WormMine

WSWS298

An integrated data resource for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00219660 Gene Name  linc-19
Sequence Name  ? C44B11.8 Organism  Caenorhabditis elegans
Automated Description  Enriched in egg-laying apparatus; mu_int_L; neurons; and spermathecal-uterine junction based on single-cell RNA-seq and RNA-seq studies. Is affected by several genes including cyd-1; etr-1; and hsf-1 based on RNA-seq studies. Biotype  SO:0001641
Genetic Position  III :-7.46762± Length (nt)  ? 1131
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00219660

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:C44B11.8 C44B11.8 714   III: 3150222-3151352
 

Other

0 CDSs

0 RNAi Result

24 Allele

Public Name
gk962532
gk964281
WBVar01329798
WBVar01329797
gk962959
gk962958
WBVar01938562
WBVar01415924
WBVar01938563
WBVar00233572
WBVar00233571
gk390177
WBVar01667338
gk386439
gk913538
WBVar01667339
WBVar02003290
gk697547
gk600524
gk601935
gk604903
WBVar02034031
WBVar01785213
WBVar01989898

1 Chromosome

WormBase ID Organism Length (nt)
III Caenorhabditis elegans 13783801  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00219660 3150222 3151352 1

2 Data Sets

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

1 Downstream Intergenic Region

WormBase ID Name Sequence Name Length (nt) Chromosome Location Organism
intergenic_region_chrIII_3151353..3151808   456 III: 3151353-3151808 Caenorhabditis elegans

