WormMine

WS295

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00077455 Gene Name  Y69H2.17
Sequence Name  ? Y69H2.17 Organism  Caenorhabditis elegans
Automated Description  Enriched in neurons based on RNA-seq; single-cell RNA-seq; and microarray studies. Is affected by several genes including etr-1; hsf-1; and hpl-2 based on RNA-seq and microarray studies. Is affected by four chemicals including allantoin; Sirolimus; and rifampin based on RNA-seq and microarray studies. Is predicted to encode a protein with the following domains: CUB domain and Spermadhesin, CUB domain superfamily. Biotype  SO:0001217
Genetic Position  :± Length (nt)  ? 1453
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00077455

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:Y69H2.17.1 Y69H2.17.1 676   V: 18684937-18686389
 

Other

1 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:Y69H2.17 Y69H2.17 513   V: 18685060-18685114

4 RNAi Result

WormBase ID
WBRNAi00021340
WBRNAi00076839
WBRNAi00082829
WBRNAi00082839

90 Allele

Public Name
gk963271
gk963489
gk963304
gk963809
gk963637
gk963292
gk963480
WBVar02124279
gk574146
gk776681
gk324761
gk862211
gk360360
gk808319
gk603173
gk713980
gk702138
gk667883
gk949804
WBVar01750042
WBVar00061070
WBVar00061075
WBVar01597059
WBVar01597058
WBVar01597067
WBVar01597066
WBVar01597065
WBVar01597064
WBVar01597063
WBVar01597062

1 Chromosome

WormBase ID Organism Length (nt)
V Caenorhabditis elegans 20924180  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00077455 18684937 18686389 1

2 Data Sets

Name URL
WormBaseAcedbConverter  
C. elegans genomic annotations (GFF3 Gene)  

