Genomics
3 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:T14F9.4c.1 | T14F9.4c.1 |
1332
 |
X: 2211051-2218101 |
| Transcript:T14F9.4a.1 | T14F9.4a.1 |
2174
|
X: 2215630-2218988 |
| Transcript:T14F9.4b.1 | T14F9.4b.1 |
819
|
X: 2217174-2218101 |
Other
3 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:T14F9.4c | T14F9.4c |
1332
|
X: 2211051-2211095 |
| CDS:T14F9.4b | T14F9.4b |
819
|
X: 2217174-2217302 |
| CDS:T14F9.4a | T14F9.4a |
1284
|
X: 2215633-2215752 |
125 Allele
| Public Name |
|---|
| gk963725 |
| gk963864 |
| WBVar02048627 |
| WBVar01757616 |
| WBVar02052537 |
| gk758264 |
| gk433121 |
| gk586205 |
| gk710775 |
| WBVar01757615 |
| WBVar01987301 |
| WBVar02034661 |
| gk736135 |
| cxTi9184 |
| WBVar01757614 |
| WBVar01757613 |
| WBVar01757612 |
| WBVar01600995 |
| WBVar01600998 |
| WBVar01600996 |
| WBVar01600997 |
| gk753407 |
| gk735032 |
| ok1941 |
| gk753408 |
| gk273076 |
| gk273075 |
| cu9 |
| WBVar01979645 |
| gk469510 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00003968 | 2211051 | 2218988 | 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_2218989..2219011 | 23 | X: 2218989-2219011 | Caenorhabditis elegans |
238 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 | |
| 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 no food was present | DESeq(version 1.10.1), FDR < 0.05. | WBPaper00050726:OsmoticStress_regulated_NoFood |
| Transcripts that showed significantly increased expression in csr-1a(tor159) comparing to in N2 at 25C. | DESeq2, fold change > 2, p-value < 0.05. | WBPaper00061753:csr-1(tor159)_upregulated_25C | |
| Bacteria: E.faecalis strain OG1RF | Transcripts that showed significantly increased expression after infection by E. faecalis OG1RF. | Ballgown was used to calculate differential expression of genes using FPKM data and to generate tables with fold change and P values. Genes were shortlisted with a cutoff of 2-fold change and P values of less than 0.05. | WBPaper00059754:E.faecalis_OG1RF_upregulated |
| Transcripts that showed significantly increased expression glp-1(e2141); TU3401 animals comparing to in TU3401 animals. | Fold change > 2, FDR < 0.01. | WBPaper00065993:glp-1(e2141)_upregulated | |
| 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 higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc). | DESeq2, fold change >= 2, FDR <= 0.01. | WBPaper00056826:SGP_biased | |
| 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 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 expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:intestine_expressed | |
| Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:pharynx_expressed | |
| Transcripts 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 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 | |
| Transcripts that showed significantly increased expression after four-day-old young adult worms were placed on NGM plates seeded with OP50 in the presence 5% Agaro-oligosaccharides(AGO) for 24 h, comparing to animals grown in the absence of AGO. | Fold change > 2. | WBPaper00064306:Agaro-oligosaccharides_upregulated | |
| Transcripts that showed significantly increased expression in sin-3(tm1276) comparing to in N2. | DESeq2, fold change > 2, p-value < 0.01. | WBPaper00061203:sin-3(tm1276)_upregulated | |
| Transcripts that showed significantly increased expression in aak-1(tm1944);aak-2(ok524) animals comparing to in N2. | DEseq 1.18.0, adjusted p-value < 0.05. | WBPaper00056471:aak-1(tm1944);aak-2(ok524)_upregulated | |
| 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 at the intestine cells of daf-2(e1370) comparing to the intestine cells of N2 animals at L2 larva stage. | DESeq2 (version 1.24.0), fold change >= 2, FDR < 0.05 | WBPaper00064632:daf-2(e1370)_upregulated_intestine | |
| Transcripts that showed significantly increased expression in adr-1(tm668) and adr-1(gv6) comparing to in N2 at L4 larva stage. | DESeq FDR <= 0.05 | WBPaper00056617:adr-1_upregulated_L4_transcript | |
| Transcripts that showed significantly increased expression after treatment with TPEN (2.5uM and 5uM) from L1 to L4 larva. | N.A. | WBPaper00051498:zinc-reduction_upregulated | |
| 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 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 cco-1(RNAi) comparing to in vector control animals. | The limma package47 was used for differential expression. Genes with a Benjamini-Hochberg adjusted P-value <0.05 and an absolute log fold change of 2 were considered differentially expressed. | WBPaper00053402:cco-1(RNAi)_upregulated | |
| 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 |
| Genes that showed oscillating mRNA expression level throughout the 16 hour time courses from L3 larva to young adult. | The following three lines of R code were used to perform the classification: increasing <-2*amplitude-PC1 < -1.7; oscillating <-!increasing & (amplitude > 0.55); flat <-!increasing & !oscillating; Note that the amplitude of a sinusoidal wave corresponds to only half the fold change between trough and peak. | WBPaper00044736:oscillating_dev_expression |
15 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr1031892 | Tiling arrays expression graphs | |||
