Genomics
5 Transcripts
| Class | WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|---|
| MiRNAPrimaryTranscript | Transcript:C05G5.6.2 | C05G5.6.2 |
891
 |
X: 14743590-14744480 |
| MiRNAPrimaryTranscript | Transcript:C05G5.6.3 | C05G5.6.3 |
707
|
X: 14743590-14744296 |
| MiRNAPrimaryTranscript | Transcript:C05G5.6.1 | C05G5.6.1 |
1732
|
X: 14743590-14745321 |
| MiRNA | Transcript:C05G5.6b | C05G5.6b |
22
|
X: 14744191-14744212 |
| MiRNA | Transcript:C05G5.6a | C05G5.6a |
22
|
X: 14744234-14744255 |
Other
52 Allele
| Public Name |
|---|
| gk964260 |
| gk964029 |
| gk962707 |
| gk964028 |
| gk963810 |
| gk963581 |
| WBVar01928581 |
| q782 |
| tm11366 |
| gk301756 |
| gk501874 |
| gk301755 |
| WBVar01760444 |
| ma422ma423 |
| h11385 |
| WBVar00085527 |
| WBVar00085529 |
| WBVar00085528 |
| WBVar00085531 |
| WBVar01679712 |
| WBVar00085530 |
| WBVar00085532 |
| zen162 |
| zen165 |
| zen168 |
| WBVar01942208 |
| zen171 |
| WBVar01942207 |
| ma393 |
| ma388 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00002285 | 14743590 | 14745321 | -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_chrX_14740120..14743589 | 3470 | X: 14740120-14743589 | Caenorhabditis elegans |
47 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| 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 | |
| Transcripts that showed significantly decreased expression in atfs-1(cmh15) (null allele) animals comparing to in N2 animals at L4 larva stage. | edgeR, fold change > 2, FDR < 0.05 | WBPaper00060909:atfs-1(cmh15)_downregulated | |
| Transcripts that showed differential expression between 24 and 26 hours post hatching L2d and dauer committed larvae of daf-9(dh6), triggered by the dafachronic acid (DA) growth hormone. Cluster 3 genes increased expression transiently at 26 hour post hatching. | Benjamini Hochberg corrected q-value < 0.01. | WBPaper00053388:dauer_regulated_Cluster3 | |
| 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 | |
| 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 increased expression in daf-2(e1370) neurons comparing to in N2 neurons at day 8adult stage. | DESeq2, FDR < 0.05, fold change > 2. | WBPaper00066978:daf-2(e1370)_upregulated_neuron | |
| Transcripts that showed significantly increased expression in daf-16(mu86);daf-2(e1370) neurons comparing to in daf-2(e1370) neurons at day 8adult stage. | DESeq2, FDR < 0.05, fold change > 2. | WBPaper00066978:daf-16(mu86)_upregulated_neuron | |
| Transcripts that showed significantly decreased expression in whole animal day 1 N2 adults comparing to in whole animal day 8 N2 adults. | DESeq2, FDR < 0.05, fold change > 2. | WBPaper00066978:Day1Adult_vs_Day8Adult_downregulated_neuron | |
| Transcripts that showed significantly increased expression in ints-1(RNAi) animals comparing to control RNAi animals, at late L3 larva stage. | DESeq2, v1.12.0, fold change > 2, FDR < 0.05 | WBPaper00057068:ints-4(RNAi)_upregulated | |
| Bacteria infection: Pseudomonas aeruginosa PA14. 24 hours of exposure. | Small RNAs (21-26nt) that showed significantly increased expression after L4 animals were exposed to P .aeruginosa strain PA14 for 24 hours. | DESeq2, FDR < 0.05 | WBPaper00056868:P.aeruginosa_upregulated_smallRNA |
| Bacteria diet: Sphingomonas aquatilis Yellow. Fed for 30 generations. | Transcripts that showed significantly increased expression after fed by bacteria Sphingomonas aquatilis (Yellow) for 30 generations comparing to animals fed by E. coli OP50. | DESeq2 fold change > 2, p-value < 0.01. | WBPaper00061007:S.aquatilis_upregulated |
| Transcripts that showed significantly increased expression in jmjd-5(zr1234) comparing to in N2 animals. | DESeq2, adjusted p value < 0.01 and absolute log2FC > = 1. | WBPaper00062156:jmjd-5(zr1234)_upregulated | |
| Transcripts that showed significantly decreased expression in numr-1/2(RNAi) animals comparing to control RNAi animals, at late L3 larva stage. | DESeq2, v1.12.0, fold change > 2, FDR < 0.05 | WBPaper00057068:numr-1(RNAi)_downregulated | |
