WormMine

WSWS298

An integrated data resource for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00194667 Gene Name  Y105C5A.1271
Sequence Name  ? Y105C5A.1271 Organism  Caenorhabditis elegans
Automated Description  Enriched in RID; RIG; and RIGL based on RNA-seq and single-cell RNA-seq studies. Is affected by several genes including atfs-1; rrf-3; and pptr-1 based on RNA-seq and microarray studies. Is affected by five chemicals including methylmercury hydroxide; rifampin; and Psoralens based on RNA-seq studies. Biotype  SO:0000336
Genetic Position  :± Length (nt)  ? 1082
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00194667

Genomics

0 Transcripts

 

Other

0 CDSs

0 RNAi Result

29 Allele

Public Name
gk964078
gk964500
gk962765
gk963378
gk963590
gk963377
gk963795
gk962529
gk963948
gk480064
gk508658
gk400149
WBVar00197567
gk344140
gk568974
WBVar01657377
gk963791
WBVar02054098
WBVar00577635
WBVar01821700
WBVar01798297
WBVar01798296
WBVar01807065
WBVar01807064
gk220277
WBVar02022447
gk220278
WBVar01734000
WBVar01734001

1 Chromosome

WormBase ID Organism Length (nt)
IV Caenorhabditis elegans 17493829  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00194667 15649825 15650906 -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_chrIV_15649361..15649824   464 IV: 15649361-15649824 Caenorhabditis elegans

