WormMine

WS295

Intermine data mining platform for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00271694 Gene Name  T10E9.14
Sequence Name  ? T10E9.14 Organism  Caenorhabditis elegans
Automated Description  Predicted to enable mRNA binding activity. Human ortholog(s) of this gene implicated in congenital myopathy 9A and congenital myopathy 9B. Is an ortholog of human FXR1 (FMR1 autosomal homolog 1). Biotype  SO:0001217
Genetic Position  Length (nt)  ? 1089
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00271694

Genomics

2 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:T10E9.14b.1 T10E9.14b.1 851   I: 6531983-6533071
Transcript:T10E9.14a.1 T10E9.14a.1 817   I: 6531983-6533031
 

Other

2 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:T10E9.14a T10E9.14a 549   I: 6532187-6532323
CDS:T10E9.14b T10E9.14b 543   I: 6532187-6532317

0 RNAi Result

14 Allele

Public Name
gk962858
gk962706
gk963902
gk429550
gk593692
gk852750
gk703780
gk558649
gk335361
gk540549
gk777384
h16091
tm5258
gk113185

1 Chromosome

WormBase ID Organism Length (nt)
I Caenorhabditis elegans 15072434  

1 Chromosome Location


Feature . Primary Identifier
Start End Strand
WBGene00271694 6531983 6533071 -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_chrI_6531964..6531982   19 I: 6531964-6531982 Caenorhabditis elegans

18 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals. Fold change > 2, FDR < 0.05 WBPaper00064088:Day-1-adult_vs_L4_upregulated_fem-3(q20)
  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)
  Transcripts that showed significantly increased expression in day 3 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals. Fold change > 2, FDR < 0.05 WBPaper00064088:Day-3-adult_vs_L4_upregulated_fem-3(q20)
  Transcripts that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage. DESeq2, fold change > 2, FDR < 0.05. WBPaper00066594:ilc-17.1(syb5296)_upregulated
  Transcripts that showed significantly decreased expression in animals with germline-specific inx-14(RNAi) comparing to in aniamls fed with control vector, both exposed to PA14 infection. DESeq2. Differentially-expressed genes (DEG) were identified based on two criteria: FDR (False discovery rateusing Benjamini-Hochberg adjusted p-values) < 0.01 and absolute value of log2(Fold Change) > 1. WBPaper00066146:germline-inx-14(RNAi)_downregulated_PA14
  Transcripts that showed significantly decreased expression in hda-2(ok1479) comparing to in N2 animals. DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2. WBPaper00062159:hda-2(ok1479)_downregulated
  Transcripts that showed significantly decreased 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_downregulated_neural
  Transcripts enriched in purified oocyte P bodies comparing to in the whole animal. DESeq2, FDR < 0.05, fold change > 2. WBPaper00065975:P-body_vs_WholeAnimal_enriched
  Top 300 transcripts enriched in ABalaaaarl, ABalaaaarr 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:RME_LR_parent
  Top 300 transcripts enriched in ABarpaaa 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:ABarpaaa_lineage
  Top 300 transcripts enriched in arcade cell 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:Arcade_cell_anterior_and_posterior
  Transcriptions that showed significantly decreased expression in hsf-1(RNAi) comparing to empty vector injection into rrf-3(pk1426);daf-2(e1368) animals. Genes with an absolute fold changeof at least 2 and standard p-values below 0.05 were considered as differentially expressed. WBPaper00062193:hsf-1(RNAi)_downregulated
  Transcripts that showed significantly decreased expression in sin-3(syb2172) comparing to in N2 gonads at young adult stage. DESeq2, fold change > 2, FDR < 0.05. WBPaper00066085:sin-3(syb2172)_downregulated
  Top 300 transcripts enriched in ABalaaaala, ABalaapaaa 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:AIN_parent
  Top 300 transcripts enriched in ABalapppaa 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:Neuroblast_ALA_RMED
  Top 300 transcripts enriched in ABalapaapa, ABalaapppa 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_parent
  Transcripts that showed significantly decreased expression in lsl-1(ljm1) comparing to in N2 animals. DESeq2, q-value <= 0.01 and fold change >= 2. WBPaper00062587:lsl-1(ljm1)_downregulated
  Transcripts that showed significantly decreased expression in lsl-1(tm4769) comparing to in N2 animals. DESeq2, q-value <= 0.01 and fold change >= 2. WBPaper00062587:lsl-1(tm4769)_downregulated

2 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr2024293 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).  
    Expr2006079 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).  

5 GO Annotation

Annotation Extension Qualifier
  enables
  enables
  enables
  enables
  enables

0 Homologues

1 Locations


Feature . Primary Identifier
Start End Strand
WBGene00271694 6531983 6533071 -1

5 Ontology Annotations

Annotation Extension Qualifier
  enables
  enables
  enables
  enables
  enables

0 Regulates Expr Cluster

1 Sequence

Length
1089

1 Sequence Ontology Term

Identifier Name Description
gene  

0 Strains

1 Upstream Intergenic Region

WormBase ID Name Sequence Name Length (nt) Chromosome Location Organism
intergenic_region_chrI_6533072..6534083   1012 I: 6533072-6534083 Caenorhabditis elegans