Genomics
14 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:F49E11.1c.1 | F49E11.1c.1 |
3520
 |
IV: 13009158-13035955 |
| Transcript:F49E11.1b.1 | F49E11.1b.1 |
3594
|
IV: 13009158-13035953 |
| Transcript:F49E11.1k.1 | F49E11.1k.1 |
3317
|
IV: 13009158-13035803 |
| Transcript:F49E11.1g.1 | F49E11.1g.1 |
2403
|
IV: 13009158-13034518 |
| Transcript:F49E11.1h.1 | F49E11.1h.1 |
1608
|
IV: 13024534-13034518 |
| Transcript:F49E11.1l.1 | F49E11.1l.1 |
1545
|
IV: 13024534-13034826 |
| Transcript:F49E11.1e.1 | F49E11.1e.1 |
1721
|
IV: 13026206-13033951 |
| Transcript:F49E11.1f.1 | F49E11.1f.1 |
3620
|
IV: 13027172-13035961 |
| Transcript:F49E11.1i.1 | F49E11.1i.1 |
1572
|
IV: 13031334-13034518 |
| Transcript:F49E11.1m.1 | F49E11.1m.1 |
1509
|
IV: 13031334-13034826 |
| Transcript:F49E11.1a.1 | F49E11.1a.1 |
3232
|
IV: 13031334-13035951 |
| Transcript:F49E11.1d.1 | F49E11.1d.1 |
1428
|
IV: 13031644-13033951 |
| Transcript:F49E11.1j.1 | F49E11.1j.1 |
1473
|
IV: 13031644-13034518 |
| Transcript:F49E11.1n.1 | F49E11.1n.1 |
1410
|
IV: 13031644-13034826 |
Other
14 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:F49E11.1b | F49E11.1b |
2454
|
IV: 13009158-13009229 |
| CDS:F49E11.1c | F49E11.1c |
2391
|
IV: 13009158-13009229 |
| CDS:F49E11.1g | F49E11.1g |
2403
|
IV: 13009158-13009229 |
| CDS:F49E11.1f | F49E11.1f |
1518
|
IV: 13027264-13027303 |
| CDS:F49E11.1i | F49E11.1i |
1572
|
IV: 13031334-13031382 |
| CDS:F49E11.1m | F49E11.1m |
1509
|
IV: 13031334-13031382 |
| CDS:F49E11.1d | F49E11.1d |
1428
|
IV: 13031644-13031768 |
| CDS:F49E11.1n | F49E11.1n |
1410
|
IV: 13031644-13031768 |
| CDS:F49E11.1a | F49E11.1a |
1527
|
IV: 13031334-13031382 |
| CDS:F49E11.1e | F49E11.1e |
1506
|
IV: 13026421-13026448 |
| CDS:F49E11.1h | F49E11.1h |
1608
|
IV: 13024534-13024618 |
| CDS:F49E11.1j | F49E11.1j |
1473
|
IV: 13031644-13031768 |
| CDS:F49E11.1k | F49E11.1k |
2340
|
IV: 13009158-13009229 |
| CDS:F49E11.1l | F49E11.1l |
1545
|
IV: 13024534-13024618 |
38 RNAi Result
429 Allele
| Public Name |
|---|
| otn10062 |
| gk964278 |
| gk964078 |
| gk963546 |
| gk963547 |
| gk964500 |
| gk962765 |
| gk432705 |
| gk372194 |
| gk684528 |
| gk427829 |
| gk592212 |
| gk747005 |
| gk535183 |
| gk736677 |
| gk474293 |
| gk821759 |
| gk809201 |
| gk768157 |
| gk842961 |
| gk566518 |
| gk491606 |
| gk768158 |
| gk552178 |
| gk693064 |
| gk322979 |
| gk882995 |
| gk656852 |
| gk483068 |
| gk858705 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00003150 | 13009158 | 13035961 | 1 |
4 Data Sets
| Name | URL |
|---|---|
| WormBaseAcedbConverter | |
| GO Annotation data set | |
| C. elegans genomic annotations (GFF3 Gene) | |
| Panther orthologue and paralogue predictions |
161 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Genes with expression altered >= 3-fold in dpy-10(e128) mutants. | Data across the wild type series was analyzed using the Significance analysis of Microarrays (SAM) algorithm (to calculate the False Discovery Rate (FDR)). | WBPaper00035873:dpy-10_regulated | |
| Transcripts that showed significantly increased expression in L1 neural cells comparing to in adult neural cells. | DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction. | WBPaper00060811:L1_vs_adult_upregulated_neural | |
| 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 | |
| mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis. | Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05. | WBPaper00045420:fertilization_downregulated_transcript | |
| 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 |
| 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 altered expression in cat-1(RNAi) animals comparing to control animals injected with empty vector. | p-value <= 0.05 | WBPaper00066902:cat-1(RNAi)_regulated | |
| Proteins interacting with NHR-49-GFP according to co-IP and LC-MS. | N.A. | WBPaper00064071:NHR-49_interacting | |
| Transcripts expressed in the epithelial tissues surrounding the pharynx that includes the arcade and intestinal valve (AIV) cells, according to PAT-Seq analysis using Pbath-15-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:arcade_intestinal-valve_expressed | |
| Transcripts expressed in body muscle, according to PAT-Seq analysis using Pmyo-3-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:body-muscle_expressed | |
| Transcripts expressed in GABAergic neuron, according to PAT-Seq analysis using Punc-47-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:GABAergic-neuron_expressed | |
| Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:hypodermis_expressed | |
| Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:intestine_expressed | |
| Transcripts expressed in NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:NMDA-neuron_expressed | |
| Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:pharynx_expressed | |
| Genes with expression level regulated by genotype (N2 vs CB4856) and age at old adults stage (214 hours at 24 centigrade). | For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR). | WBPaper00040858:eQTL_age_regulated_aging | |
| Genes with expression level regulated by genotype (N2 vs CB4856) and age at L3 larva and Late reproduction stage (96 hours at 24 centigrade). | For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR). | WBPaper00040858:eQTL_age_regulated_developing | |
| Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:seam_expressed | |
| Genes with expression level regulated by genotype (N2 vs CB4856) at L3 larva and Late reproduction stage (96 hours at 24 centigrade). | For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR). | WBPaper00040858:eQTL_regulated_developing | |
| Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals. | Fold change > 2, FDR < 0.05 | WBPaper00064088:Day-3-adult_vs_L4_downregulated_glp-1(e2141) | |
| Bacteria diet: Sphingomonas aquatilis Yellow. Fed for 30 generations. | Transcripts that showed significantly decreased 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_downregulated |
| Transcripts detected in germline isolated from day-1 adult hermaphrodite animals. | All three experiments have CPM >= 1. | WBPaper00067147:germline_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 2 mix) vs BT407 12h), according to RNAseq. | Cuffdiff, ajusted p-value < 0.01. | WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h |
| 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 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 increased expression in 10-days post L4 adult hermaphrodite N2 grown at 20C, comparing to in 1-day post L4 adult hermaphrodite N2 animals grown at 20C. | CuffDiff, fold change > 2. | WBPaper00065096:Day10_vs_Day1_upregulated | |
| Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy. | Cufflinks | WBPaper00065120:body-muscle-transcriptome | |
| 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 | |
| Proteins that showed significantly decreased expression after 1-day-old wild type adults were exposed to cisplatin (300ug per mL) for 6 hours. | The differential expression analysis was performed in R. Differentially expressed proteins were identified by using a two-sided t-test on log-transformed data. | WBPaper00065373:Cisplatin_downregulated_WT |
13 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Picture: Fig 2. | Expr4905 | Endogenous MBK-2 and EGG-3 colocalize on the cortex of growing oocytes. Two MBK-2 fusions (GFP:MBK-2 and MBK-2:HIS) colocalize with endogenous EGG-3 on the cortex in metaphase I embryos and in discrete cytoplasmic puncta during the second meiotic division. In 2-cell and later embryos, EGG-3 was rarely detected, whereas GFP:MBK-2 and endogenous MBK-2 persisted in the cytoplasm of all blastomeres and on P granules until at least the 20-cell stage. Comparison of total EGG-3 levels to cytoplasmic GFP:MBK-2 levels confirmed that degradation of EGG-3 correlates with increased GFP:MBK-2 in the cytoplasm. | ||
| Expr4577 | WGA-G and MBK-2 colocalized in the cortex of oocytes in the proximal germline and in the cortex of newly fertilized embryos. Furthermore, cortical WGA-G and MBK-2 punctae were completely coincident at anaphase of meiosis I. MBK-2 localizes to centrosomes and chromosomes by first mitosis, at which point, WGA-G punctae are no longer detected. | |||
| Expr1031486 | Tiling arrays expression graphs | |||
| Expr2388 | mbk-2::gfp reporter constructs were expressed in subsets of tissues, including the nervous system, body wall muscle, and the pharynx. | |||
| Expr1151671 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr12976 | mbk-2 showed strong expression in the syncytial region of the gonad and in embryos, the reporter showed a complete lack of expression in oocytes. | |||
| Expr2013432 | 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). | |||
| Expr2031666 | 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). | |||
| Expr2389 | MBK-2::GFP was excluded from the nucleus. | |||