| Transcripts that showed significantly increased expression in hsp-6(mg585) comparing to in N2 at L4 larva stage. | EdgeR, fold change > 2, FDR < 0.001. | WBPaper00056290:hsp-6(mg585)_upregulated | |
| Transcripts that showed significantly decreased expression in BAT525 [hmg-3 (tm2539) / dpy-5(e61) unc-13(e1091) I.] comparing to in N2 at 1-day post L4 adult hermaphrodite stage | DESeq 2, fold change > 4, adjusted p-value < 0.05. | WBPaper00055013:hmg-3(bar24)_downregulated | |
| Potental DAF-12 target genes identified by ChIP-chip analysis performed on strain ALF4 [daf-12 | Affymetrix TAS software that computed for each probe estimates of fold enrichment (in linear scale) over hybridization with input DNA. At the same time, TAS calculated for each probe a p-value by applying a Wilcoxon signed rank test. A threshold of 2.5 was selected, which corresponds to probe intensities approximately 2.5 times stronger on the ChIP array than on the Input array. Additional TAS threshold parameters were MinRun=180 bp, MaxGap=300 bp. TAS analysis showed that the selected threshold of 2.5 corresponds approximately to a p-value of 0.01. | WBPaper00040221:DAF-12_target_ALF4 | |
| Transcripts that showed significantly decreased expression in nfki-1(cer1) animals at L4 larva stage, comparing to in N2 animals. | Differentially expressed genes between wild type and knockouts were explored using DESeq2 R package (v.1.20.0) considering a threshold of adjusted p value < 0.01. | WBPaper00060445:nfki-1(cer1)_downregulated_L4 | |
| Transcripts that showed significantly increased expression in mdt-15(mg584gf) comparing to in N2 at L4 larva stage. | EdgeR, fold change > 2, FDR < 0.001. | WBPaper00056290:mdt-15(mg584)_upregulated | |
| Genes that showed significantly increased expression after exposure to 1mg/L MWCNTs from L1 larva to young adult. | Transcripts with false discovery rate-corrected p-values < 0.05 and fold change > 2 were defined as differentially expressed. | WBPaper00049377:MWCNT_upregulated | |
| Transcripts that were enriched in muscle in young adult animals, according to trans-splicing-based RNA tagging (SRT) and RNAseq. | DESeq and Benjamini-Hochberg adjusted p-values were used. | WBPaper00050053:muscle_enriched_Day4 | |
| Transcripts that showed significantly increased expression in animals exposed to 2.5mM ketamine since L1 larva stage. | DESeq2 (1.20.0), fold change > 2, p-value < 0.05. | WBPaper00064788:ketamine_upregulated | |
| Transcripts that showed significantly increased expression in spt-16(RNAi) comparing to in vector control worm at L4 larva stage. | DESeq 2, fold change > 4, adjusted p-value < 0.05. | WBPaper00055013:spt-16(RNAi)_downregulated | |
| Transcripts that showed significantly decreased expression in ikb-1(nr2027) animals at L4 larva stage, comparing to in N2 animals. | Differentially expressed genes between wild type and knockouts were explored using DESeq2 R package (v.1.20.0) considering a threshold of adjusted p value < 0.01. | WBPaper00060445:ikb-1(nr2027)_downregulated_L4 | |
| Transcripts that showed significantly decreased expression in set-26(tm2467) animals comparing to in N2. | edgeR, 5% FDR. | WBPaper00054410:set-26(tm2467)_downregulated | |
| Micro RNAs that showed significantly decreased expression in day 8 adults comparing to in day 1 adults in intestine. | Differentially expressed miRNAs were identified using DEGseq based on unique molecular identifier (UMI). A minimum UMI sum of 10 in 3 replicates was set as the threshold of expression. MiRNAs with more than five reads were defined as expressed. Differential expression of miRNAs was analysed by t-test (P value < 0.05 and fold-change > 1.5 or < 0.67) after Box-Cox transformation. MiRNA targets were identified by TargetScanWorm (Release 6.2) and Pearson Correlation Coefficient smaller than -0.2. | WBPaper00066447:Day8_vs_Day1_downregulated_intestine | |
| Transcripts that were enriched in muscle in day 12 animals, according to trans-splicing-based RNA tagging (SRT) and RNAseq. | DESeq and Benjamini-Hochberg adjusted p-values were used. | WBPaper00050053:muscle_enriched_Day12 | |
