Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:R13A5.5.1 | R13A5.5.1 |
921
 |
III: 7555660-7558041 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:R13A5.5 | R13A5.5 |
609
|
III: 7555661-7555973 |
41 RNAi Result
31 Allele
| Public Name |
|---|
| gk964518 |
| gk963887 |
| sw1 |
| WBVar01265579 |
| WBVar01990179 |
| WBVar01628815 |
| unk27 |
| WBVar00065668 |
| gk178507 |
| WBVar01645475 |
| gk549154 |
| gk409004 |
| gk328403 |
| gk421903 |
| gk771914 |
| gk663497 |
| gk551024 |
| gk905002 |
| gk601956 |
| ok737 |
| pk20 |
| gk329480 |
| gk523633 |
| gk795973 |
| gk640979 |
| gk351514 |
| WBVar01837889 |
| gk390210 |
| WBVar01837888 |
| gk357296 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00000437 | 7555660 | 7558041 | 1 |
3 Data Sets
| Name | URL |
|---|---|
| WormBaseAcedbConverter | |
| GO Annotation data set | |
| C. elegans genomic annotations (GFF3 Gene) |
1 Downstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrIII_7558042..7562171 | 4130 | III: 7558042-7562171 | Caenorhabditis elegans |
140 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons. | DESeq. False discovry rate (FDR) < 0.1. | WBPaper00048988:neuron_expressed | |
| Genes significantly enriched (> 2x, FDR < 5%) in a particular cell-type versus a reference sample of all cells at the same stage. | 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_larva_enriched | |
| 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 |
| 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 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:bodywall-muscle_L1-larva_expressed | |
| Transcripts that showed significantly decreased expression at 5-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites. | DESeq2, fold change > 2, FDR < 0.05 | WBPaper00065835:Day5_vs_Day1_downregulated | |
| 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 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 sin-3(tm1276) comparing to in N2. | DESeq2, fold change > 2, p-value < 0.01. | WBPaper00061203:sin-3(tm1276)_upregulated | |
| Genes that showed significantly increased expression in daf-2(e1370);hel-1(gk148684) comparing to in hel-1(gk148684) | 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_hel-1(gk148684)-background | |
| 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 | |
| Transcripts that showed significantly decreased expression in 10-days post L4 adult hermaphrodite npr-8(ok1439) animals grown at 20C, comparing to in N2 animals. | CuffDiff, fold change > 2. | WBPaper00065096:npr-8(ok1439)_downregulated_Day10_20C | |
| 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 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 mbl-1(syb4345), referred to as mbl-1long(ex7+), comparing to in N2 at L4 larva stage. | DESeq2, Fold change > 2 and FDR < 0.05 | WBPaper00066410:mbl-1(syb4345)_upregulated | |
| Genes that showed expression levels higher than the corresponding reference sample (L3/L4 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:dopaminergic-neurons_L3-L4-larva_expressed | |
| 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 | |
| Genes that showed expression levels higher than the corresponding reference sample (L3/L4 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:hypodermis_L3-L4-larva_expressed | |
| Genes significantly enriched (> 2x, FDR < 5%) in a particular cell-type versus a reference sample of all cells at the same stage. | 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_larva_enriched | |
| Genes that showed expression levels higher than the corresponding reference sample (L3/L4 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:PVD-OLL-neurons_L3-L4-larva_expressed | |
| Transcripts that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage. | DESeq2, fold change > 2, FDR < 0.05. | WBPaper00066594:ilc-17.1(syb5296)_upregulated | |
| Transcripts that showed significantly increased expression in srbc-48(ac23);kyIs262;fer-1(b232ts) comparing to in kyIs262;fer-1(b232ts), 24h after infection with P.aeruginosa. | DESeq2, FDR <0.05, fold change > 2. | WBPaper00059664:srbc-48(ac23)_upregulated | |
| Transcripts that showed significantly decreased 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_downregulated |
38 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2009860 | 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). | |||
| Expr1030247 | Tiling arrays expression graphs | |||
| Clone: pUL#JRH/AH08 | Expr7642 | Expression is first seen in comma stage embryos with four pairs of nuclei in anterior regions. Expression is seen postembryonically in the dorsal nerve cord, plus a cell in nerve ring. Expression is also seen in the adult vulva. | ||