| Expr3804 | GFP:MBK-2 relocalizes abruptly from the cortex to cortical puncta in anaphase/telophase of meiosis I and progressively from cortical puncta to the cytoplasm during meiosis II and meiotic exit. Consistent with two distinct steps of relocalization, embryos arrested before or during metaphase I maintain GFP:MBK-2 uniformly at the cortex, whereas embryos arrested in metaphase II maintain GFP:MBK-2 in cortical puncta, with some puncta in the cytoplasm (20/24 zyg-11(RNAi) gonads). In spe-9 eggs, GFP:MBK-2 progressed from the cortex into cortical puncta and the cytoplasm as in wild-type embryos, suggesting that meiotic exit, rather than meiosis II, is critical. In wee-1.3(RNAi) oocytes, relocalization of GFP:MBK-2 to cortical puncta and to the cytoplasm occurred precociously in oocytes . This premature relocalization was blocked by CDK-1 and MAT-1 depletion. Authors concluded that GFP:MBK-2 relocalizes from the cortex to the cytoplasm in a two-step process linked to progression past metaphase I and possibly to meiotic exit. | |||
| Expr1018585 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr2692 | GFP:MBK-2 foci was detected in 0/9 embryos undergoing metaphase or anaphase of meiosis I, in 3/4 embryos in telophase of meiosis I or prophase of meiosis II, and in 18/18 embryos in metaphase or anaphase of meiosis II. After pronuclear formation, the foci disappeared quickly in a posterior-to-anterior wave. GFP:Histone H2B fusion was used to precisely stage embryos expressing GFP:MBK-2. GFP:MBK-2 was found predominantly at the cell periphery (cortex) in a uniform pattern. In later zygotes, GFP:MBK-2 distribution changed abruptly from uniform to punctate, with GFP:MBK-2 apparently coalescing into many discrete cortical foci. By mitosis, GFP:MBK-2 was found predominantly on centrosomes and chromosomes, in a pattern that persisted in all blastomeres up to at least the eight-cell stage. In the germline blastomeres P2, P3, and P4, GFP:MBK-2 also appeared to associate with P granules. Seventy-eight percent of mat-1(RNAi) embryos (n=292) maintained GFP:MBK-2 uniformly distributed at the cortex, as it is in oocytes and newly fertilized zygotes. The remainder typically had fewer foci than wild-type. mat-1 encodes CDC27, an APC subunit required for the metaphase-to-anaphase transition. Thus, redistribution of MBK-2 into cortical foci occurs just prior to the second meiotic division, and depends on progression past metaphase of meiosis I. | |||
| Expr3274 | In fertilized embryos, GFP-MBK-2 foci were first observed on the cortex at 4.3 +/- 0.7 min (n = 4) after the start of anaphase I chromosome segregation. The appearance of cortical foci of GFP-MBK-2 in unfertilized, spe-9 embryos was delayed until 12.3 +/- 2.1 min (n = 3) after the start of anaphase I chromosome separation. The timing of GFP-MBK-2 redistribution was also measured in fertilized and unfertilized embryos expressing only GFP-MBK-2 and using exit from the spermatheca as a reference point. In these experiments, cortical foci of GFP-MBK-2 appeared 13.7 +/- 1.9 min (n = 9) after spermatheca exit in fertilized embryos and 22.4 +/- 3.0 min (n = 8) after spermatheca exit in unfertilized embryos. These results indicate that the redistribution of GFP-MBK-2 was delayed by approximately 9 min in the absence of fertilization. |
48 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| occurs in(GO:0005737)|occurs in(GO:0005938) | enables |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| occurs in(GO:0005737)|occurs in(GO:0005938) | enables |
| enables | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| enables | |
| located_in | |
| located_in | |
| occurs in(WBbt:0004422),happens during(GO:0030010) | involved_in |
| occurs in(WBbt:0004422),happens during(GO:0030010) | involved_in |
| involved_in | |
| involved_in |
8 Homologues
| Type |
|---|
| orthologue |
| orthologue |
| orthologue |
| orthologue |
| least diverged orthologue |
| least diverged orthologue |
| least diverged orthologue |
| least diverged orthologue |
48 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| occurs in(GO:0005737)|occurs in(GO:0005938) | enables |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| enables | |
| occurs in(GO:0005737)|occurs in(GO:0005938) | enables |
| enables | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in | |
| enables | |
| enables | |
| located_in | |
| located_in | |
| occurs in(WBbt:0004422),happens during(GO:0030010) | involved_in |
| occurs in(WBbt:0004422),happens during(GO:0030010) | involved_in |
| involved_in | |
| involved_in |
30 Strains
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrIV_12995987..13009157 | 13171 | IV: 12995987-13009157 | Caenorhabditis elegans |
