WormMine: Gene WBGene00000528

• WormBase Gene ID: WBGene00000528
• Gene Name: clh-1
• Sequence Name: T27D12.2
• Brief Description: clh-1 encodes two CLC-type chloride channels via alternative splicing, homologous to human CLC1 (OMIM:118425) and CLC2 (OMIM:600570); CLH-1a and CLH-1b are required for maintenance of normal body shape; null mutations of clh-1 cause abnormal alae and a wider body than normal, with the body phenotype being reversible by culture medium of high osmolarity.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable voltage-gated chloride channel activity. Predicted to be involved in chloride transport. Predicted to be located in plasma membrane. Expressed in several structures, including amphid sensillum; anterior hypodermis; cephalic sheath cell; spermatheca; and vulval cell. Human ortholog(s) of this gene implicated in idiopathic generalized epilepsy 11; myotonia congenita (multiple); and primary hyperaldosteronism. Is an ortholog of human CLCN1 (chloride voltage-gated channel 1) and CLCN2 (chloride voltage-gated channel 2).
• Biotype: SO:0001217
• Genetic Position: II :4.08004 ±0.003234
• Length (nt): 9955

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00000528

Genomics

7 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T27D12.2e.1	T27D12.2e.1	3095	II: 11846507-11854743
Transcript:T27D12.2b.1	T27D12.2b.1	3063	II: 11846508-11854745
Transcript:T27D12.2a.1	T27D12.2a.1	3066	II: 11846515-11854743
Transcript:T27D12.2f.1	T27D12.2f.1	2553	II: 11846859-11851673
Transcript:T27D12.2g.1	T27D12.2g.1	2586	II: 11846859-11851673
Transcript:T27D12.2c.1	T27D12.2c.1	2922	II: 11846859-11856461
Transcript:T27D12.2d.1	T27D12.2d.1	2736	II: 11846859-11856461

Other

7 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T27D12.2e	T27D12.2e	2742	II: 11846859-11846974
CDS:T27D12.2c	T27D12.2c	2922	II: 11846859-11846974
CDS:T27D12.2d	T27D12.2d	2736	II: 11846859-11846974
CDS:T27D12.2a	T27D12.2a	2721	II: 11846859-11846974
CDS:T27D12.2b	T27D12.2b	2709	II: 11846859-11846974
CDS:T27D12.2f	T27D12.2f	2553	II: 11846859-11846974
CDS:T27D12.2g	T27D12.2g	2586	II: 11846859-11846974

3 RNAi Result

• WBRNAi00054307
• WBRNAi00019329
• WBRNAi00077546

219 Allele

• gk963801
• gk963053
• gk962684
• gk963539
• qa901
• qa900
• WBVar00246501
• gk962823
• WBVar01605168
• WBVar01605169
• WBVar01377317
• WBVar01377306
• WBVar01547221
• WBVar01547223
• h8915
• WBVar02029281
• WBVar00229890
• WBVar00229889
• WBVar00229887
• WBVar01405782
• WBVar01405781
• WBVar00105999
• WBVar00106001
• WBVar00106000
• WBVar02033679
• gk156016
• gk156015
• gk156018
• gk156017
• gk156014

1 Chromosome

• WormBase ID: II
• Organism: Caenorhabditis elegans
• Length (nt): 15279421

1 Chromosome Location

• Feature . Primary Identifier: WBGene00000528
• Start: 11846507
• End: 11856461
• Strand: -1

3 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrII_11846036..11846506
• Length (nt): 471
• Chromosome Location: II: 11846036-11846506
• Organism: Caenorhabditis elegans