| Expr10740 | CEH-13 was present in almost all neurons of the pharyngeal nerve ring and ventral nerve cord at the adult stage. For example, several amphid neurons, such as ASK, ASI, ASH, and ASJ, were positive for GFP fluorescence. Moreover, we found that a few posteriorly localized neurons, such as the PHB phasmid neuron, also accumulate CEH-13. | |||
| Expr15563 | ||||
| Expr2562 | Another notable aspect of ceh-13 expression in ray complexes 5, 7, and 9 was its cell-specific regulation. At the beginning of L4, the highest levels of protein were present in A- and B-type neurons, intermediate levels in the support cells, and lowest levels in hypodermal cells. Protein levels were higher in hyp7 than in hyp5,9. Upon tail retraction, expression in hyp7 was transiently upregulated and maintained high until mid-L4. At this point, there was upregulation of expression in st5, 7, and 9 and downregulation in all neuroblasts, as well as in hyp7. During tail morphogenesis in late L4 and in the course of ray shaping, significant upregulation of cytoplasmic CEH-13::GFP reporter levels occurred in structural cells, particularly around the papillae. In tests for ceh-13 expression in the sensory rays, ray-specific CEH-13 and CEH-13::GFP expression was detected shortly after the L3 moult, concomitantly with completion of the last divisions of the precursor cells. The protein initially exhibited uniform cytoplasmic distribution, then rapidly accumulated in the nuclei. On the basis of the complex patterning and dynamics of expression, two aspects of activity could be defined. In the first, ceh-13 was expressed in the A-type neurons of all rays, although lower levels were seen in the ventral ray groups 2, 4, and 8. This expression persisted until mid-L4 and was switched off thereafter except in ray 9. Thus, with the exception of R9A, detectable levels of protein were no longer present in the A-type neurons by the time of ray morphogenesis and the emergence of papillae. In the second aspect, CEH-13 and CEH-13::GFP were specifically expressed in the dorsal ray groups 5, 7, and 9, where they were present in all cells after completion of the last division of the precursor cells. Detectable levels of protein rapidly disappeared from the hypodermal cells in groups 5 and 9 but persisted in the hypodermal cell of 7 until the beginning of tail retraction. Three other ceh-13-expressing cells, R(5,7,9).aap, underwent apoptotic cell death shortly after division of the anterior neuroblasts that generated them. Thus, at the beginning of tail retraction, remaining ceh-13 activity could be observed exclusively in ray groups 5, 7, and 9, i.e., in B-type neurons of 5 and 7, in the A-type neuron of 9, and in the structural cells of 5, 7, and 9. The first expression of CEH-13 in the male tail was detected during the third larval stage (L3) in B_gamma. Upon division of the B_gamma cell, the protein became equally distributed between the anterior and posterior daughters B_gamma.a and B_gamma.p, but subsequently disappeared in B_gamma.p. CEH-13 and CEH-13::GFP expression in B_gamma.a was accompanied by subcellular redistribution of the protein, with an increase in nuclear and a decrease in cytoplasmic accumulation. After division of B_gamma.a, CEH-13 exhibited exclusive nuclear localisation in the two daughters B_gamma.al and B_gamma.ar. Also during L3, sex independent expression of CEH-13 in the tail region could be observed in an asymmetric neuron tentatively identified as Ql.ap. In the L4, several additional unidentified expressing cells were observed. | Expression was both cytoplasmic and nuclear, and the nuclear expression appeared stronger in the region of the nucleolus. | ||
| Expr12542 | ceh-13 was expressed in both ALM and PLM neurons. | |||
| Expr12585 | ceh-13 was expressed in both ALM and PLM neurons, although the expression in PLM was much weaker. | |||
| Expr15184 | In wild type, cnd-1p::mCherry and ceh-13p::GFP showed a complex and partially overlapping expression pattern in the retrovesicular ganglion and ventral nerve cord, with around two cells co-expressing cnd-1 and ceh-13 in the ganglion and an average of 4.1 cells co-expressing in the ventral nerve cord. | |||
