WormMine

WS295

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00198737 Gene Name  T04C9.8
Sequence Name  ? T04C9.8 Organism  Caenorhabditis elegans
Automated Description  Enriched in neurons based on RNA-seq studies. Is affected by several genes including fzo-1; lpd-3; and ogt-1 based on RNA-seq studies. Biotype  SO:0001263
Genetic Position  :± Length (nt)  ? 139
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00198737

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:T04C9.8 T04C9.8 139   III: 5989353-5989491
 

Other

0 CDSs

0 RNAi Result

6 Allele

Public Name
gk964518
gk175795
gk964338
gk964339
WBVar01445982
WBVar02053287

1 Chromosome

WormBase ID Organism Length (nt)
III Caenorhabditis elegans 13783801  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00198737 5989353 5989491 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_5989492..5991643   2152 III: 5989492-5991643 Caenorhabditis elegans

9 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 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 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
  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 increased expression in zcIs13; twnEx320[Punc-119-ds-fzo-1] comparing to in zcIs13[Phsp-6-gfp] animals. Fold change >= 1.5. WBPaper00061409:neuronal-fzo-1(RNAi)_upregulated
  Transcripts that showed significantly increased expression in lpd-3(ok2138) comparing to in N2 animals. DESeq2, fold change > 4, FDR < 0.05. WBPaper00064661:lpd-3(ok2138)_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
  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

0 Expression Patterns

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00198737 5989353 5989491 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
139

1 Sequence Ontology Term