Genomics
19 Transcripts
Other
19 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:C30D11.1i | C30D11.1i |
2238
 |
III: 4115385-4115393 |
| CDS:C30D11.1a | C30D11.1a |
2490
|
III: 4121464-4121724 |
| CDS:C30D11.1k | C30D11.1k |
2292
|
III: 4124822-4124884 |
| CDS:C30D11.1l | C30D11.1l |
2061
|
III: 4124822-4124884 |
| CDS:C30D11.1d | C30D11.1d |
2418
|
III: 4131277-4131465 |
| CDS:C30D11.1j | C30D11.1j |
2697
|
III: 4131277-4131465 |
| CDS:C30D11.1e | C30D11.1e |
2406
|
III: 4134230-4134406 |
| CDS:C30D11.1p | C30D11.1p |
2397
|
III: 4134230-4134406 |
| CDS:C30D11.1q | C30D11.1q |
2166
|
III: 4134230-4134406 |
| CDS:C30D11.1f | C30D11.1f |
2376
|
III: 4138712-4138858 |
| CDS:C30D11.1s | C30D11.1s |
2136
|
III: 4138712-4138858 |
| CDS:C30D11.1b | C30D11.1b |
2466
|
III: 4126594-4126830 |
| CDS:C30D11.1c | C30D11.1c |
2592
|
III: 4128501-4128863 |
| CDS:C30D11.1g | C30D11.1g |
2145
|
III: 4138712-4138858 |
| CDS:C30D11.1h | C30D11.1h |
2001
|
III: 4138712-4138858 |
| CDS:C30D11.1m | C30D11.1m |
2283
|
III: 4124822-4124884 |
| CDS:C30D11.1n | C30D11.1n |
2052
|
III: 4124822-4124884 |
| CDS:C30D11.1o | C30D11.1o |
2175
|
III: 4134230-4134406 |
| CDS:C30D11.1r | C30D11.1r |
2367
|
III: 4138712-4138858 |
21 RNAi Result
416 Allele
| Public Name |
|---|
| gk172211 |
| WBVar01262749 |
| WBVar01262753 |
| WBVar01262758 |
| WBVar01262754 |
| WBVar01262755 |
| WBVar01262756 |
| WBVar01262757 |
| sy557 |
| sy670 |
| sy673 |
| sy674 |
| WBVar01606998 |
| WBVar01541709 |
| gk445095 |
| WBVar01825487 |
| WBVar01656509 |
| WBVar01827646 |
| h6510 |
| h17933 |
| h9938 |
| h17759 |
| h17758 |
| h13728 |
| h3330 |
| h18207 |
| cxTi9970 |
| gk952892 |
| e1597n1214 |
| e1597 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00006830 | 4115385 | 4147278 | 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_4147279..4147424 | 146 | III: 4147279-4147424 | Caenorhabditis elegans |
142 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 |
| 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 | |
| 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 | |
| Genes significantly enriched in NSM neurons (isolated by FACS) versus the reference, according to RNAseq analysis towards total RNA. | Gene expression quantification and differential expression was analyzed using cufflinks v2.2.1. Enriched contains only genes significantly enriched (differentially expressed >= 2.4 fold in total RNA or >= 3.2 fold in DSN treated total RNA) in the NSM neurons versus the reference. | WBPaper00045974:NSM_enriched_totalRNA_RNAseq | |
| 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 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 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) | |
| 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 | |
| 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 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 altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage. | DESeq | WBPaper00053302:stavudine_24h_regulated | |
| 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 | |
| Genes that showed expression levels higher than the corresponding reference sample (L2 all cell 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:A-class-motor-neurons_L2-larva_expressed | |
| Transcripts that showed significantly increased expression in hpk-1(pk1393) comparing to in N2 at adult day 2. | DESeq 2, fold change > 2, FDR < 0.05. | WBPaper00065581:hpk-1(pk1393)_upregulated | |
| Genes down-regulated following nhr-25(RNAi). | Pair-wise significance testing (mutant/RNAi vs. wild-type/vector) was performed using the Bioconductor package limma and p-values were initially corrected for multiple testing using the false discovery rate (FDR) method of Benjamini and Hochberg. Authors defined differential expression as log2(ratio) >= 0.848 with the FDR set to 5%, and p-value <= 0.001. | WBPaper00045015:nhr-25(RNAi)_downregulated | |
