Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:R107.8.1 | R107.8.1 |
4555
 |
III: 9060221-9071472 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:R107.8 | R107.8 |
4290
|
III: 9060402-9060524 |
26 RNAi Result
254 Allele
| Public Name |
|---|
| gk964518 |
| gk963887 |
| otn11116 |
| otn8588 |
| otn9816 |
| q269 |
| otn13112 |
| gk401353 |
| gk435981 |
| gk578972 |
| gk866024 |
| gk371803 |
| gk720489 |
| gk473657 |
| gk724335 |
| gk919740 |
| gk397625 |
| gk574993 |
| gk889402 |
| gk739493 |
| gk562368 |
| gk733661 |
| gk912277 |
| gk527711 |
| gk477974 |
| gk917499 |
| gk485071 |
| gk551031 |
| gk460422 |
| gk899471 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00003001 | 9060221 | 9071472 | -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_9060182..9060220 | 39 | III: 9060182-9060220 | Caenorhabditis elegans |
152 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 | |
| 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 expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:intestine_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 |
| 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 |
| Maternal class (M): genes that are called present in at least one of the three PC6 replicates. | A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing. | [cgc5767]:expression_class_M | |
| 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 |
| Transcripts that showed significantly increased expression in alg-1(gk214), comparing to in N2. | DESeq2, Fold change > 1.5. | WBPaper00051404:alg-1(gk214)_upregulated | |
| Significantly upregulated genes from clk-1(qm30) microarrays using SAM algorithm with an FDR < 0.1 from adult-only chips. | SAM algorithm with an FDR < 0.1. | WBPaper00033065:clk-1(qm30)_upregulated | |
| Transcripts that showed significantly increased expression in animal with pgph-2 overepxreesion [pgph-2p-pgph-2; myo-2p-mcherry] in glucose excess condition. | Genes with anadjusted P-value <= 0.05 found by DESeq2 were assigned as differentially expressed. | WBPaper00065926:pgph-2(overepxreesion)_upregulated_glucose | |
| Transcripts that showed significantly increased expression in xrep-4(lax137). | DESeq2. Genes were selected if their p value < 0.01. | WBPaper00066062:xrep-4(lax137)_upregulated | |
| Reduced humidity (98% relative humidity). | Genes that were down-regulated after one day exposure to reduced humidity (98% relative humidity) according to microarray analysis. | Multiple hypothesis testing with the Benjamini-Hochberg correction was applied on calculated p-values. A change in the expression level was considered to be significant if the adjusted p-value was less than 0.001. | WBPaper00044578:reduced-humidity_downregulated_microarray |
| Transcripts that showed significantly increased expression in daf-2(e1370) comparing to in N2. | Differential gene expression analysis was performed using the quasi-likeli-hood framework in edgeR package v. 3.20.1 in R v. 3.4.1. | WBPaper00053810:daf-2(e1370)_upregulated | |
| Growth temperature | Transcripts that are significantly downregulated at 15C compared to both 25C and 20C, with no statistical difference between 25C and 20C, in worms feeding B. subtilis PY79. | DESeq2 and EdgeR, adjusted p-value < 0.05. | WBPaper00053814:15C_downregulated_PY79 |
| 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:GABAergic-motor-neurons_L2-larva_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 detected in germline isolated from day-1 adult hermaphrodite animals. | All three experiments have CPM >= 1. | WBPaper00067147:germline_expressed | |
| Genes that were not enriched in either spermatogenic fem-3(q96gf) nor oogenic fog-2(q71) gonads, according to RNAseq analysis. | To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq. | WBPaper00045521:Gender_Neutral | |
| Transcripts that showed altered expression from P0 to F2 generation animals after N2 parental generation were treated with antimycin, but not in damt-1(gk961032) P0 to F2 animals after the parenal generaton were treated with antimycin. | N.A. | WBPaper00055862:antimycin_damt-1(gk961032)_regulated | |
| Transcripts that showed significantly decreased expression in nhl-2(ok818) comparing to in N2 at 25C. | EdgeR, FDR < 0.05, fold change < 0.5. | WBPaper00055971:nhl-2(ok818)_25C_upregulated | |
| Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(+), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage. | DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2. | WBPaper00050859:upregulated_P-granule(-)GFP(+)_vs_control_day2-adult | |
| Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(-), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage. | DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2. | WBPaper00050859:upregulated_P-granule(-)GFP(-)_vs_control_day2-adult | |
| Transcripts that showed significantly increased expression in pgl-1(ct131) animals (isolated from SS0002[pgl-1(ct131)him-3(e1147)], comparing to in control animals SS1174, at 1-day post L4 adult hermaphrodite stage. | DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2. | WBPaper00050859:upregulated_pgl-1(ct131)_vs_control_day1-adult | |
| Heat shock: 34C 30min. | Transcripts that showed significantly increased expression in L2 larva stage C. elegans animals after incubated in a 34C water bath for 30min. | DESeq2 v 1.18.1, fold change > 2, FDR < 0.01. | WBPaper00058955:heatshock_upregulated_CE |
| Transcripts that showed significantly altered expression after 24 hour exposure to nitroguanidine (NQ). | Multivariate permutation tests with random variance model implemented in BRB-Array Tools version 4.5 were performed to infer differentially expressed genes (DEGs). One thousand random permutations were computed per chemical class (i.e., a group of 16 arrays or samples). The confidence level of false discovery rate assessment was set at 80%, and the maximum allowed portion of false-positive genes was 10%. | WBPaper00055899:nitroguanidine_regulated | |
| 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:hypodermis_L1-larva_expressed | |
| Transcripts unqiuely expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:intestine_enriched |
30 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr1031398 | Tiling arrays expression graphs | |||
| Expr1200164 | Data from the TransgeneOme project | |||
| Reporter gene fusion type not specified. | Expr3287 | Occasional LIN-12::GFP expression was observed in the RIG neurons of young larvae. Expression of LIN-12::GFP was detected in approximately 25% of L1/L2 animals. | ||
| Authors only analyzed the expression pattern of LIN-12 before and during intestinal twist. The patterns describe are not observed in embryos from lin-12(n941) hermaphrodites or from lin-12(RNAi) hermaphrodites, and are thus specific for LIN-12. | Expr1040 | LIN-12 expression is first detected at very low, but above background, levels in each of the cells in the E4 intestinal primordium. By the E8 stage, LIN-12 appears most abundant in cells in the right half of the primordium, and is present at lower or undetectable levels in cells in the left half. The left-right asymmetry in LIN-12 expression persists to the E16 stage, when dynamic changes in LIN-12 expression occur along the anterior-posterior axis of the primordium. At the E16 stage, LIN-12 is prominent in punctate structures near the midline of the primordium; these structures resemble in shape, position and timing of appearance the 'apical vesicles' described in an ultrastructural study of the primordium. | ||
| This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope). | Expr631 | LacZ staining is first detected in both Z1.pp and Z4.aa and is seen in Z1.ppp, Z4.aaa, Z1.ppa and Z4.aap. All four cells continue to express until the middle of the L2 stage during AC/VU decision and then expression is restricted to either Z1.ppp or Z4.aaa, with expression observed in presumptive VU (Z1.ppa and Z4.aap) but not in presumptive AC. This is consistent with GFP fluorescence observed. lin-12::lacZ staining disappears in the VUs; staining reappears in their daughters just after division. The level of lin-12::lacZ expression from early L2 until the Vulva Precursor Cells (VPCs) divide in the L3 is uniform in all 6 VPCs. lin-12::lacZ reporter is also expressed in all twelve of the granddaughters of the VUs. There appears to be a time during the early L3 stage when the VUs no longer express the lin-12::lacZ reporter gene. During L3, beta-gal activity is detected in two sheath cells in each gonad arm: sheath cells No. 1 (Z1.paaa, Z1.apa, Z4.pap, and Z4.appp). During early L4 stage, eight more sheath cells express the transgene: sheath cells No. 2 (Z1.paapaaa, Z1.appaaa, Z4.paappp, and Z4.appappp) and sheath cells No. 3 (Z1.paapaap, Z1.appaap, Z4.paappa, and Z4.appappa). Staining is almost always observed in sheath cells No. 1 in the L3 and L4 stages as well as in the young adult. Only a subset of animals consistently express the reporter gene in sheath cells No. 2. Staining in sheath cells No. 3 are never detected once