| In situ hybridization showed that ceh-13 mRNA was not present at early embryonic stages. It appeared first in E.p and then in the AB.xxxp cells, only a short time before CEH-13. Transgenic Marker: rol-6(su1006). Subcellular localization: : Nuclear in E.p, cytoplasmic in AB.xxxp. Nuclear in E.p and Ab.xxxp daughters. In situ hybridization showed that ceh-13 mRNA was not present at early embryonic stages. It appeared first in E.p and then in the AB.xxxp cells, only a short time before CEH-13. Transgenic Marker: rol-6(su1006). | Expr513 | Expressed weakly in intestinal precursor, E.p, at 26-cell stage embryo at the beginning of gastrulation. Expressed in E.p and AB.xxxp daughters and in D.a and D.p. See Expression pattern 512 for expression later in development. | Nuclear in E.p, cytoplasmic in AB.xxxp. Nuclear in E.p and Ab.xxxp daughters. | |
| Feature : "ceh-13/lin-39_temp_I1" | Expr11423 | Region I1 drove expression in seam cells, starting with the embryo and continuing through to young adults. | ||
| Feature : "ceh-13/lin-39_temp_I0" | Expr11422 | Region I0 drove expression in the ventral posterior coelomocytes and the two anterior inner longitudinal muscles of the male tail. | ||
| Removal of the most upstream 1.5-kb HindIII fragment from pMF1 did not affect the expression pattern. The 3.4-kb HindIII fragment (enh3.4) is responsible for a large part of the normal embryonic ceh-13 expression pattern. The 1.2-kb HindIII fragment (enh1.2) is located more proximal to the coding region of pMF1. This fragment appears not to be required for embryonic expression, but drives expression of a GFP reporter gene in larvae and adults, for example, in the male tail. Reporter gene fusion type not specified. The enhancer region of ceh-13 contains different regulatory regions that are responsible for various aspects of the developmental expression pattern of this gene. | Expr1771 | pMF1, like the endogenous ceh-13 gene, is first expressed at the onset of gastrulation in the posterior daughters of the intestinal precursor cell E (Ep) and of the AB descendants ABxxx (ABxxxp). During later embryogenesis, CEH-13::GFP is detected in many different tissues and cell types. At the comma stage, for example, it is expressed in the lateral hypodermal cells H2 and V2, in anterior dorsal hypodermal and body wall muscle cells and in cells of the prospective ventral nerve cord (VNC). | ||
| Feature : "ceh-13.enh3.4" WBsf919526 | Expr11275 | The 3.4-kb HindIII fragment is responsible for a large part of the normal embryonic ceh-13 expression pattern. If cloned into pPD107.94, a gfp reporter gene plasmid containing a minimal promoter derived from the pes-10 gene, enh3.4 was able to drive an early embryonic GFP expression pattern indistinguishable from that of the endogenous ceh-13. In comma-stage embryos, enh3.4 recapitulated a large part of the normal ceh-13 expression pattern, including expression in cells of the future VNC and embryonic dorsal hypodermal and body wall muscle cells.However, we also observed some ectopic reporter gene expression in the posterior endoderm and in a few non identified cells of the posterior part of comma-stage embryos. | ||
| Feature : "ceh-13.enh740" WBsf919528 | Expr11276 | The terminal 740 bp (enh740) of enh3.4, when cloned into pPD107.94, were sufficient to initiate the correct early embryonic expression pattern. During the comma stage, however, enh740 failed to induce important aspects of the GFP expression pattern seen with the entire enh3.4. Particularly, GFP expression in embryonic dorsal body wall muscle cells and cells of the future VNC was missing. | ||
| Feature : "ceh-13/lin-39_temp_N11" | Expr11421 | Region N11 was in the proximal promoter region of ceh-13 and drove expression in the anterior hypodermis of late embryos. | ||
| Expr514 | E.p and daughters during gastrulation, then fades during morphogenesis. No staining seen in larval or adult intestine; AB.xxxp and their daughters during gastrulation; D.a and D.p during gastrulation; unidentified anterior embryonic cells, other cells in AB, MS and D lineages throughout embryogenesis. Strongly expressed in H2L, H2R, V1L, V1R at comma stage embryo. Also seen in anterior dorsal hypodermal cells and anterior body wall muscle cells at comma stage Embryo. Ventral nerve cord, lateral hypodermal and dorsal hypodermal cells show strong expression at L1. H2L and H2R show weak expression at L1. V1.pxx cells do not show expression at L1, but all V1 through V4 descendants show expression at L2. Expressed in male tail at unspecified stage. | |||
| Reporter gene fusion type not specified. See Expr1771 for expression pattern of pMF1 and enhancer analysis. The enhancer region of ceh-13 contains different regulatory regions that are responsible for various aspects of the developmental expression pattern of this gene. | Expr1772 | enh3.4 was able to drive an early embryonic GFP expression pattern indistinguishable from that of the endogenous ceh-13. In comma-stage embryos, enh3.4 recapitulated a large part of the normal ceh-13 expression pattern, including expression in cells of the future VNC and embryonic dorsal hypodermal and body wall muscle cells. However, some ectopic reporter gene expression was observed in the posterior endoderm and in a few nonidentified cells of the posterior part of comma-stage embryos. | ||
