WormMine: Gene WBGene00219650

• WormBase Gene ID: WBGene00219650
• Gene Name: linc-56
• Sequence Name: C14A11.12
• Organism: Caenorhabditis elegans
• Automated Description: Enriched in neurons based on RNA-seq and single-cell RNA-seq studies. Is affected by several genes including mter-4; etr-1; and osm-3 based on RNA-seq studies. Is affected by Zidovudine based on RNA-seq studies.
• Biotype: SO:0001641
• Genetic Position: X :-12.8781±
• Length (nt): 755

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00219650

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C14A11.12	C14A11.12	755	X: 2822754-2823508

Other

0 CDSs

0 RNAi Result

12 Allele

• gk963725
• WBVar00076532
• WBVar00076530
• WBVar00076531
• gk274426
• WBVar02047683
• gk693230
• gk682858
• WBVar02044398
• WBVar01822271
• WBVar02026839
• gk274427

1 Chromosome

• WormBase ID: X
• Organism: Caenorhabditis elegans
• Length (nt): 17718942

1 Chromosome Location

• Feature . Primary Identifier: WBGene00219650
• Start: 2822754
• End: 2823508
• Strand: 1

2 Data Sets

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

0 Downstream Intergenic Region

29 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
	Single-cell RNA-Seq cell group 84_0 expressed in neuron.	scVI 0.6.0	WBPaper00065841:84_0
	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 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 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
	Transcripts that showed significantly decreased expression in whole animal day 1 N2 adults comparing to in whole animal day 8 N2 adults.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00066978:Day1Adult_vs_Day8Adult_downregulated_neuron
	Transcripts that showed significantly increased expression in sma-2(rax5) comparing to in N2 at 1-day post-L4 adult hermaphrodite	HTseq-count was used to count reads mapped to each gene and counting data was imported to EdgeR for statistical analysis. Statistical significance was defined by adjusted P value (false discovery rate, FDR) of <0.05.	WBPaper00053184:sma-2(rax5)_upregulated
	Transcripts that showed significantly increased expression in sma-4(rax3) comparing to in N2 at 1-day post-L4 adult hermaphrodite	HTseq-count was used to count reads mapped to each gene and counting data was imported to EdgeR for statistical analysis. Statistical significance was defined by adjusted P value (false discovery rate, FDR) of <0.05.	WBPaper00053184:sma-4(rax3)_upregulated
Bacteria infection: Pseudomonas aeruginosa PA14. 24 hours of exposure at 25C.	Transcripts that showed significantly decreased expression in N2 animals with 24 hours of exposure to P. aeruginosa PA14 for 24 hrs at 25C, comparing to N2 animals without exposure to PA14.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00058948:PA14_downregulated
	Transcripts that showed significantly decreased expression in gonad cyd-1(RNAi) animals in daf-2(e1370) at late L4 stage.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00067493:gonad-cyd-1(RNAi)_downregulated_daf-2(e1370)
	Transcripts that showed significantly altered expression after 24 hour exposure to zidovudine (AZT) starting at L1 lava stage.	DESeq	WBPaper00053302:zidovudine_24h_regulated
Temperature Shift: 25C vs 15C for 16 hours at L4 larva stage.	Transcripts that showed significantly increased expression in AFD neurons comparing to in whole animals.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00065158:AFD_enriched
	Transcripts that showed significantly decreased expression in mter-4(syb3662 syb3403) comparing to in N2.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00061995:mter-4(syb3662syb3403)_downregulated
Feeding for 4 hours after L1 arrest.	Transcripts that showed significantly decreased expression after 4 hours of feeding of starvation-induced arrested L1 rsks-1(ok1255) animals, comparing to animals continue to starve.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00067518:food_downregulated_rsks-1(ok1255)
	Transcripts that showed significantly increased expression in osm-3(p802) comparing to in N2 animals grown on OP50.	fold change > 2, FDR < 0.05	WBPaper00066858:osm-3(p802)_upregulated_OP50
	Transcripts that showed differential expression between 24 and 26 hours post hatching L2d and dauer committed larvae of daf-9(dh6), triggered by the dafachronic acid (DA) growth hormone. Cluster 4 genes increased expression transiently during dauer commitment.	Benjamini Hochberg corrected q-value < 0.01.	WBPaper00053388:dauer_regulated_Cluster4
	Single-cell RNA-Seq cell group 121_0 expressed in neuron.	scVI 0.6.0	WBPaper00065841:121_0
Heat shock: 35C for 1 hour.	Transcripts that showed significantly decreased expression immediately after 1-day post L4 adult hermaphrodite endu-2(tm4977) animals were exposed to 35C for 1 hour.	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:Heat-Shock_downregulated_endu-2(tm4977)
	Transcripts that showed significantly increased expression in sensory neuron (labeled by iaIs25[Pgcy-37::GFP + unc-119(+)]) comparing to in whole worm.	Fold change > 2, p-value < 0.05.	WBPaper00060661:sensory-neuron_enriched
	Single-cell RNA-Seq cell group 104_0 expressed in neuron.	scVI 0.6.0	WBPaper00065841:104_0
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)
	Single-cell RNA-Seq cell group 47_0 expressed in neuron.	scVI 0.6.0	WBPaper00065841:47_0
	Transcripts of noncoding genes that showed significantly decreased 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_depleted_noncoding-RNA
	Single-cell RNA-Seq cell group 47_1 expressed in neuron.	scVI 0.6.0	WBPaper00065841:47_1
	Single-cell RNA-Seq cell group 63_0 expressed in neuron.	scVI 0.6.0	WBPaper00065841:63_0
	Single-cell RNA-Seq cell group 87_0 expressed in neuron.	scVI 0.6.0	WBPaper00065841:87_0
	Single-cell RNA-Seq cell group 106_0 expressed in neuron.	scVI 0.6.0	WBPaper00065841:106_0

0 Expression Patterns

0 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00219650
• Start: 2822754
• End: 2823508
• Strand: 1

0 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 755

1 Sequence Ontology Term