155 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts of coding 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_coding-RNA
	Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons.	DESeq. False discovry rate (FDR) < 0.1.	WBPaper00048988:neuron_expressed
adult vs dauer larva	Transcripts that showed differential expression in adult vs dauer lava in N2 animals at 20C.	N.A.	WBPaper00050488:adult_vs_dauer_regulated_N2_20C
	mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis.	Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05.	WBPaper00045420:fertilization_downregulated_transcript
	TGF- Dauer pathway adult transcriptional targets. Results obtained by comparing the microarray results of the dauer-constitutive mutants daf-7(e1372), daf-7(m62), and daf-1(m40) with dauer-defective mutants daf-3(mgDf90), daf-5(e1386), and daf-7(e1372);daf-3(mgDf90) double mutants at the permissive temperature, 20C, on the first day of adulthood.	SAM	WBPaper00031040:TGF-beta_adult_upregulated
	Transcripts that showed significantly increased expression glp-1(e2141); TU3401 animals comparing to in TU3401 animals.	Fold change > 2, FDR < 0.01.	WBPaper00065993:glp-1(e2141)_upregulated
Bacteria infection: Enterococcus faecalis	Genes with increased expression after 24 hours of infection by E.faecalis Fold changes shown are pathogen vs OP50.	For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated.	WBPaper00038438:E.faecalis_24hr_upregulated_TilingArray
	Transcripts that showed significantly higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc).	DESeq2, fold change >= 2, FDR <= 0.01.	WBPaper00056826:SGP_biased
	Transcripts expressed in body muscle, according to PAT-Seq analysis using Pmyo-3-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:body-muscle_expressed
	Transcripts expressed in GABAergic neuron, according to PAT-Seq analysis using Punc-47-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:GABAergic-neuron_expressed
	Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:hypodermis_expressed
	Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_expressed
	Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_daf-16(mu86);glp-1(e2141)
	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 increased expression in day 1 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_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)
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_6h
	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 increased expression in hrde-1(tm1200) animals, comparing to in N2, after growing at 25C for five generations (late generation).	CuffDiff2	WBPaper00051265:F4_hrde-1(tm1200)_upregulated
	Transcripts that showed significantly increased expression in aak-1(tm1944);aak-2(ok524) animals comparing to in N2.	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:aak-1(tm1944);aak-2(ok524)_upregulated
	Transcripts that showed significantly decreased 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_downregulated
Heat Shock: 35C 4 hours at L4 larva stage.	Transcripts that showed significantly decreased expression after L4 larva N2 animals were heat stressed at 35C for 4 hours	DESeq2	WBPaper00057154:HeatShock_downregulated_mRNA
	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 depleted in purified oocyte P bodies comparing to in whole oocytes.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00065975:P-body_vs_oocyte_depleted
	Transcripts depleted in purified oocyte P bodies comparing to in the whole animal.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00065975:P-body_vs_WholeAnimal_depleted
	Transcripts that showed significantly increased expression in sftb-1(cer6) deletion homozygous comparing to to in N2 animals at L4 larva stage.	DESeq2, fold change > 2	WBPaper00058725:sftb-1(cer6)_downregulated
	Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
Reduced humidity (98% relative humidity).	Genes that were down-regulated after one day exposure to reduced humidity (98% relative humidity) according to microarray analysis.	Multiple hypothesis testing with the Benjamini-Hochberg correction was applied on calculated p-values. A change in the expression level was considered to be significant if the adjusted p-value was less than 0.001.	WBPaper00044578:reduced-humidity_downregulated_microarray
	Transcripts that showed significantly increased 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)_upregulated_PA14
	Genes that showed oscillating mRNA expression level throughout the 16 hour time courses from L3 larva to young adult.	The following three lines of R code were used to perform the classification: increasing <-2*amplitude-PC1 < -1.7; oscillating <-!increasing & (amplitude > 0.55); flat <-!increasing & !oscillating; Note that the amplitude of a sinusoidal wave corresponds to only half the fold change between trough and peak.	WBPaper00044736:oscillating_dev_expression

9 Expression Patterns

• Primary Identifier: Expr1030315
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr15673
• Pattern: It has previously been reported that clh-1 is expressed in hypodermal cells, seam cells, D-cells of the vulva, and neuronal and glial cells of the head (Grant et al., 2015; Nehrke et al., 2000). These expression patterns were confirmed with a transcriptional reporter (clh-1p::nls4::mTFP). Of the head neurons, at least ASE, AWA, and AWC sensory neurons expressed the reporter.

• Primary Identifier: Expr12665
• Pattern: clh-1 is expressed in the AMsh cell body and processes. In addition to AMsh glia, expression of GFP was observed in other cells in the head, including 3 sets of neurons located posterior to the C. elegans nerve ring, as was previously reported (Nehrke et al., 2000).

• Primary Identifier: Expr1121
• Pattern: Seam cells and hypodermal cells of the head, epithelial D-cell of the vulva, spermatheca, neurons in the head ganglia, and posterior intestinal cells.

• Primary Identifier: Expr978
• Remark: Reporter gene fusion type not specified.
• Pattern: lacZ staining was clearly observed only in hypodermal cells, called seam cells. These cells extend along the lateral sides of the worm bodies and form two seam syncytia in adults. On the other hand, the transgenic worms carrying pTO17-13 strongly expressed the protein in hypodermal cells localized in their vulvae and heads, together with the enhanced expression in seam cells.

• Primary Identifier: Expr2010228
• 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: Expr2028470
• 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: Expr1157851
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1013381
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

11 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00000528
• Start: 11846507
• End: 11856461
• Strand: -1

11 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 9955

1 Sequence Ontology Term

• Name: gene

5 Strains

• WBStrain00031546
• WBStrain00040609
• WBStrain00040608
• WBStrain00051724
• WBStrain00051725

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrII_11856462..11861028
• Length (nt): 4567
• Chromosome Location: II: 11856462-11861028
• Organism: Caenorhabditis elegans