| Transcripts that showed significantly decreased expression in set-9(rw5) animals comparing to in N2. | edgeR, 5% FDR. | WBPaper00054410:set-9(rw5)_downregulated | |
| Micro RNAs that showed significantly decreased expression in day 8 adults comparing to in day 1 adults in hypodermis. | Differentially expressed miRNAs were identified using DEGseq based on unique molecular identifier (UMI). A minimum UMI sum of 10 in 3 replicates was set as the threshold of expression. MiRNAs with more than five reads were defined as expressed. Differential expression of miRNAs was analysed by t-test (P value < 0.05 and fold-change > 1.5 or < 0.67) after Box-Cox transformation. MiRNA targets were identified by TargetScanWorm (Release 6.2) and Pearson Correlation Coefficient smaller than -0.2. | WBPaper00066447:Day8_vs_Day1_downregulated_hypodermis | |
| miRNAs that showed significantly increased expression in pry-1(mu38) comparing to in N2. | Fold change > 2, FDR < 0.05 | WBPaper00057033:pry-1(mu38)_upregulated | |
| MicroRNAs that showed significantly decreased expression in alg-5(ram2), comparing to in N2. | DESeq2, Fold change > 1.5. | WBPaper00051404:alg-5(ram2)_downregulated_miRNA |
20 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr12867 | GFP expression appeared in the seam cells at the very beginning of the L4 stage and continued on through adulthood. GFP was never seen in the seam cells before the L3-to-L4 transition in a wild-type background (100%, n 80 animals). Seam cell expression of let-7::gfp is significant as let-7 is normally required for seam cell development. Nontemporally regulated GFP expression was observed in other parts of the worm, including the pharynx, intestinal cells, muscle cells, and neurons. | |||
| Expr15759 | ||||
| Expr12021 | During the L1 and L2 stages, Plet-7::gfppest expression is detected primarily in the intestine, the pharynx, and some neurons. Beginning in the L3, Plet-7::gfppest expression is detected in seam and vulva precursor cells, as well as the body wall muscle, in addition to the tissues observed in L1/L2 stage animals. Plet-7::gfppest is expressed strongly in the vulva and seam during the L4. | |||
| Expr8408 | Expression detected from late embryos to adults. In late embryos to L1, expression is seen in dnc and intestine. From L2 to adults, expression is detected in almost all tissues except germline; specifically muscle, rectum, vulva, spermatheca, pharynx, intestine, vnc, dnc, nerve ring, hypodermis. | |||
| Expr10882 | The let-7 promoter drives GFP expression in AVM and ALM touch neurons in L2-stage and YA animals. Expression of the mature let-7 micro-RNA is almost undetectable from embryonic to L2 stages and becomes apparent at L3. lin-41 is broadly expressed in the nervous system at the L2 stage. GFP expression is seen in the head ganglion, tail neurons, SDQR, AVM, ALM, and ventral cord motor neurons. | |||
| Picture: Fig 2A. | Expr8397 | Northern blot temporal expression: L3 to adult. | ||
| plet-7A::GFP and plet-7B::GFP expression differs in intestine, hypodermal, and seam cells. | Expr10699 | let-7 primary transcripts are first detected at the end of the first larval stage and exhibit pulses of expression near the molt of each larval stage. Both of the plet-7::GFP constructs drove temporally regulated expression, initially observed at the end of the first larval stage (L1). Starting in late L1 (~10 h at 25°C), robust GFP was seen in muscle and neuronal cells in the head, including the nerve ring. Midway through L2, GFP accumulated in the neurons and muscle cells of the tail, body wall muscle (BWM), and ventral nerve cord (VNC). Beginning in L3, all transgenic lines began to express GFP in vulva precursor cells. After the onset of GFP expression in a particular tissue, it was maintained until adults became gravid with embryos (~52 h at 25° C). GFP was not detected in the germ line. Although plet-7A::GFP and plet-7B::GFP transgenics showed similar spatio-temporal expression patterns in most cell types, they were not entirely overlapping. In hypodermal and seam cells, the plet-7B::GFP reporter produced a robust GFP signal at the L3 stage. However, plet-7A::GFP animals exhibited only weak, transient expression of GFP in the hypodermal cells beginning at the L3 stage. Early in the second stage of development, all intestinal cells showed high expression of GFP in plet-7B::GFP transgenic animals, while GFP was undetectable in the intestine of plet-7A::GFP transgenic animals. | ||
