Genomics
22 Transcripts
Other
16 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:R10E4.2k | R10E4.2k |
1116
 |
III: 4277142-4277371 |
| CDS:R10E4.2m | R10E4.2m |
1317
|
III: 4277142-4277380 |
| CDS:R10E4.2o | R10E4.2o |
1125
|
III: 4277142-4277380 |
| CDS:R10E4.2q | R10E4.2q |
1431
|
III: 4277142-4277371 |
| CDS:R10E4.2d | R10E4.2d |
297
|
III: 4277354-4277371 |
| CDS:R10E4.2e | R10E4.2e |
306
|
III: 4277354-4277380 |
| CDS:R10E4.2j | R10E4.2j |
951
|
III: 4277354-4277371 |
| CDS:R10E4.2a | R10E4.2a |
1074
|
III: 4277354-4277380 |
| CDS:R10E4.2b | R10E4.2b |
1230
|
III: 4277354-4277380 |
| CDS:R10E4.2c | R10E4.2c |
453
|
III: 4277354-4277380 |
| CDS:R10E4.2f | R10E4.2f |
1065
|
III: 4277354-4277371 |
| CDS:R10E4.2g | R10E4.2g |
1143
|
III: 4277354-4277371 |
| CDS:R10E4.2i | R10E4.2i |
1221
|
III: 4277354-4277371 |
| CDS:R10E4.2l | R10E4.2l |
1395
|
III: 4277142-4277380 |
| CDS:R10E4.2n | R10E4.2n |
1239
|
III: 4277142-4277380 |
| CDS:R10E4.2r | R10E4.2r |
1275
|
III: 4277354-4277380 |
55 Allele
| Public Name |
|---|
| otn9732 |
| WBVar00245902 |
| WBVar01262919 |
| WBVar01262920 |
| ct49 |
| WBVar00059141 |
| gk403 |
| WBVar01709963 |
| WBVar01952136 |
| WBVar01396721 |
| gk426 |
| gk960901 |
| WBVar01994971 |
| WBVar01994970 |
| gk705238 |
| gk683920 |
| gk577657 |
| ma265 |
| gk516818 |
| gk688057 |
| gk624704 |
| ma315 |
| gk927574 |
| ma316 |
| gk378501 |
| gk620958 |
| gk804168 |
| gk907912 |
| gk545749 |
| gk711142 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00006331 | 4276196 | 4280224 | -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_chrIII_4272511..4276195 | 3685 | III: 4272511-4276195 | Caenorhabditis elegans |
252 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 |
| Genes that showed increased expression in wdr-5(ok1417) comparing with in N2. | Statistical analysis for misexpression was performed using a moderated t test from the package limma. All genes with a false discovery rate (FDR) of <= 5% (p <= 0.05) were selected as differentially regulated. | WBPaper00045861:wdr-5(ok1417)_upregulated | |
| Bacteria: E.faecalis strain OG1RF | Transcripts that showed significantly increased expression after infection by E. faecalis OG1RF. | Ballgown was used to calculate differential expression of genes using FPKM data and to generate tables with fold change and P values. Genes were shortlisted with a cutoff of 2-fold change and P values of less than 0.05. | WBPaper00059754:E.faecalis_OG1RF_upregulated |
| Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin and 250uM Allantoin from day 1 to day 3 adult hermaphradite. | DESeq2(v1.14.1), fold change > 2, p-value < 0.05 | WBPaper00055354:Rifampicin-Allantoin_upregulated | |
| 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 increased expression after animals were treated with 100uM Psora and 250uM Allantoin from day 1 to day 3 adult hermaphradite. | DESeq2(v1.14.1), fold change > 2, p-value < 0.05 | WBPaper00055354:Psora-Allantoin_upregulated | |
| Transcripts that showed significantly increased expression after animals were treated with 100uM Rapamycin and 50mM Metformin from day 1 to day 3 adult hermaphradite. | DESeq2(v1.14.1), fold change > 2, p-value < 0.05 | WBPaper00055354:Rapamycin-Metformin_upregulated | |
| 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 | |
| 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 that showed significantly increased expression in hda-1(RNAi) embryos comparing to control animals. | DESeq2, fold change > 2, FDR < 0.05. | WBPaper00067044:hda-1(RNAi)_upregulated | |
| Transcripts expressed in vulva. | FPKM >= 1. | WBPaper00064122:vulva_transcriptome | |
| 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 | |
| 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 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 12h), according to RNAseq. | Cuffdiff, ajusted p-value < 0.01. | WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h |
| 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 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 | |
| Bacteria infection: Staphylococcus aureus MW2. 4 hours of exposure. | Transcripts that showed significantly increased expression after N2 animals had 4 hours of infection by Staphylococcus aureus (MW2). | DEseq 1.18.0, adjusted p-value < 0.05. | WBPaper00056471:S.aureus-4h_upregulated_N2 |
8 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2035265 | 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). | |||
| Expr1032555 | Tiling arrays expression graphs | |||
| Expr13294 | SUP-26::Flag is ubiquitously expressed and cytoplasmically localized in later stages of embryonic development. In addition to germ cells, SUP-26::FLAG is expressed in the somatic gonad in the distal tip cell (DTC) and the hermaphrodite spermatheca. | SUP-26::Flag is expressed in the maternal germline and is maternally contributed to early embryos. SUP-26::Flag preferentially localizes to perinuclear bodies by the 24-cell stage; these were confirmed to be germline P granules by costaining with P-granule markers. | ||
| Based on data from the Nematode Expression Pattern DataBase (http://nematode.lab.nig.ac.jp), in situ hybridization experiments using either sup-26a or sup-26b cDNA as probes reveal that the sup-26 messages are absent from early meiotic-stage germ cells but are present in oocytes. Picture: Fig. 2. | Expr9139 | SUP-26::GFP was expressed in most, if not all, somatic cells, starting from the early gastrula through adulthood. There was no apparent difference in SUP-26::GFP expression patterns between male and hermaphrodite L4 larvae or adults. | SUP-26::GFP localized to the cytoplasm and was largely excluded from the nucleus. | |
| Expr12220 | sup-26 is expressed in the PVD and broadly throughout development excluding the germ line, which often silences repetitive DNA such as the extrachromosomal arrays generated by DNA microinjection in worms. | |||
| Expr12235 | SUP-26 translational fusion to GFP is localized to the cytoplasm. SUP- 26::GFP is restricted to the cytoplasm of the cell body and is not found in dendrites. SUP-26 has a striking perinuclear enrichment with intermediate-sized puncta, located further from the nucleus but still within the cell body. | |||
| Expr1155379 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr2017129 | 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). |
14 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| enables | |
| enables | |
| enables | |
| enables | |
| located_in | |
| located_in | |
| involved_in | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| part_of | |
| located_in |
12 Homologues
| Type |
|---|
| least diverged orthologue |
| least diverged orthologue |
| least diverged orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| least diverged orthologue |
| least diverged orthologue |
14 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| enables | |
| enables | |
| enables | |
| enables | |
| located_in | |
| located_in | |
| involved_in | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| part_of | |
| located_in |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrIII_4280225..4283599 | 3375 | III: 4280225-4283599 | Caenorhabditis elegans |
