Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:T05A6.1.1 | T05A6.1.1 |
809
 |
II: 7811240-7812105 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:T05A6.1 | T05A6.1 |
555
|
II: 7811259-7811467 |
52 RNAi Result
11 Allele
| Public Name |
|---|
| gk963801 |
| gk963053 |
| gk962682 |
| gk941931 |
| gk132 |
| gk673821 |
| gk549685 |
| gk575569 |
| gk403392 |
| gk147665 |
| gk883742 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00000516 | 7811240 | 7812105 | 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_chrII_7812106..7812602 | 497 | II: 7812106-7812602 | Caenorhabditis elegans |
283 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Genes with expression altered >= 3-fold in dpy-10(e128) mutants. | Data across the wild type series was analyzed using the Significance analysis of Microarrays (SAM) algorithm (to calculate the False Discovery Rate (FDR)). | WBPaper00035873:dpy-10_regulated | |
| 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 |
| 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 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 | |
| Transcripts that showed significantly increased expression in eft-2(RNAi) animals at N2 background. | DESeq2, fold change > 2 and p-value < 0.01. | WBPaper00067953:eft-2(RNAi)_upregulated_N2 | |
| Transcripts that showed significantly increased expression in eft-2(RNAi) animals at zip-2(tm4248) background. | DESeq2, fold change > 2 and p-value < 0.01. | WBPaper00067953:eft-2(RNAi)_upregulated_zip-2(tm4248) | |
| Transcripts that showed significantly increased expression in eif-2alpha(RNAi) animals at N2 background. | DESeq2, fold change > 2 and p-value < 0.01. | WBPaper00067953:eif-2alpha(RNAi)_upregulated_N2 | |
| Transcripts that showed significantly increased expression in eif-2alpha(RNAi) animals at zip-2(tm4248) background. | DESeq2, fold change > 2 and p-value < 0.01. | WBPaper00067953:eif-2alpha(RNAi)_upregulated_zip-2(tm4248) | |
| 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 | |
| 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 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 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 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 | |
| Bacteria: Pseudomonas donghuensis HYS | Transcripts that showed significantly increased expression after 24 hours of infection by Pseudomonas donghuensis HYS with deletion of ferric uptake regulator (FUR), comparing to control animals exposed to OP50. | DESeq2, fold change > 2, FDR < 0.05. | WBPaper00068216:FUR_vs_OP50_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 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 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 | |
| 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 |
| Genes that showed significantly increased expression in daf-2(e1370) comparing to in N2. | To identify DEGs, Students t test and the log2 median ratio test were performed to compute t values and median ratios for all the annotated genes. The adjusted P values from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjusted P values from the individual tests were combined to compute the overall P values using Stouffers method , and genes with overall P < 0.05 and fold change > 1.5 were selected as DEGs. | WBPaper00047131:daf-2(e1370)_upregulated_N2-background | |
| Transcripts that showed significantly changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals. | Sleuth | WBPaper00051558:aging_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 |
13 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr4691 | GFP was detected in epidermal cells including the head epidermal cells hyp1 to hyp5, the hyp7 syncytium, the tail epidermal cells hyp8 to hyp11, and the ventral Pn.p cells. GFP expression was also detected in the excretory duct cell. | |||
| Gene_regulation: The amount of anti-CKI-1 signal per distal nucleus in cul-2(ek1) gonads is 13-fold higher than in the wild type (13 plusminus 10 arbitrary units (a.u.), n = 50, versus 1.0 plusminus 0.9 a.u., n = 36). | Expr4746 | In the distal mitotic germ cells of wild-type animals, the amount of CKI-1 is low. As germ cells enter meiosis, the level of CKI-1 increases, with the highest intensity being observed in oocyte nuclei. | ||
| Expr4662 | cki-1 expression, detected by a cki-1 promoter::GFP fusion gene, was much higher in the Z1.aa/Z4.pp cells than in the Z1.ap/Z4.pa cells. | |||
| Expr1030306 | Tiling arrays expression graphs | |||