the nuclei have migrated for out along the arm. Staining is observed in 12 sheath cells during the late L3/early L4 stages soon after they are born. As the cells move out the gonad arm, staining is only detected in one member of pair No. 1 and one member of pair No. 2 in each arm. Staining is detected during L4 in up to eight spermathecal cells [Z1.papaa(a/p) (d/v), Z4.apaaa(a/p)(d/v), Z1.pappp(a/p)(d/v) and Z4.apapp(a/p)(d/v)] in each arm. The progenitors of these cells [Z1.papaa(a/p), Z4.apaaa(a/p), Z1.pappp(a/p) and Z4.apapp(a/p)] also express the reporter gene. During the L2 and early L3 stages, lin-12::lacZ is expressed in all six VPCs. LacZ staining is detected in all 12 daughters of the VPCs (Pn.px stage), and is then restricted to P5.ppa, P5.ppp, P7.paa and P7.pap. High level of GFP expression is seen in the daughters of P5.p and P7.p but not in the daughters of p6.p. Variable level of GFP is detected in the daughters of P3,p, P4.p and P8.p. In the VPC granddaughters GFP is detected in P5.ppa, P5.ppp, P7.paa and P7.pap. Weak staining is detected in two of the granddaughters of P5.p and P7.p, the L cells, but is undetected in their progeny. Expression is always detected in the other two granddaughters of P5.p and P7.p, the N and T cells. There is no staining in the T descendants of P6.p cells. The N cells do not divide and staining is detected in both N cells throughout vulval morphogenesis in the L4 stage and in young adults. Staining can be detected in the T daughters in the L4 stage and in young adults. The parents of the SM/bm precursor cells; M.vlp and M.vrp and their dorsal equivalents, M.dlp and M.drp all express lin-12 reporter gene. After division of the parent cells, the SM/bm precursor cells and their dorsal equivalents also express the reporter gene as do the sisters of these cells. Expression is detected in both the SM and bm cells on the left and right sides of the animal. Staining persists in these cells on the ventral side even after it is no longer detectable in the cells of the dorsal side. [M.vrpa, M.vlpa, M.vrpp, M.vlpp, M.drpa, M.dla, M.drpp and M.dlpp]. Expression is detected in a discrete subset of cells during embryogenesis. Staining was only observed in pairs or groups of cells from the 28-cell stage to about the 400-cell stage. Two of the cells that express the gene in the >300-cell embryo may be the intestinal valve cells. Expression is seen in a discrete subset of cells in the ventral nerve cord of L1 larvae. There are three small nuclei that stain in the head region that may be G2, W, the excretory duct cell, G1 or the neuroblast that is the equipotent equivalent of the excretory cell. Staining was observed in the excretory cell. | ||
| Expr16149 | Focusing on larval development, we found that LIN-12::mNG::3xFlag was expressed in all postembryonic mesoderm progenitor cells at the 4M and 8M stages, but was only localized to the nucleus in ventral M-lineage cells, consistent with functions in dorsoventral patterning of the M lineage (Foehr & Liu, 2008). LIN-12::mNG::3xFlag was subsequently visible in somatic gonad cells and in several PN.p cells where lin-12 regulates cell fates (reviewed by Sternberg, 2005). LIN-12::mNG::3xFlag was visible at the cell membrane and in internalized punctae in the P3.p - P8.p cells but localized to the nucleus only in P5.p and P7.p. Following vulval precursor cell patterning, LIN-12::mNG::3xFlag was highly expressed in numerous somatic gonad cells, with nuclear localization in several spermatheca and uterine precursor cells. | |||
| Expr10737 | lin-12(1in_1408) displayed a highly differentiated, characteristic expression pattern in the VPC lineages. The expression was already evident in comma-stage embryos. Several glowing cells of different types were seen along the anteroposterior body axis at the twofold embryonic stage. At the L1 stage, lin-12(1in_1408) was expressed in all Pn.p cells. Some unidentified cells in the head and tail regions were also gfp-positive at this stage. By the early L2 stage, lin-12(1in_1408) expression remained strong only in the P(3-8).p cells. Unlike the other Pn.p cells, they remain unfused with the hypodermal syncytium, thereby retaining their competence to differentiate into a vulval cell type. After vulval induction at the early L3 stage, lin-12(1in_1408) was strongly expressed in P5.p and P7.p, the two VPCs that adopt 2nd vulval fates, but weakly detectable in the other VPCs, P(3-4,6,8).p. As shown earlier (Wilkinson and Greenwald, 1995; 276 Levitan and