| Feature : "ceh-13/lin-39_temp_N3" | Expr11417 | Region N3 was expressed in the hypodermal hyp7 cells in the late embryo and early L1 larvae as well as in the V cells, P cells, and ventral nerve cord of the early L1 through L3 larvae. | ||
| Feature : "ceh-13/lin-39_temp_N4" | Expr11418 | Region N4 is in the proximal promoter region of lin-39; it drove expression in the ventral mid-body of the early embryo shortly after gastrulation. During early larval development N4 also drove expression in V6. | ||
| Feature : "ceh-13.enh450" WBsf919527 | Expr11274 | The most upstream located 450 bp (enh450) of enh3.4 were sufficient to drive most aspects of the normal ceh-13 expression pattern in comma-stage embryos. enh450 was able to drive GFP expression in dorsal body wall muscle cells and cells of the future VNC. Interestingly, the strong endodermal expression observed with enh740 was not induced by these constructs, suggesting that enh740 and enh450 are responsible for different aspects of ceh-13 expression during the comma stage. The most important difference between enh740 and enh450, however, is that early embryonic GFP expression induced by enh740, could not be detected with the two enh450-containing constructs. | ||
| Feature : "ceh-13/lin-39_temp_N7" | Expr11419 | Region N7 drove expression in the posterior bodywall muscle cells, starting in the late embryo and continuing through adulthood, and in the diagonal and longitudinal muscles of the male tail. | ||
| Feature : "ceh-13/lin-39_temp_N9" | Expr11420 | Region N9 drove previously reported embryonic expression, along with previously unreported anterior body wall muscle expression in L4 larvae and adults. | ||
| Feature : "ceh-13/lin-39_temp_W2" | Expr11426 | W2, a large region spanning N7, N8, and N9, directs expression in both the anterior and posterior body wall muscles, demonstrating additive coexpression of N7 and N9. | ||
| Feature : "ceh-13/lin-39_temp_N1" | Expr11415 | The intronic element N1 drove expression in vulval muscle, starting during the L4 larval stage and continuing through the adult. | ||
| Feature : "ceh-13/lin-39_temp_N2" | Expr11416 | Region N2 was expressed in the ventral nerve cord during the L1 larval stage. Expression of region N2 was also seen in some P cells and in the neural precursor Q cells. | ||
| Expr16256 | For ceh-13, we found that the fosmid-based reporter wgIs756[ceh-13::EGFP] was only expressed in the embryos and no significant GFP signal was detected in larvae or adult animals. However, Tihanyi et al. reported that a transcriptional reporter ceh-13p::GFP, which contains 8.1 kb sequence upstream of the start codon, was expressed in larval stages and in many cell lineages during development. To investigate this discrepancy, we generated a GFP knock-in at the ceh-13 locus through CRISPR/Cas9-mediated gene editing and found that the expression of endogenous ceh-13::GFP was only observed in the early embryos, similar to wgIs756[ceh-13::EGFP]. Although we occasionally observed very weak ceh-13::GFPexpression in some presumably ventral nerve cord motor neurons in adults, we werenot able to consistently identify the neurons that showed the weak GFP signal. So, we concluded that the expression of ceh-13 is mostly restricted to the embryonic stages, and its expression in terminally differentiated cells is rather weak and may be below our detection limit. | |||
| Expr1020412 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr2028100 | 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). | |||
| Original chronogram file: chronogram.1115.xml | [R13A5.5:gfp] transcriptional fusion. | Chronogram108 |
12 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| involved_in | |
| located_in | |
| involved_in | |
| involved_in | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| located_in | |
| located_in | |
| located_in |
12 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| involved_in | |
| located_in | |
| involved_in | |
| involved_in | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| located_in | |
| located_in | |
| located_in |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrIII_7545156..7555659 | 10504 | III: 7545156-7555659 | Caenorhabditis elegans |