| See Expr837, 839, 840 for Expr_pattern of the same locus. | Expr838 | In embryos, PEB-1 protein was strongly detected in the nuclei of many cells in the developing pharynx. Staining was first detected at the comma stage. Some pharyngeal cells do not express PEB-1, observed a cluster of nuclei that do not contain PEB-1 near the center of the developing pharynx, a region containing many of the pharyngeal neurons. Strong pharyngeal staining persisted through the remainder of embryogenesis. PEB-1 staining was also observed outside the pharynx in several cells near the rectum and in the tail and at lower level in hypodermal nuclei. In early larvae, PEB-1 protein is easily detectable in the pharynx, as well as in a subset of nonpharyngeal. Consistently observed PEB-1 protein in the nuclei of all pharyngeal muscles, marginal cells, epithelial cells, gland cells, and pharyngeal-intestinal valve cells. Notably, authors did not observe PEB-1 staining in any pharyngeal neurons. Pharyngeal PEB-1 staining decreased in late larvae until it became undetectable in adults. PEB-1 protein expression was also observed in some tissues outside the pharynx in larvae and adults. In general, the nonpharyngeal expression was weaker than expression in the pharynx, and it appeared dynamic during the worm life cycle. In larvae, PEB-1 antibody staining was reproducibly observed in several cells near the rectum and in hypodermal nuclei in the tail and in the developing vulva and surrounding cells. Authors also observed protein expression in several nuclei in the head and tail that were provisionally identified as hypodermal nuclei. In older larvae and adults, the rectal and vulval expression decreased, but PEB-1 staining was visible in germ-line cells. This expression is consistent with Northern blots indicating that peb-1 mRNA is expressed in the germ line. | PEB-1 protein was strongly detected in the nuclei. | |
| Reporter gene fusion type not specified. See Expr837, 838, 840 for Expr_pattern of the same locus. | Expr839 | Very strong beta-galactosidase expression in the pharynx from the comma stage of embryogenesis through late larval stages, and frequent expression was observed in muscle cells and marginal cells, while less frequent expression was observed in epithelial cells and the pharyngeal intestinal valve cells. Reporter expression was also observed outside the pharynx in a pattern similar to that of the endogenous PEB-1 protein. | ||
| Reporter gene fusion type not specified. | Expr3374 | Expressed in both sexes pharynx; male tail; herm vulva. | ||
| Expr3389 | Expressed in pharynx and gonad (L2 to Adult). | |||
| Expr1200173 | Data from the TransgeneOme project | |||
| Expr12258 | Like endogenous PEB-1, GFP::PEB-1 was expressed in the pharynx and hypodermis beginning at the comma stage of embryogenesis and was tightly localized to nuclei throughout development. Expression was also observed in the gut, and in some cases body wall muscle and seam cells, where PEB-1 antibody staining was not reproducibly detected. | |||
| See Expr837, 838, 839 for Expr_pattern of the same locus. | Expr840 | peb-1 mRNA accumulation in the pharynx. Did not observe localized peb-1 mRNA accumulation outside the pharynx. | ||
| Expr1800 | Expressed in pharynx. | |||
| Interestingly, Y is replaced in the hindgut by P12.pa, a descendant of the only P cell in which PEB-1 protein expression was detected in L1 larvae. No detailed description on cellular expression patterns in pharynx, try to find those information in Expr838. | Expr3462 | In summary, PEB-1 accumulated in L1 larvae in the nuclei of all hypodermal cells and the epithelial cells lining the rectal lumen. As in the pharynx, PEB-1 was not detectable in neuroblasts or differentiated neurons. PEB-1-expressing cells are not obviously related by cell type or lineage. Rather, one striking common feature of these cells is that they contact the cuticle on the exterior of the worm or lining the pharyngeal or rectal lumen. Like in the pharynx, PEB-1 was first detected in the hypodermal nuclei in comma stage embryos (approximately 400 min) and remained detectable until hatching. In 1 1/2-fold stage embryos, the PEB-1 protein was detected in the nuclei of most, if not all, hypodermal cells including hyp5, hyp6, and hyp7 and the H, P, and V cells. After hatching, PEB-1 remained detectable in most hypodermal cells although it decreased in later larvae and was undetectable in adults. In the L1 lateral hypodermis, the PEB-1 protein was detected in H0, H1, H2, V1 to V6, and T, and their anterior and posterior daughters, as well as in the nuclei of the hyp7 syncytium. PEB-1 was also detected in many of the dorsal and ventral hypodermal nuclei in the head and the ventral hypodermal nuclei in the tail. Notably, PEB-1 was not detected in larval P cells. In addition, PEB-1 was not detected in other neuroblasts including Q and T.p. PEB-1 was also expressed in cells lining the lumen of the hindgut. In 1 1/2-fold embryos (approximately 420 min), PEB-1 was detected in many nuclei near the posterior of the embryo. These likely include both the posterior hypodermal cells and hindgut cells, although these cells cannot be easily distinguished at this stage. In L1 larvae, PEB-1 was detected in many of the non-neuronal nuclei surrounding the rectal lumen, including K, K', U, F, B, and Y. PEB-1 was not detected in the rectal-intestinal valve or the anal depressor muscle. As in other tissues, the PEB-1 protein remained detectable in the hindgut throughout larval development but became progressively less abundant and undetectable in adults. Importantly, this progressive decrease in PEB-1 expression also occurs in Y, which withdraws from the hypodermis during late larval development to become a neuron. | nuclei | |
| Expr1022290 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr1156914 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| See Expr838, 839, 840 for Expr_pattern of the same locus. | Expr837 | peb-1 mRNA is detected throughout the C. elegans life cycle on Northern blots hybridized with the full-length peb-1 cDNA. A single band of approximately 2300 nucleotides is most abundant in embryos and early larvae and decreases substantially in later larval stages. In wild-type adult hermaphrodites, much of the peb-1 mRNA appears to be expressed in the germ line. peb-1 mRNA expression levels after normalization (in arbitrary units): embryos, 11.3; L1, 13.3; L2/L3, 7.1; L4, 1.0; adults, 1.2 | ||
| Expr2033049 | 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). | |||
| Expr2014815 | 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). |
8 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| located_in | |
| located_in | |
| involved_in | |
| located_in | |
| enables | |
| involved_in | |
| enables | |
| enables |