Greenwald, 1998), lin-12 expression remained on in the P5.p and P7.p granddaughters by the late L3 stage. In addition to the P5.p and P7.p descendants, we found obvious fluorescence in the daughters of other VPCs, and even in the P6.p granddaughters [the daughters of P(3,4,8).p fuse with the hypodermis]. Nevertheless, expression of lin-12(1in_1408) was constantly intense in the P5.p and P7.p lineages, as compared with other VPC lineages. At the L2 and early L3 stages, lin-12(1in_1408) is also expressed in the two AC/VU precursors. Later, when lin-12(1in_1408) expression became increased in P5.p and P7.p relative to the other VPCs, transgene activity was seen in the presumptive VU cell, but not in the AC. During the L4 stage, expression of lin-12(1in_1408) was gradually lost from the P6.p lineage; only the P(5,7).p descendants retained GFP fluorescence in the developing vulval tissue. It is worth to note that lin-12(1in_1408) was also active in certain hypodermal and intestinal cells throughout larval development, presumably due to background expression of the vector. In adult hermaphrodites, lin-12(1in_1408) expression could not be detected. The only exception was presented by a few unidentified cells in the posterior body part, probably due to background expression. | |||
| Expr10738 | At the comma stage embryo, faint lin-12(2in_490) fluorescence is detected in cells that are located ventrally along the anteroposterior body axis. These cells represent P blast precursors. At the L1-L2 stages, lin-12(2in_490) was abundantly expressed in the ventral nerve cord. Most, if not all, ventral nerve cord neurons expressed lin-12(2in_490), and both neurons and axonal bundles were glowing. These cells maintained a robust lin-12(2in_490) expression throughout larval development. | |||
| Reporter gene fusion type not specified. | Expr1613 | Reproducible beta-galactosidase expression was first observed in 24 cells at the 55-cell (32-AB-cell) stage in embryos carrying the lin-12::lacZ construct; variable staining was observed at the 28-, 46- and 50-cell stages. The positions of the beta-galactosidase-expressing cells suggested that all 24 expressing cells at the 55-cell stage were AB-derived. laser-ablation of AB in the 2-cell embryo eliminated all beta-galactosidase expression at a time corresponding to the wild-type 55-cell (32-AB-cell) stage. In intact transgenic embryos, beta-galactosidase expression persisted through at least one round of cell division. Again, because an engineered beta-galactosidase with a short half-life was used in the construction of the translational fusion, this observation may reflect continued expression of the lin-12 reporter. There were no reporter expression in either ABplaa or ABplpa. However, lin-12 expression was observed in the descendants of both of these cells. lin-12-expressing cells included ABplaaa and ABplpapp. | ||
| Expr13452 | LIN-12::GFP is expressed in the presumptive G2 and W but not in the presumptive duct or pore at ventral enclosure. | |||
| Starting plasmid pLB30 fully rescues lin-12(null) mutant. Integrated strain arIs41[lin-12::GFP] yields mostly wild-type hermaphrodites, with <5% showing weak lin-12 gain-of-function phenotype. | Expr544 | LIN-12::GFP protein is initially detectable in both Z1.ppp and Z4.aaa, and later in development becomes detectable in the presumptive VU but not in the presumptive AC. The LIN-12:: GFP protein is initially detectable in all six VPCs. However, in the mid-L3 stage, at the time of VPC specification, LIN-12::GFP is reduced in P6.p relative to the other VPCs, notably with respect to P5.p and P7.p. High LIN-12::GFP accumulation is always seen in the daughters of P5.p and P7.p, but LIN-12::GFP accumulation is not seen in the daughters of P6.p. There is variable accumulation of LIN-12::GFP in the daughters of P3.p, P4.p and P8.p. | In Z1.ppp and Z4.aaa, and in other gonadal cells, LIN-12::GFP is detectable over the entire surface of cells. However, in the VPCs, LIN-12::GFP is visible in the perinuclear region, which is probably endoplasmic reticulum/Golgi, and at the ventral (apical) surface and at the junctions between VPCs. | |
| Expr10804 | Transgenic animals carrying the lin-12::SL2::mCherry construct showed mCherry expression in a number of cell types including both the vm2 muscle cells and the vulval epithelial cells. Strikingly, no detectable lin-12 expression was observed in vm1 muscle cells. | |||
