs. in N2 day 1 adults without heat shock. | edgeR, fold change > 2, FDR < 0.05 | WBPaper00066900:hsf-1(sy441)_upregulated | |
Fungi infection: Myzocytiopsis humicola | Transcripts that showed significantly altered expression 12 hours after animals were infected by M. humicola. | Differentially expressed genes as determined by Kallisto and Sleuth (pval<0.01, qval<0.1). | WBPaper00060871:M.humicola-infection_12h_regulated |
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 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 | |
mitochondrial sulfide delivery molecule (mtH2S) AP39 | Transcripts that showed significantly increased expression in N2 animals treated with mitochondrial sulfide delivery molecule (mtH2S) AP39 starting from 1-day-post L4 until 11 days post L4. | DESeq2, fold change > 2, FDR < 0.05 | WBPaper00065835:mtH2S-AP39-D0-treatment_upregulated_Day11 |
Genes up regulated in alg-1(gk214) comparing to in N2. | Differential expression was assessed using an empirical Bayes statistics using the eBayes function. | WBPaper00040823:alg-1(gk214)_upregulated | |
Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals. | Fold change > 2, FDR < 0.05 | WBPaper00064088:Day-1-adult_vs_L4_upregulated_daf-16(mu86);glp-1(e2141) | |
Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals. | Fold change > 2, FDR < 0.05 | WBPaper00064088:Day-1-adult_vs_L4_upregulated_fem-3(q20) | |
Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals. | Fold change > 2, FDR < 0.05 | WBPaper00064088:Day-1-adult_vs_L4_upregulated_glp-1(e2141) | |
Transcripts that showed significantly increased expression in day 3 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals. | Fold change > 2, FDR < 0.05 | WBPaper00064088:Day-3-adult_vs_L4_upregulated_fem-3(q20) | |
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 that showed significantly increased expression after 24 hours of induction of human beta Amyloid at young adult stage | A 2-fold change in expression level and a false discovery rate analog of p < 0.05. | WBPaper00064130:Beta-Amyloid_24h_upregulated_mRNA | |
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 in sin-3(tm1276) comparing to in N2. | DESeq2, fold change > 2, p-value < 0.01. | WBPaper00061203:sin-3(tm1276)_upregulated | |
Bacteria diet: Comamonas aquatica DA1887 vs. E. coli OP50 | Transcripts that showed significantly decreased expression in N2 L3 larva animals fed with Comamonas aquatica strain DA1887, comparing to in N2 L3 larva animals fed with E. coli OP50. | edgeR, fold change > 2, p-value < 0.05. | WBPaper00067248:C.aquatica_downregulated_L3 |
starvation 12 hours | Transcripts that showed significantly increased expression in dissected intestines of N2 L1 larva that were starved for 12 hours, comparing to fed animals. | EdgeR, FDR < 0.05, fold change >= 2. | WBPaper00067259:starvation_upregulated_intestine |
Transcripts that showed significantly decreased expression in morc-1(tm6048) animals, comparing to in N2, after growing at 25C for five generations (late generation). | CuffDiff2 | WBPaper00051265:F4_morc-1(tm6048)_downregulated | |
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 increased expression in nhr-114(gk849) comparing to wild type animals at L4 larva. | DESeq2 1.26.0, fold change > 2, FDR < 0.05. | WBPaper00064539:nhr-114(gk849)_upregulated |
9 Expression Patterns
Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
---|---|---|---|---|
Expr1031179 | Tiling arrays expression graphs | |||
Expr1118 | The tissue distribution of HSP43 is localized to specific cells of the vulva, to the spermathecal valve and junctions between cells of the spermathecal cage. It is also concentrated in regions of contact between muscle cells or between muscle cells and the overlying hypodermis. In males, HSP43 was also found to be concentrated in specialized structures of the tail, including rays, copulatory spicules and other structures too poorly resolved to permit reliable identification. This signal was HSP43-specific, and not due to autofluorescence of tail structures, since it was abolished when the antibody was pre-incubated with excess HSP43 protein. | |||
Picture: Figure 2. This pattern appears identical with that reported for monoclonal antibody MH5, which labels fibrous organelles containing hemidesmosomes associated with the hypodermis, where it contacts the muscle cells. Similar patterns, but differing in some details, were noted with monoclonal antibodies MH4 and MH46. The specificity of the antiserum for HSP43 is demonstrated by the loss of signal when the antibody is pre-incubated with excess pure recombinant HSP43. | Expr8560 | At the same developmental stages, HSP43 staining was seen in desmosomes of cells which make up the spermathecal cage and the spermathecal valve. L2 larvae, which lack vulva and spermatheca, showed prominent HSP43 staining anteriorly in the pharyngealintestinal valve, a structure made up of six cells coupled by a system of desmosomes, and posteriorly in a discreet region probably corresponding to the intestinalrectal valve. In both control and heat-shocked adult and L4 larvae a low level of staining was seen throughout the body, together with very strong, specific, staining in the vulva and spermatheca. In the vulval region, HSP43 was localized in the adherens junctions of vulval epithelial cells, but absent from vulval muscle. Images taken in different focal planes of the vulval region revealed HSP43 staining in the utse cells and in the uv1 cells. | In the vulval region, HSP43 was localized in the adherens junctions of vulval epithelial cells, In all post-embryonic stages, HSP43 staining was observed in a very regular punctate pattern over body-wall muscle, the columns of labelled spots running circumferentially along the muscle quadrant and the signal being more intense where the muscle cells contact each other. Individual bands could be resolved as doublets separated by a narrow space. | |
Expr15505 | HSP-43 was highly and exclusively expressed in the epidermis and displayed distinct parallel short stripe patterns characteristic of C elegans hemidesmosomes. | |||
Expr2012626 | 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). | |||
Expr1026872 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
Expr1200270 | Data from the TransgeneOme project | |||
Expr2030862 | 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). | |||
Expr1144614 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 |
5 GO Annotation
Annotation Extension | Qualifier |
---|---|
enables | |
located_in | |
located_in | |
involved_in | |
involved_in |
29 Homologues
Type |
---|
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
orthologue |
5 Ontology Annotations
Annotation Extension | Qualifier |
---|---|
enables | |
located_in | |
located_in | |
involved_in | |
involved_in |
1 Upstream Intergenic Region
WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
---|---|---|---|---|---|
intergenic_region_chrX_6235544..6235778 | 235 | X: 6235544-6235778 | Caenorhabditis elegans |