WormMine: Gene WBGene00004830

• WormBase Gene ID: WBGene00004830
• Gene Name: slo-1
• Sequence Name: Y51A2D.19
• Brief Description: slo-1 encodes a voltage- and calcium-activated potassium (BK) channel; SLO-1 activity is required for muscle inactivation: mutants have wild-type levels of motor activity, but have less smooth movement and tend to stop and reverse direction; SLO-1 is expressed in neurons and in body wall and vulval muscle; SLO-1 localization in proximity to the EGL-19 L-type calcium channel in muscle membrane is mediated by the dystrophin-associated protein complex (DAPC) and the ISLO-1 adapter protein with which SLO-1 physically interacts and also colocalizes with in muscle membrane.
• Organism: Caenorhabditis elegans
• Automated Description: Enables calcium-activated potassium channel activity and voltage-gated potassium channel activity. Involved in several processes, including behavioral response to ethanol; nematode pharyngeal pumping; and sarcomere organization. Located in M band; striated muscle dense body; and synapse. Expressed in several structures, including AWC; body wall musculature; non-striated muscle; pharyngeal neurons; and somatic nervous system. Used to study Duchenne muscular dystrophy and alcohol use disorder. Human ortholog(s) of this gene implicated in Alzheimer's disease; idiopathic generalized epilepsy; paroxysmal nonkinesigenic dyskinesia 3; and spermatogenic failure. Is an ortholog of human KCNMA1 (potassium calcium-activated channel subfamily M alpha 1).
• Biotype: SO:0001217
• Genetic Position: V :16.7585 ±0.028814
• Length (nt): 15952

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004830

Genomics

13 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y51A2D.19c.1	Y51A2D.19c.1	3719	V: 18492261-18508212
Transcript:Y51A2D.19b.1	Y51A2D.19b.1	3673	V: 18492261-18508205
Transcript:Y51A2D.19k.1	Y51A2D.19k.1	3733	V: 18492261-18508205
Transcript:Y51A2D.19e.1	Y51A2D.19e.1	3785	V: 18492261-18508212
Transcript:Y51A2D.19a.1	Y51A2D.19a.1	3733	V: 18492267-18508205
Transcript:Y51A2D.19f.1	Y51A2D.19f.1	3423	V: 18492306-18507934
Transcript:Y51A2D.19g.1	Y51A2D.19g.1	3417	V: 18492306-18507934
Transcript:Y51A2D.19h.1	Y51A2D.19h.1	3357	V: 18492306-18507934
Transcript:Y51A2D.19i.1	Y51A2D.19i.1	3483	V: 18492306-18507934
Transcript:Y51A2D.19j.1	Y51A2D.19j.1	3462	V: 18492306-18507934
Transcript:Y51A2D.19l.1	Y51A2D.19l.1	3396	V: 18492306-18507934
Transcript:Y51A2D.19m.1	Y51A2D.19m.1	3441	V: 18492306-18507934
Transcript:Y51A2D.19d.1	Y51A2D.19d.1	3747	V: 18492306-18508198

Other

13 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y51A2D.19a	Y51A2D.19a	3423	V: 18492306-18492460
CDS:Y51A2D.19b	Y51A2D.19b	3357	V: 18492306-18492460
CDS:Y51A2D.19c	Y51A2D.19c	3396	V: 18492306-18492460
CDS:Y51A2D.19e	Y51A2D.19e	3462	V: 18492306-18492460
CDS:Y51A2D.19m	Y51A2D.19m	3441	V: 18492306-18492460
CDS:Y51A2D.19d	Y51A2D.19d	3483	V: 18492306-18492460
CDS:Y51A2D.19f	Y51A2D.19f	3423	V: 18492306-18492460
CDS:Y51A2D.19g	Y51A2D.19g	3417	V: 18492306-18492460
CDS:Y51A2D.19h	Y51A2D.19h	3357	V: 18492306-18492460
CDS:Y51A2D.19i	Y51A2D.19i	3483	V: 18492306-18492460
CDS:Y51A2D.19j	Y51A2D.19j	3462	V: 18492306-18492460
CDS:Y51A2D.19k	Y51A2D.19k	3417	V: 18492306-18492460
CDS:Y51A2D.19l	Y51A2D.19l	3396	V: 18492306-18492460