| Expr12248 | let-7 promoter directed temporal gfp expression in the seam cells of transgenic animals at the early L4 stage and in the adult. let-7 was observed in the anchor cell at L3 and in the distal tip cells at the adult stage. lin-4 and let-7 were weakly expressed in the anchor cell, which is required for proper vulval patterning, and in the P5.p, P6.p, and P7.p cells that will later differentiate into the mature vulva. | |||
| Expr9613 | Fluorescence was observed at the end of the L1 stage in transgenic worms that express GFP fused to the pri-let-7B start site. Detection of GFP mRNA, driven by both let-7 promoter A and B sequences in the transgenic worms, mirrored that of endogenous let-7 primary transcripts, indicating that expression of let-7 is repressed largely at the transcriptional level from embryogenesis until the late L1 stage. Consistent with the reporter analysis, pri-let-7 was first observed during the late L1 stage. We detected all three pri-let-7 isoforms, and coordinate expression of these isoforms oscillated throughout development. The low levels of pri-let-7 at most mid-larval time points and the slight shifts in the timing of pri-let-7 expression between experiments indicate that expression of endogenous pri-let-7 transcripts is dynamic, and that even slight changes in culture conditions can affect the rate of development and thus pri-let-7 expression. GFP mRNA levels of the let-7 promoter reporter oscillated with a frequency identical to that of endogenous pri-let-7 expression, suggesting that transcriptional mechanisms largely control the cycling pattern of pri-let-7 expression. Consistent with previous reports, pre- and mature let-7 RNAs were undetectable until the L3 stage. In the L3 and L4 stages, levels of pre-let-7 oscillated in parallel to those of pri-let-7, while mature let-7 accumulated to a relatively constant level. | |||
| Expr12251 | For each of the mir::GFP-pest reporters (Plin-4::GFP-pest, Plet-7::GFP-pest, mir-1::GFP-pest) post-embryonic GFP-pest expression was first detected at approximately 14 hours post L1 arrest. Once transcriptionally activated, Plin-4::GFP-pest and Plet-7::GFP-pest reporters peak in expression by 18-20 hours and diminish with similar kinetics. For animals expressing the Plet-7::GFP-pest reporter GFP-pest expression was monitored for longer periods after release from L1 arrest. Consistent with the highly pulsatile nature of this expression pattern, GFP-pest expression was reinitiated at 30 hours, which correlates with the later portions of the L2 stage. While transcriptional activation of the Pmir-1::GFP-pest reporter was also initiated at 14 hours post-L1 arrest, the peak of Pmir-1::GFPpest expression occurred at a later time point, and diminished with slower kinetics, as compared to Plin-4::GFP-pest and Plet-7::GFP-pest expression.The majority of animals which harbor the Plin-4::GFP-pest transgene cease GFP-pest expression by L3 ecdysis and resume expression by the mid-L4 stage. The pulse of Plin-4::GFP-pest expression at the L4 stage extends through the early portion of young adulthood and completely overlaps with the lethargus period in all animals. Plet-7::GFP-pest expression followed a similar pattern. However, GFP-pest expression was more variable at the L3-to-L4 transition and L4-specific induction of this transgene was primarily restricted to the lethargus period. In contrast to the expression profiles of the lin-4 and let-7 reporters, induction of Pmir-1::GFP-pest expression began during, or immediately after, L3 ecdysis and persisted into the L4 stage. A second pulse of Pmir-1::GFP-pest expression completely overlapped with the L4 lethargus period and continued into early adulthood. Collectively, these results suggest that the expression patterns of lin-4, let-7 and mir-1 are dynamic throughout development and that the cyclical transcription of these miRNAs is mediated by their cognate promoter sequences. | |||