| Expression of reporters containing 2 or 6 kb of sequences upstream of the gene was not observed in the embryonic gut lineage. It has been shown that cell- or tissue-specific cis-regulatory elements of the Drosophila string/cdc25 gene, a developmentally controlled cell cycle regulator, extend over a 30 kb interval. Thus, it is conceivable that the spatiotemporal expression of cki-1 is also controlled by an extended stretch of cis-regulatory elements. The 20 kb region upstream of the cki-1 gene does not contain any predicted protein coding sequences and it is possible that a cis-acting element required for embryonic gut expression may reside 6kb upstream of the gene. Indeed, we found that when a cki-1 reporter gene was co-transformed with two cosmids containing ~30 kb of sequence upstream of the gene, the resultant extrachromosomal array, which is presumably generated by homologous recombination of the introduced DNA, expresses GFP in the gut cells at around the comma stage. However, the level of expression is too low and variable to identify in which gut cells GFP is expressed. Moreover, the cosmid T05A6, which contains about 11 kb upstream sequence of the cki-1 gene, can rescue the gut hyperplasia in mnDf100 embryos. | Expr2640 | cki-1 reporter expression is first detectable in a group of cells of the pharynx and nervous system at about six hours post-fertilization. This represents the time at which most cells in the embryo become postmitotic. Following this initial burst of expression, reporter expression expands to include most of the anteriorly located cells. | ||
| In the absence of food expression is very high in arrested larvae and then fades by 8-12h post-feeding. See Table 2 in the article cgc3201 for the stage/tissue type expression patterns of this locus. Lineage expression: SM lineage. This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope). | Expr608 | First detected at comma stage in pharyngeal primordium as pharyngeal muscles begin terminal differentiation. Strong expression is detected in most cells during late embryogenesis when cells are either differentiating or undergoing cell cycle arrest prior to hatching. At hatching and in L1 animals maintained in absence of food expression detected in Q, M, Z1, Z4 and V cells. Expression in these cells fades after feeding when cell division resumes. Strong expression is observed in many postmitotic neurons and muscle cells. Stronger expression is detected in newly differentiated cells and then gradually decreases. cki-1 also expressed in dauer larvae. 1. Lateral hyodermal V lineage: V cells show strong expression until they divide in the mid L1 (fluorescence decreases significantly). Seam cells express at quite high levels during resting phases between molts and at a reduced level during division. Expression increases at L4 (coincident with seam cell terminal differentiation). 2. sex myoblasts (SM)lineage: High level of expression observed during SM migration, reduced during SM division and high again as the sex muscles differentiate. 3. P lineage: L1-molt progeny of Pn.a neuroblasts express high levels of cki-1::gfp. 4. Somatic gonad: Expression in Z1 and Z4 diminishes prior to cell division in mid-L1. Strong expression in Z1.aa and Z4.pp, the distal tip cells, beginning in L2, undetectable in the rest of Z1/Z4 lineage until the late L3 and early L4. Expression in somatic gonad increases dramatically at the onset of terminal differentiation. 5. Intestine: After L1-molt expression in intestine is seen throughout the larval stages 6. Vulva precursor cells: cki-1::gfp expression first detected in vulva precursor cells (VPCs) in late L1 or early L2 and peaks at L2 molt. | ||
| Expr12576 | Using single molecule fluorescent in situ hybridization (smFISH), high levels of transcript for cki-1 (Cip/Kip family CDK inhibitor), which promotes G1 arrest, were found in the anchor cell. | |||
| Expr2010031 | 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). | |||
| Expr2028272 | 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). | |||
| Expr1156061 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr1026898 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr10546 | In pat-3(+) rescued animals, the appearance of CKI-1::GFP is a distinct fluorescent spot within a round green nucleus, suggesting nuclear and nucleolar localization. | |||
| Expr2998 | Nuclear CKI-1-GFP was detected in the VPCs of wild-type animals during late L1, the time at which the decision to arrest divisions is made. |
20 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| occurs_in(WBbt:0005792),happens_during(GO:0002119) | involved_in |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| occurs_in(WBbt:0005792),happens_during(GO:0002119) | involved_in |
| occurs_in(WBbt:0004522) | involved_in |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| occurs_in(WBbt:0004522),happens_during(GO:0000080) | involved_in |
| involved_in | |
| involved_in | |
| involved_in | |
| located_in | |
| enables | |
| involved_in | |
| enables |
11 Homologues
| Type |
|---|
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
20 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| occurs_in(WBbt:0005792),happens_during(GO:0002119) | involved_in |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| occurs_in(WBbt:0005792),happens_during(GO:0002119) | involved_in |
| occurs_in(WBbt:0004522) | involved_in |
| located_in | |
| located_in | |
| located_in | |
| located_in | |
| occurs_in(WBbt:0004522),happens_during(GO:0000080) | involved_in |
| involved_in | |
| involved_in | |
| involved_in | |
| located_in | |
| enables | |
| involved_in | |
| enables |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrII_7809410..7811239 | 1830 | II: 7809410-7811239 | Caenorhabditis elegans |
