WormMine: Gene WBGene00194866

• WormBase Gene ID: WBGene00194866
• Gene Name: Y41C4A.22
• Sequence Name: Y41C4A.22
• Organism: Caenorhabditis elegans
• Automated Description: Enriched in ASG; ASGL; ASGR; PHB; and neurons based on single-cell RNA-seq and RNA-seq studies. Is affected by several genes including etr-1; hpl-2; and spr-5 based on RNA-seq studies.
• Biotype: SO:0001217
• Genetic Position: :±
• Length (nt): 1210

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00194866

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y41C4A.22.1	Y41C4A.22.1	369	III: 11695275-11696484

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y41C4A.22	Y41C4A.22	264	III: 11695342-11695420

0 RNAi Result

31 Allele

• gk963887
• gk964363
• gk964364
• gk963799
• WBVar00180293
• WBVar00180294
• WBVar00180292
• WBVar01646695
• gk337638
• tm8951
• WBVar01448902
• gk464095
• gk408119
• WBVar01939854
• gk562399
• gk384905
• gk656217
• WBVar01270447
• WBVar01270446
• WBVar00566204
• WBVar02057340
• WBVar01852392
• WBVar01852391
• WBVar01919420
• WBVar01852390
• WBVar01507925
• WBVar01542354
• WBVar01952881
• gk186740
• WBVar01548869

1 Chromosome

• WormBase ID: III
• Organism: Caenorhabditis elegans
• Length (nt): 13783801

1 Chromosome Location

• Feature . Primary Identifier: WBGene00194866
• Start: 11695275
• End: 11696484
• Strand: 1

2 Data Sets

• WormBaseAcedbConverter
• C. elegans genomic annotations (GFF3 Gene)

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrIII_11696485..11696572
• Length (nt): 88
• Chromosome Location: III: 11696485-11696572
• Organism: Caenorhabditis elegans

14 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased 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_upregulated_neural
	Transcripts enriched in ASG according to single cell RNAseq.	Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched.	WBPaper00061651:ASG_enriched
	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
	Single-cell RNA-Seq cell group 71_0 expressed in neuron.	scVI 0.6.0	WBPaper00065841:71_0
	Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
	Transcripts that showed significantly decreased expression in hpl-2(tm1489) comparing to in N2 animals.	DESeq2, adjusted p-value < 0.05, log2 fold change > 2 or < -2.	WBPaper00054493:hpl-2(tm1489)_downregulated
	Transcripts of coding genes that showed significantly increased expression in muscle.	DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed.	WBPaper00062325:muscle_enriched_coding-RNA
moderate static magnetic field	Transcripts that showed significantly decreased expression after exposure to moderate static magnetic field.	N.A.	WBPaper00064509:static-magnetic-field_downregulated
	Transcripts that showed significantly increased expression in cco-1/cox-5B(RNAi) animals comparings to animals injected with vector control.	LimmaVoom. The genes with a BenjaminiHochbergadjusted P value < 0.05 were defined as statistically significant. Genes whose expressions were significantly upregulated with log2FC > 0.393.	WBPaper00064637:cox-5B(RNAi)_upregulated
	Transcripts that showed significantly increased expression in FACS sorted neuron cells (labelled by pan-neuronal GFP) from edIs6[unc-119::GFP + rol-6(su1006)]; thoc-5(wy822) comparing to in edIs6.	DESeq2, log2 fold change > 2, adjusted p-value < 0.005.	WBPaper00055103:thoc-5(wy822)_upregulated
	Transcripts that showed significantly decreased expression in alg-1(gk204) comparing to in N2 at 5-days post L4 adult hermaphrodites.	DESeq, fold change > 2, adjusted p-value < 0.05.	WBPaper00054758:alg-1(gk204)_downregulated
	Top 300 transcripts enriched in ASGL, ASGR 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:ASG
	Transcripts enriched in PHB according to single cell RNAseq.	Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched.	WBPaper00061651:PHB_enriched
	Transcripts that showed significantly decreased expression in spr-5(by101);met-2(n4256) L1 animals comparing to in N2 control.	DeSeq2 (v.2.11.40.2), p < 0.05.	WBPaper00060886:spr-5(by101);met-2(n4256)_downregulated

3 Expression Patterns

• Primary Identifier: Expr2025665
• Pattern: 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).

• Primary Identifier: Expr1159848
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2007429
• Pattern: 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).

0 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00194866
• Start: 11695275
• End: 11696484
• Strand: 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 1210

1 Sequence Ontology Term