| Expr15707 | The translational LIN-12::GFP reporter was expressed on the apical membrane of the VPCs, while the LIN-18::GFP and PAT-3::GFP translational reporters localized predominantly to the basolateral compartment. | |||
| Expr10798 | lin-31p::cfp and LIN-12::GFP are expressed in multipotent VPCs during larval (L)2 stage and before induction in the L3 stage. lin-31p::cfp expression remains high in VPCs of dauer larvae. LIN-12::GFP remains expressed in VPCs in dauer larvae. | |||
| Expr1155347 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr12808 | lin-12::gfp expression was not detected in M lineage cells at the 1-M and 2-M stages. However, at the 4-M to 8-M stages, lin-12::gfp expression was observed in all M-derived cells, with the same intensity in both the dorsal and the ventral sides. At the 10-M stage and later, lin-12::gfp is still detected in both dorsal and ventral M-derived cells, but become more restricted along the anteroposterior axis. lin-12::gfp appears to be gradually lost in the anterior M lineage cells, but retained in the posterior M lineage cells that are the precursors of CCs (M.dlpa and M.drpa) and BWMs (M.dlpp and M.drpp) on the dorsal side and precursors of SM/BWMs (M.vlpa and M.vrpa) and BWMs (M.vlpp and M.vrpp) on the ventral side. | |||
| Expr11590 | LIN-12::GFP is present and membrane-localized in all SM sub-lineage cells from the 2-SM stage through the 8-SM stage. At the 16-SM stage the expression of LIN-12::GFP becomes restricted to the four SM descendants that are fated to become VM2s. As these cells begin to differentiate into VM2s, LIN-12::GFP becomes nuclear localized. Thus LIN-12 is present and activated in cells fated to become VM2s. LIN-12 is present in M.vlpaaap, M.vlpaapa, M.vrpaaap and M.vrpaapa cells. | |||
| Expr2013158 | 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). | |||
| Expr1026633 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr16148 | As expected, LIN-12::mNG::3xFlag localized primarily to the cell membrane, along with localized cytoplasmic domains that may represent endosomes. | |||
| Expr16150 | localized to the nucleus in ventral M-lineage cells | |||
| Expr16151 | LIN-12::mNG::3xFlag was visible at the cell membrane and in internalized punctae in the P3.p - P8.p cells but localized to the nucleus only in P5.p and P7.p. | |||
| Expr16152 | LIN-12::mNG::3xFlag was visible at the cell membrane and in internalized punctae in the P3.p - P8.p cells but localized to the nucleus only in P5.p and P7.p. | |||
| Expr16153 | LIN-12::mNG::3xFlag was highly expressed in numerous somatic gonad cells, with nuclear localization in several spermatheca and uterine precursor cells. | |||
| Expr2031390 | 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). | |||
| Expr15083 | GFP::LIN-12 showed a membrane localization pattern and showed co-localization with autophagic vesicles. | |||
| Original chronogram file: chronogram.621.xml | [R107.8:gfp] transcriptional fusion. | Chronogram1701 | ||
| Expr11942 | LIN-12::GFP accumulates at the apical membrane and in puncta at or below the membrane reminiscent of endocytic vesicles observed in C. elegans oocytes, coelomocytes and synaptic vesicles in neurons. In fact, simultaneous staining with an early endocytic marker showed that at least some of the LIN-12::GFP puncta are early endosomes. | |||
| Original chronogram file: chronogram.470.xml | [R107.8:gfp] transcriptional fusion. | Chronogram1588 | ||
| This information was extracted from published material (Archana Sharma-Oates, Andrew Mounsey and Ian A. Hope). | Expr773 | lin-12 transcript is abundant in early embryos but a substantial amount is seen in mid embryos as well. lin-12 transcript is abundant in embryos, present in a low level during larva development and in adults. |
51 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| part_of | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| enables | |
| enables | |
| enables | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| occurs_in(WBbt:0005785) | involved_in |
| involved_in | |
| involved_in |
12 Homologues
| Type |
|---|
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| orthologue |
51 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| part_of | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| enables | |
| enables | |
| enables | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| occurs_in(WBbt:0005785) | involved_in |
| involved_in | |
| involved_in |
40 Strains
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrIII_9071473..9074703 | 3231 | III: 9071473-9074703 | Caenorhabditis elegans |