37 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  Transcripts that showed significantly decreased expression in atfs-1(cmh15) (null allele) animals comparing to in N2 animals at L4 larva stage. edgeR, fold change > 2, FDR < 0.05 WBPaper00060909:atfs-1(cmh15)_downregulated
  Transcripts that showed significantly increased expression in rrf-3(pk1426) comparing to in N2 at embryo stage. DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01. WBPaper00056169:rrf-3(pk1426)_upregulated_embryo
  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 significantly increased expression in hda-1(RNAi) embryos comparing to control animals. DESeq2, fold change > 2, FDR < 0.05. WBPaper00067044:hda-1(RNAi)_upregulated
  Transcripts that showed significantly increased expression in cco-1(RNAi) comparing to in vector control animals. The limma package47 was used for differential expression. Genes with a Benjamini-Hochberg adjusted P-value <0.05 and an absolute log fold change of 2 were considered differentially expressed. WBPaper00053402:cco-1(RNAi)_upregulated
  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 increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(+), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage. DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2. WBPaper00050859:upregulated_P-granule(-)GFP(+)_vs_control_day2-adult
  Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(-), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage. DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2. WBPaper00050859:upregulated_P-granule(-)GFP(-)_vs_control_day2-adult
  Transcripts that showed significantly increased expression in ints-5(RNAi) comparing to in N2. DESeq2 and edgeR. WBPaper00056284:ints-5(RNAi)_upregulated
  Transcripts that showed significantly increased expression in spr-1(ok2144) comparing to in N2. DESeq2, fold change > 2, p-value < 0.01. WBPaper00061203:spr-1(ok2144)_upregulated
  Transcripts that showed significantly increased expression in sams-3(RNAi) comparing to N2 animals injected with empty vector. Deseq FDR < 0.01, fold change > 2. WBPaper00065005:sams-3(RNAi)_upregulated
  Transcripts that showed significantly increased expression in ints-1(RNAi) animals comparing to control RNAi animals, at late L3 larva stage. DESeq2, v1.12.0, fold change > 2, FDR < 0.05 WBPaper00057068:ints-4(RNAi)_upregulated
  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
  Transcripts that showed altered expression in cat-2(RNAi) animals comparing to control animals injected with empty vector. p-value <= 0.05 WBPaper00066902:cat-2(RNAi)_regulated
  Transcripts that showed significantly increased expression in N2 animals exposed to 0.1mM Paraquat from hatching to reaching adult stage. DESeq2 version 1.22.2, p < 0.05 WBPaper00064716:paraquat_upregulated
  Transcripts that showed significantly increased expression in ints-4(RNAi) animals treated with 300uM CdCl2 from L1 to late L3 larva stage, comparing to control RNAi animals with the same Cadmium treatment. DESeq2, v1.12.0, fold change > 2, FDR < 0.05 WBPaper00057068:ints-4(RNAi)_upregulated_Cadmium
  Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin, 50uM Rifampicin and 100uM Psora from day 1 to day 3 adult hermaphradite. DESeq2(v1.14.1), fold change > 2, p-value < 0.05 WBPaper00055354:Rapamycin-Rifampicin-Psora_downregulated
  Transcripts that showed significantly increased expression in UR156 dmd-3(ok1327) him-5(e1490) males comparing to in CB4088 him-5(e1490) males at L4 stage. DESeq2, fold change > 2, FDR < 0.01 WBPaper00067232:dmd-3(ok1327)_upregulated_male
  Transcripts that showed significantly decreased expression in eat-2(ad465) comparing to in N2. Student's t-test, fold change > 2, p-value < 0.05. WBPaper00055386:eat-2(ad465)_downregulated
  Transcripts that showed significantly increased expression in shk-1(yum1003) comparing to in N2 animals. DESeq2 v1.36.0, fold change > 2, FDR < 0.05. WBPaper00067803:shk-1(yum1003)_upregulated
  Transcripts that showed significantly decreased expression in atfs-1(et18) comparing to in N2 animals at L4 larva stage. edgeR, fold change > 2, FDR < 0.05 WBPaper00060909:atfs-1(et18)_downregulated
  Transcripts that showed significantly increased expression in fhod-1(tm2363) comparing to in N2 animals. Differentially expressed genes (defined by false discovery rate (FDR) step up <= 0.05, fold change >1.5) were identified by Gene-Specific Analysis. WBPaper00060634:fhod-1(tm2363)_upregulated
  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
  Transcripts that showed significantly decreased expression in sma-3(wk30) comparing to in N2. EdgeR fold change > 2, FDR < 0.05. WBPaper00067781:sma-3(wk30)_downregulated
  Transcripts that showed significantly increased expression in strain CER276 sftb1(cer39[Q552P, R643C,K718E]) comparing to in N2 animals at L4 larva stage. DESeq2, fold change > 2 WBPaper00058725:sftb-1(cer39)_upregulated
heat shock: 33C 30min Transcripts that showed significantly increased expression in hsf-1(RNAi) animals, after heat shock at 33 C for 30min, comparing to in hsf-1(RNAi) 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:HeatShock_upregulated_hsf-1(RNAi)
  Genes regulated by unc-39(hp701). Authors compared genes enriched in FACS sorted GFP+ cells (RID, ALA, AIY, CAN and a sheath cell) vs. whole animal in WT hpIs202[Pceh-10GFP] (WT enriched sets), and genes enriched in FACS sorted GFP+ cells (ALA, AIY, CAN and a sheath cell) vs. whole animal in unc-39(hp701) hpIs202[Pceh-10GFP] (unc-39 enriched sets) at L2 larva stage. This set of genes are WT enriched but not unc-39 enriched, suggesting they are enriched in RID neurons. DESeq WBPaper00050496:unc-39(hp701)_regulated
  Transcripts that showed significantly increased expression in rrf-3(pk1426) comparing to in N2 at L2 larva stage. DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01. WBPaper00056169:rrf-3(pk1426)_upregulated_L2
  Transcripts that showed significantly increased expression in ints-2(RNAi) comparing to in N2. DESeq2 and edgeR. WBPaper00056284:ints-2(RNAi)_upregulated
  Transcripts that showed significantly increased expression in uaf-1(n4588) comparing to in N2 at embryo stage. DEGSeq 1.18.0, p < 0.05, fold change > 2. WBPaper00055364:uaf-1(n4588)_upregulated

0 Expression Patterns

0 GO Annotation

0 Homologues

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00194667 15649825 15650906 -1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

Length
1082

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_chrIV_15650907..15652036   1130 IV: 15650907-15652036 Caenorhabditis elegans