0 Downstream Intergenic Region

36 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  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 of coding genes that showed significantly decreased expression in muscle. DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed. WBPaper00062325:muscle_depleted_coding-RNA
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
  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
  Single-cell RNA-Seq cell group 71_0 expressed in neuron. scVI 0.6.0 WBPaper00065841:71_0
  Transcripts that showed significantly increased expression in ogt-1(ok1474) neuronal cells isolated by FACs comparing to in FACs isolated neuronal cells from wild type. DESeq2, fold change > 2, FDR < 0.05. WBPaper00066485:ogt-1(ok1474)_upregulated_neuron
  Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin and 250uM Allantoin from day 1 to day 3 adult hermaphradite. DESeq2(v1.14.1), fold change > 2, p-value < 0.05 WBPaper00055354:Rifampicin-Allantoin_upregulated
  Transcripts that showed significantly decreased expression in hpl-2(tm1489) comparing to in N2 animals. DESeq2, adjusted p-value < 0.05, log2 fold change > 2 or < -2. WBPaper00054493:hpl-2(tm1489)_downregulated
  Transcripts that showed significantly decreased expression in eat-2(ad1116) comparing to in N2 at 3-days post L4 adult hermaphrodite animals. DESeq2(v1.14.1), fold change > 2, p-value < 0.05 WBPaper00055354:eat-2(ad1116)_downregulated
  Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin and 250uM Allantoin from day 1 to day 3 adult hermaphradite. DESeq2(v1.14.1), fold change > 2, p-value < 0.05 WBPaper00055354:Rapamycin-Allantoin_downregulated
Heat shock: 34C 30min. Transcripts that showed significantly increased expression in L2 larva stage C. elegans animals after incubated in a 34C water bath for 30min. DESeq2 v 1.18.1, fold change > 2, FDR < 0.01. WBPaper00058955:heatshock_upregulated_CE
  Transcripts that showed significantly 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 increaseded expression in sma-3(wk30) comparing to in N2 at L2 larva stage. Differentiallyexpressed genes between the different genotypes were identified using limma-voom. Fold change > 2. WBPaper00062491:sma-3(wk30)_upregulated
  Genes found to be regulated in daf-16(mgDf50) by resveratrol treatment with p < 0.01. N.A. WBPaper00026929:Resveratrol_regulated_daf-16
  Transcripts that showed significantly increased expression in xpf-1(tm2842) comparing to in N2 animals. DESeq2 1.14.1, fold change > 2, FDR < 0.01. WBPaper00062497:xpf-1(tm2842)_upregulated
Temperature Shift: 25C vs 15C for 16 hours at L4 larva stage. Transcripts that showed significantly increased expression in AFD neurons comparing to in whole animals. DESeq2, fold change > 2, FDR < 0.05. WBPaper00065158:AFD_enriched
  Transcripts that showed significantly decreased expression in unc-70(cas983) comparing to in N2 at L1 larva stage. DESeq2, fold change >= 2, FDR <= 0.05 WBPaper00057041:unc-70(cas983)_downregulated
Temperature Shift: 25C vs 15C for 16 hours at L4 larva stage. Transcripts that showed significantly increased expression in AFD neurons at lin-15(n765ts); oyIs95 animals shifted from 20C to 25C for 16 hours at L4 larva stage, comparing to animals shifted from 20C to 15C for 16 hours at L4 larva stage. DESeq2, fold change > 2, FDR < 0.05. WBPaper00065158:25C_vs_15C_upregulated_AFD
  Transcripts that showed significantly increased expression in alg-1(gk204) comparing to in N2 at 5-days post L4 adult hermaphrodites. DESeq, fold change > 2, adjusted p-value < 0.05. WBPaper00054758:alg-1(gk204)_upregulated
  Transcripts that showed significantly altered expression at RMG neurons in camt-1(ok515) animals comparing to in wild type AX1888-1 strain. RNA-seq data were mapped using PRAGUI - a Python 3-based pipeline for RNA-seq data analysis. WBPaper00061902:camt-1(ok515)_regulated_RMG
Mating for 24 hours with oleic acid supplement. Transcripts that showed significantly decreased expression after glp-1(e2141) hermaphrodites mated for 24 hours with oleic acid supplement. Two-class SAM analysis WBPaper00061572:oleic-acid-specific_mating_downregulated
  Transcripts that showed significantly increased expression in PVD neurons isolated from TV22833 wyIs840(ser2prom3::daf-12a(rh273)::gfpnovo2, Pmyo-2::gfp); wyIs592(ser2prom3::myr-gfp), comparing to in PVD neurons isolated from animals that only expressed wyIs592. Cufflinks 2.2.1 WBPaper00058678:DAF-12_upregulated_PVD
  Top 300 transcripts enriched in RIAL, RIAR according to single cell RNAseq. Top 300 enriched transcripts were determined by log2.ratio of the tpm in the cell type vs the tpm in the other cells * the log2 of the cell.type tpm. WBPaper00061340:RIA
  Genes enriched in neuronal miRNA-induced silencing complexes (miRISC) as detected by immunoprecipitations and microarray analysis. Testable genes were defined as having reliable signals in two different biological replicates using the Agilent microarray chip. Multiple probes for the same gene were removed, keeping the probe with the lowest p-value as defined by a one-tailed t-test comparing all testable probes versus probes towards a designated gene. The testable data was then supplemented with the enrichment values (as percent ranks) of a fifth replicate, from another microarray platform GPL5883 (which had a single probe for each gene), and statistical significance was re-calculate. p < 0.001 was the final cutoff. WBPaper00042548:miRISC_enriched
  Top 300 transcripts enriched in AVEL, AVER according to single cell RNAseq. Top 300 enriched transcripts were determined by log2.ratio of the tpm in the cell type vs the tpm in the other cells * the log2 of the cell.type tpm. WBPaper00061340:AVE
  Transcripts significantly enriched in AVK neurons comparing to all cell types at L1 larva stage. edgeR, FDR < 0.001, fold change > 2. WBPaper00055565:AVK_enriched
  Transcripts that showed significantly increased expression in hsf-1(RNAi) comparing to in wild type animals injected with vector. Differential mRNA expression using DESeq2. mRNAs with a FDR < 0.05 and fold change > 2 considered differentially expressed. WBPaper00066232:hsf-1(RNAi)_upregulated_WT

3 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr2026481 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).  
    Expr1161493 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015  
    Expr2008239 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).  

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00077455 18684937 18686389 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
1453

1 Sequence Ontology Term