WormMine

WSWS298

An integrated data resource for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00271415 Gene Name  T05A7.13
Sequence Name  ? T05A7.13 Organism  Caenorhabditis elegans
Automated Description  Predicted to enable alpha-(1->3)-fucosyltransferase activity. Predicted to be involved in fucosylation. Biotype  SO:0001217
Genetic Position  :± Length (nt)  ? 1666
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1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00271415

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:T05A7.13.1 T05A7.13.1 1110   II: 4659713-4661378
 

Other

1 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:T05A7.13 T05A7.13 1110   II: 4659713-4660217

1 RNAi Result

WormBase ID
WBRNAi00018186

26 Allele

Public Name
gk963801
gk963053
WBVar01603748
WBVar01437554
gk141269
gk141267
gk141268
WBVar01783129
gk512152
gk378242
gk340397
gk501466
gk581135
WBVar01783127
gk457085
WBVar01783128
gk748741
tm10991
gk846468
gk740623
gk731396
gk836287
WBVar00171686
gk719611
gk352364
gk784504

1 Chromosome

WormBase ID Organism Length (nt)
II Caenorhabditis elegans 15279421  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00271415 4659713 4661378 -1

4 Data Sets

Name URL
WormBaseAcedbConverter  
GO Annotation data set  
C. elegans genomic annotations (GFF3 Gene)  
Panther orthologue and paralogue predictions  

1 Downstream Intergenic Region

WormBase ID Name Sequence Name Length (nt) Chromosome Location Organism
intergenic_region_chrII_4655935..4659712   3778 II: 4655935-4659712 Caenorhabditis elegans

30 Expression Clusters

Regulated By Treatment Description Algorithm Primary Identifier
  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 sin-3(tm1276) comparing to in N2. DESeq2, fold change > 2, p-value < 0.01. WBPaper00061203:sin-3(tm1276)_upregulated
  Transcripts that showed significantly decreased expression in sin-3(tm1276) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult. DESeq2, fold change > 2, adjusted p-value < 0.01 WBPaper00058598:sin-3(tm1276)_downregulated
  Transcripts that showed significantly increased 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)_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
  Genes found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014. N.A. WBPaper00026929:sir-2.1_overexpression_regulated
  Transcripts that showed significantly increased expression in endu-2(tm4977) comparing to in N2 animals at young adult stage. The DESeq2 (GalaxyVersion 2.11.40.6 + galaxy1) was used to determine differentiallyexpressed features from count tables of differential transcript abundances. log2FC > 1, FDR < 0.01. WBPaper00065749:endu-2(tm4977)_upregulated
  Transcripts that showed significantly increased expression in lin-29(n333) comparing to in N2 at day 1 adult stage. DESeq2, FDR < 0.01, fold change > 2. WBPaper00066970:lin-29(n333)_upregulated
  Transcripts that showed significantly increased expression in rict-1(mg360) comparing to in N2 at day 1 adult stage. DESeq2, FDR < 0.01, fold change > 2. WBPaper00066970:rict-1(mg360)_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 MT333 lin-29(n333) comparing to in N2 animals. DESeq2, fold change > 2, FDR < 0.01. WBPaper00067704:lin-29(n333)_upregulated
  Genes found to be regulated in daf-16(mgDf50) by resveratrol treatment with p < 0.01. N.A. WBPaper00026929:Resveratrol_regulated_daf-16
Bacteria: Pseudomonas donghuensis HYS Transcripts that showed significantly increased expression after 24 hours of infection by Pseudomonas donghuensis HYS, comparing to control animals exposed to OP50. DESeq2, fold change > 2, FDR < 0.05. WBPaper00068216:HYS_vs_OP50_upregulated
Bacteria: Pseudomonas donghuensis HYS Transcripts that showed significantly decreased expression after 24 hours of infection by Pseudomonas donghuensis HYS with deletion of ferric uptake regulator (FUR), comparing to control animals exposed to HYS. DESeq2, fold change > 2, FDR < 0.05. WBPaper00068216:FUR_vs_HYS_downregulated
  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
  Top 300 transcripts enriched in intestinal muscle, anal depressor muscle 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:mu_int_mu_anal
  Genome-wide analysis of developmental and sex-regulated gene expression profile. self-organizing map cgc4489_group_9
  Transcripts that showed significantly increased expression in lin-53(RNAi) embryos comparing to control animals. DESeq2, fold change > 2, FDR < 0.05. WBPaper00067044:lin-53(RNAi)_upregulated
  Transcripts that showed significantly decreased expression in tetraploid N2 animals after exposure to 5 uM doxorubicin for 72 hours at 15C from L1 to L4 larve stage. DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05. WBPaper00066110:Doxorubicin_downregulated_tetraploid
  Transcripts the showed altered expression after auxin induced sacy-1 depletion (24 hours of 2mM auxin treatment at 20C starting from young adult hermaphrodite stage). DESeq2 WBPaper00059334:sacy-1(depletion)_regulated
  Transcripts that showed significantly decreased expression in mab-5(e1751) without infection comparing to in N2 animals without infection. DESeq2, (FDR)-adjusted P-value < 0.05 and fold change >= 2. WBPaper00066587:mab-5(e1751)_downregulated_uninfected
Bacteria infection: Staphylococcus epidermidis Transcripts that showed significantly decreased expression in mab-5(e1239) animals exposed to S. epidermidis for 24 hours since L4 larva stage, comparing to uninfected mab-5(e1239) animals. DESeq2, (FDR)-adjusted P-value < 0.05 and fold change >= 2. WBPaper00066587:S.epidermidis_downregulated_mab-5(e1239)
  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
  Top 300 transcripts enriched in intestinal muscle, rectal muscle 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:Intestinal_and_rectal_muscle
  Transcripts that showed significantly increased expression in let-418(n3536) comparing to in N2. DESeq2, fold change > 2, p-value < 0.01. WBPaper00061203:let-418(n3536)_upregulated
  Transcripts that showed significantly increased expression in ZD101 tir-1(qd4) comparing to in N2 animals. DESeq2, fold change > 2, FDR < 0.01. WBPaper00067704:tir-1(qd4)_upregulated
Glucose rich diet. Transcripts that showed significantly increased expression in lpin-1(RNAi) animals grown on plates with additional 2% high glucose, comparing to lpin-1(RNAi) animals without additional glucose. Differentially expressed genes (fold change > 2 and adjusted p value < 0.05) were identified by using DESeq2 (v.1.22.2). WBPaper00059735:glucose_upregulated_lpin-1(RNAi)
  Single-cell RNA-Seq cell group 7_4 expressed in muscle. scVI 0.6.0 WBPaper00065841:7_4
  Top 300 transcripts enriched in MSapaaap, MSapappp, MSapapap, MSappapp, MSpppapp, MSppapap, MSppaaap, MSppappp 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:BWM_anterior
Bacteria diet: E.coli HB101 Transcripts downregulated in F3 generation of transgenic C. elegans expressing human alpha-syn in DA neurons fed HB101 0E. coli vs. OP50. Differentially expressed genes were extracted using DESeq, version 1.10.1. Assembly: PRJNA13758.WBPS13 WBPaper00065560:E.coli-HB101_downregulated_F3

2 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr2005843 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).  
    Expr2024060 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).  

2 GO Annotation

Annotation Extension Qualifier
  enables
  involved_in

23 Homologues

Type
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00271415 4659713 4661378 -1

2 Ontology Annotations

Annotation Extension Qualifier
  enables
  involved_in

0 Regulates Expr Cluster

1 Sequence

Length
1666

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_chrII_4661379..4662012   634 II: 4661379-4662012 Caenorhabditis elegans