37 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  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
  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 increased expression in rrf-3(pk1426) comparing to in N2 at L3 larva stage. DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01. WBPaper00056169:rrf-3(pk1426)_upregulated_L3
  Transcripts that showed signifcantly increased expression in pabp-2(RNAi) animals comparing to in N2 animals injected with empty vector at L1 larva stage and collected at L4 larva stage. FDR < 0.05, fold change > 2 WBPaper00067368:pabp-2(RNAi)_upregulated_N2
  Transcripts that showed significantly altered expression at URX, AQR, and PQR 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_URX-AQR-PQR
Bacteria: B.thuringiensis Transcripts in elt-2(RNAi) animals that were significantly differentially expressed at least for one time point on the non pathogenic strain Bt407 compared to E. coli OP50. Cuffdiff WBPaper00060358:B.thuringiensis_non-pathogen_regulated_elt-2(RNAi)
Bacteria: B.thuringiensis Transcripts in elt-2(RNAi) animals that were significantly differentially expressed at least for one time point and one pathogenic strain Bt247 and Bt679 compared to the non pathogenic strain Bt407. Cuffdiff WBPaper00060358:B.thuringiensis_pathogen_regulated_elt-2(RNAi)
  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 differential expression between 24 and 26 hours post hatching L2d and dauer committed larvae of daf-9(dh, triggered by the dafachronic acid (DA) growth hormone6). Cluster 2 genes' expression gradually increased into dauer. Benjamini Hochberg corrected q-value < 0.01. WBPaper00053388:dauer_regulated_Cluster2
  Transcripts that showed significantly decreased expression in hsf-1(RNAi) animals comparing to in control animals, without heat shock. Transcripts that were differentially expressed in different conditions, compared to the hsf-1(+);-HS control, were determined with CuffDiff, which uses the Benjamini-Hochberg correction for multiple testing to obtain the q-value (the FDR-adjusted the p-value). WBPaper00049942:hsf-1(RNAi)_downregulated
  Transcripts that showed significantly decreased expression in let-767(RNAi) L4 animals comparing to animals fed with empty vector. log2 fold change > 1.5 or < -1.5, p-value < 0.05 WBPaper00066679:let-767(RNAi)_downregulated
  Transcripts that showed significantly decreased expression in gonad cyd-1(RNAi) animals in daf-2(e1370) at late L4 stage. DESeq2, fold change > 2, FDR < 0.05. WBPaper00067493:gonad-cyd-1(RNAi)_downregulated_daf-2(e1370)
  Transcripts that showed significantly decreased expression in ash-2(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:ash-2(RNAi)_downregulated_WT
  Transcripts that showed significantly increased expression in N2 comparing to in skn-1 gain of function allele lax188 animals DESeq2, fold change > 2, FDR < 0.05. WBPaper00067765:skn-1(lax188)_downregulated_N2
  Transcripts that showed significantly decreased expression in cat-2(e1112);odIs77 comparing to in odIs77 control animals. EdgeR, FDR<0.01 WBPaper00060921:cat-2(e1112)_downregulated
  Transcripts that showed significantly increased expression in rrf-3(pk1426) comparing to in N2 at young adult stage. DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01. WBPaper00056169:rrf-3(pk1426)_upregulated_adult
  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
  Single-cell RNA-Seq cell group 1_2 expressed in muscle. scVI 0.6.0 WBPaper00065841:1_2
  Transcripts that showed significantly increased expression in adr-1(tm668) comparing to in N2. DESeq2, p-value < 0.05 and a fold enrichment log2fold > 0.5. WBPaper00055226:adr-1(tm668)_upregulated
  Transcripts that showed signifcantly decreased expression in ubr-5(miy31);pabp-2(RNAi) comparing to in pabp-2(RNAi) animals. FDR < 0.05, fold change > 2 WBPaper00067368:ubr-5(miy31)_downregulated_pabp-2(RNAi)
  Targets of endo-siRNA that showed significantly increased expression in BFF39[pptr-1(tm3103);Pmex-5::gfp::h2b::tbb-2 (mjIs134 II)] comparing to in SX1263[Pmex-5::gfp::h2b::tbb-2 (mjIs134 II)] dissected gonad isolated from 1-day old adult hermaphrodites. DESeq2, fold change > 2, FDR < 0.01 WBPaper00057140:pptr-1(tm3103)_upregulated
  Genes with small RNAs upregulated in all four meg-3(ax3055) meg-4(ax3052) strains comparing to N2 DESeq2 WBPaper00057162:meg-3_meg-4_upregulated_sRNA
  Transcripts that showed significantly decreased expression in tdc-1(n3419);odIs77 comparing to in odIs77 control animals. EdgeR, FDR<0.01 WBPaper00060921:tdc-1(n3419)_downregulated
  ncRNAs with significantly increased expression in cep-1(gk138) than in N2 under normal conditions, according to RNAseq. ncRNAs with more than 2 fold difference in expression are considered differentially expressed WBPaper00045380:cep-1(gk138)_upregulated_normal
  Single-cell RNA-Seq cell group 70_1 expressed in neuron. scVI 0.6.0 WBPaper00065841:70_1
  Transcripts that showed lower expression in neurons isolated from male day 2 vs day 8. DESeq2 analysis was then employed for read normalization and differential expression analysis of the counted reads. PCA analysiswas performed along with the DESeq2 package. Genes with a log2(fold-change) > 1 and p-adjusted < 0.05 were considered differentially expressed in subsequent analysis. WBPaper00066831:male-neuron_aging_upregulated
  Single-cell RNA-Seq cell group 11_3 expressed in seam. scVI 0.6.0 WBPaper00065841:11_3
  Single-cell RNA-Seq cell group 146_0 expressed in epithelium. scVI 0.6.0 WBPaper00065841:146_0
  Single-cell RNA-Seq cell group 11_0 expressed in vulva. scVI 0.6.0 WBPaper00065841:11_0
  Single-cell RNA-Seq cell group 11_1 expressed in epithelium. scVI 0.6.0 WBPaper00065841:11_1

0 Expression Patterns

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00219660 3150222 3151352 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
1131

1 Sequence Ontology Term

Identifier Name Description
gene  

1 Strains

WormBase ID
WBStrain00055036

1 Upstream Intergenic Region

WormBase ID Name Sequence Name Length (nt) Chromosome Location Organism
intergenic_region_chrIII_3143758..3150221   6464 III: 3143758-3150221 Caenorhabditis elegans