| Transcripts that showed significantly increased expression in hda-1(ne4752[3xFLAG-Degron-HDA-1]) in gonads dissected from 1-day old adult animals. | Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R. | WBPaper00061479:hda-1(ne4752)_upregulated | |
| Transcripts that showed significantly increased expression in mep-1(ne4629[MEP-1-GFP-Degron]) in gonads dissected from 1-day old adult animals. | Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R. | WBPaper00061479:mep-1(ne4629)_upregulated | |
| Transcripts that showed significantly increased expression in ubc-9(ne4833[ubc-9(G56R)] in gonads dissected from 1-day old adult animals. | Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R. | WBPaper00061479:ubc-9(ne4833)_upregulated |
10 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Picture: Fig. 5C. | Expr4896 | Punc-103::GFP transcriptional fusion was expressed in many neurons in the nervous system, including some motor neurons along the ventral cord. | ||
| Expr2035969 | 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). | |||
| Expr3815 | From this construct, unc-103 also expresses in the pharyngeal neurons (I2 and NSM), head neurons [IL1, IL2, OLL, URAD, ASH, AVD, AUA, and SIAV and OLQ, RIV, URYV, AIN, and AIA, PCA in the post-cloacal sensilla, and one of two ray neurons in rays 1, 2, 3, 4, 6, and 9. An unc-103::YFP translational fusion expressed from the 8.7 kb upstream region was also injected and it was observed that the anal depressor, spicule protractor, retractor, and other male sex muscles also expressed UNC-103; in the hermaphrodite, the vulva muscles also express the transgene. | |||
| Expr2455 | unc-103::GFP construct expressed broadly in the head and ventral cord neurons in both males and hermaphrodites. In the male tail the SPC motor neurons and the PCB postcloacal sensory neurons expressed the construct. Many neurons express the construct, but because of variability in cell position and cellular localization of the fusion protein in processes, the list of unc-103-expressing cells is far from complete. In the head region ALA, ADL, ASK, AVH, AVJ, AIN, AVA, ASJ, SMDD, SIA, ADE, and AVD express the construct. In the tail region PHA, DVC, ALN, and PVP express the construct. The unc-103 fusion protein accumulates extensively in the processes of many ventral cord neurons; however, only some cells in the AS class of excitatory neurons was identified. In the adult hermaphrodite HSN expresses the unc-103::gfp construct. | The fusion protein aggregates mostly on the cytoplasmic membrane of neuronal processes and in many, but not all, cases of cell bodies. In larval hermaphrodites and males some of the cells had cell body localization of UNC-103::GFP. | ||
| Expr1032893 | Tiling arrays expression graphs | |||
| Data came from D.J.R, J.H.T., and R. Garcia, unpublished data. Reporter gene fusion type not specified. | Expr3095 | Studies using unc-103 promoter GFP reporter constructs reveal expression of unc-103 in body-wall muscle, egg-laying muscles, pharyngeal muscles, and neurons that innervate these tissues | ||
| Expr10803 | While high level of UNC-103E::GFP expression labels both the muscle arms and the vm cell bodies, low level of transgenic expression of UNC-103E::GFP with an integrated single-copy transgene showed that UNC-103E was dramatically enriched on vm2 muscle arms. | |||
| Expr1012330 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr2017833 | 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). | |||
| Expr1145556 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 |
18 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| involved_in | |
| enables | |
| enables | |
| enables | |
| enables | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| part_of | |
| located_in | |
| located_in | |
| located_in | |
| located_in |
11 Homologues
| Type |
|---|
| least diverged orthologue |
| least diverged orthologue |
| least diverged orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| least diverged orthologue |