| Expr11388 | Both pri-let-7 and SL1-pri-let-7 were dynamically expressed during the L4 stage, starting from low levels, peaking around the time of maximum lin-42 levels, and subsequently declining. | |||
| Expr2521 | No signal detected in embryos, L1 and L2 larva. Intense signals detected in L3, L4 larva, adults, and glp-4(bn2) adults. | |||
| Previous studies did not detect the four let-7 family members until the L3 stage, but earlier expression of all four microRNAs was detected by enhancing the sensitivity of detection. | Expr3774 | When normalized to U6 expression, let-7 RNA reached half-maximal expression at about the L4 stage. | ||
| Expr12874 | Unspliced let-7 primary transcripts are expressed in L3-larvae, L4-larvae and adults. | |||
| Expr2430 | The expression and function of the let-7 RNA in C. elegans begins during the third larval stage, when the gene specifies a transition from late larval to adult cell fates, and continues at all subsequent stages. | |||
| Expr12875 | Mature let-7 RNAs are detect din L4 larvae and adult worms. | |||
| Expr2658 | Precursor miRNA: Very weak expression detected in L4. No expression detected in embryo, L1-L3 and adult. mature miRNA: Strong expression in L4 and adult. Weak expression in L3. No expression detected in embryo, L1 and L2. | |||
| Expr960 | let-7 RNA was not detected at embryonic, L1 or L2 stages; low-level expression was detected at the early L3 stage; and high-level expression was detected at the early L4 and adult stages. | |||
| Expr1669 | Expressed in L3, L4 and adults. | |||
| Figure S4. | Expr12022 | pri-let-7 miRNA transcript levels oscillate during wild-type larval development, peaking once per larval stage. |
15 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| part_of | |
| part_of | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| part_of | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| has_input(WB:WBGene00003026) | enables |
15 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| part_of | |
| part_of | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| part_of | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| has_input(WB:WBGene00003026) | enables |
6 Regulates Expr Cluster
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Proteins that showed differential expression in (B) let-7(mg279);[let-7 sponge] when comparing to (A) [let-7 sponge], and in (C) gld-1(op236); let-7(mg279);[let-7 sponge] when comparing to (A) [let-7 sponge] | N.A. | WBPaper00044501:gld-1_let-7_regulated | |
| Proteins identified by MudPIT in let-7(wt) miRNA pulldown. | Fold change > 4 enriched in miRNA pulldowns over the scrambled control, | WBPaper00064080:let-7_miRNA_interacting | |
| Transcripts upregulated consistently in let-7(n2853), lin-41(xe11) and lin-41(xe11); let-7(n2853) mutant worms, compared to wild-type worms (on RPF, ribosome-protected fragments, level) | N.A. | WBPaper00050717:let-7(n2853)_lin-41(xe11)_upregulated | |
| Genes down-regulated more than 2-fold in let-7(n2853) compared to wild-type. | Paired t-test. Expression level change of more than 2 fold is the cut-off. | WBPaper00042165:let-7_downregulated | |
| Transcripts downregulated consistently in let-7(n2853), lin-41(xe11) and lin-41(xe11); let-7(n2853) mutant worms, compared to wild-type worms (on RPF, ribosome-protected fragments, level) | N.A. | WBPaper00050717:let-7(n2853)_lin-41(xe11)_downregulated | |
| Genes up-regulated more than 2-fold in let-7(n2853) compared to wild-type. | Paired t-test. Expression level change of more than 2 fold is the cut-off. | WBPaper00042165:let-7_upregulated |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrX_14745322..14747302 | 1981 | X: 14745322-14747302 | Caenorhabditis elegans |