4 RNAi Result

• WBRNAi00007333
• WBRNAi00057136
• WBRNAi00037348
• WBRNAi00113603

462 Allele

• gk963271
• gk963489
• gk963304
• gk963809
• gk963637
• gk963292
• gk963480
• gk963970
• gk963971
• gk627200
• gk262558
• WBVar02062772
• WBVar02062774
• WBVar02062773
• WBVar02062776
• WBVar02062775
• WBVar02062778
• WBVar02062777
• WBVar02062779
• WBVar02062781
• WBVar02062780
• WBVar02062782
• otn11526
• WBVar02068917
• WBVar00247486
• WBVar00247482
• WBVar00247483
• WBVar00247484
• gk595722
• gk595721

1 Chromosome

• WormBase ID: V
• Organism: Caenorhabditis elegans
• Length (nt): 20924180

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004830
• Start: 18492261
• End: 18508212
• Strand: 1

4 Data Sets

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

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrV_18508213..18508863
• Length (nt): 651
• Chromosome Location: V: 18508213-18508863
• Organism: Caenorhabditis elegans

163 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 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
	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
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 increased expression after animals were treated with 50uM Rifampicin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin_upregulated
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	Genes significantly enriched in NSM neurons (isolated by FACS) versus the reference, according to RNAseq analysis towards total RNA.	Gene expression quantification and differential expression was analyzed using cufflinks v2.2.1. Enriched contains only genes significantly enriched (differentially expressed >= 2.4 fold in total RNA or >= 3.2 fold in DSN treated total RNA) in the NSM neurons versus the reference.	WBPaper00045974:NSM_enriched_totalRNA_RNAseq
	Transcripts expressed in NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:NMDA-neuron_expressed
	Genes with expression level regulated by genotype (N2 vs CB4856) and age at L3 larva and Late reproduction stage (96 hours at 24 centigrade).	For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR).	WBPaper00040858:eQTL_age_regulated_developing
	Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_daf-16(mu86);glp-1(e2141)
	Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_glp-1(e2141)
	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 after four-day-old young adult worms were placed on NGM plates seeded with OP50 in the presence 5% Agaro-oligosaccharides(AGO) for 24 h, comparing to animals grown in the absence of AGO.	Fold change > 2.	WBPaper00064306:Agaro-oligosaccharides_upregulated
	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
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 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
	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 detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
Gamma irradiation 100 mGY per hour for 72 hours since L1 larva.	Transcripts that showed significantly increased expression after exposure to 100mGy per hour gamma irradiation from L1 to day 1 adult hermaphrodite stage.	DESeq2, FDR <= 0.05, log2 fold change >= 0.3 or <= -0.3.	WBPaper00058958:100mGy-irradiation-72h_upregulated
	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
	Transcripts that showed significantly increased expression in hpk-1(pk1393) comparing to in N2 at adult day 2.	DESeq 2, fold change > 2, FDR < 0.05.	WBPaper00065581:hpk-1(pk1393)_upregulated
	Transcripts that showed significantly increased expression in hda-1(ne4752[3xFLAG-Degron-HDA-1]) in gonads dissected from 1-day old adult animals.	Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R.	WBPaper00061479:hda-1(ne4752)_upregulated
	Transcripts that showed significantly increased expression in mep-1(ne4629[MEP-1-GFP-Degron]) in gonads dissected from 1-day old adult animals.	Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R.	WBPaper00061479:mep-1(ne4629)_upregulated
	Transcripts that showed significantly increased expression in ubc-9(ne4833[ubc-9(G56R)] in gonads dissected from 1-day old adult animals.	Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R.	WBPaper00061479:ubc-9(ne4833)_upregulated
	Transcripts that showed significantly increased expression in mut-16(pk710), comparing to in N2 animals.	DESeq2 v. 1.22.2, adjusted p-value <= 0.05.	WBPaper00059605:mut-16(pk710)_upregulated
	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 npr-15(tm12539) comparing to in N2 at L4 larva stage.	Fold change > 2, FDR < 0.05.	WBPaper00066608:npr-15(tm12539)_upregulated
	Transcripts that showed significantly increased expression in srbc-48(ac23);kyIs262;fer-1(b232ts) comparing to in kyIs262;fer-1(b232ts), 24h after infection with P.aeruginosa.	DESeq2, FDR <0.05, fold change > 2.	WBPaper00059664:srbc-48(ac23)_upregulated
	Transcripts that showed significantly decreased expression in set-2(tm1630) animals at embryo stage, comparing to in N2 animals.	DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction.	WBPaper00060014:set-2(tm1630)_downregulated

15 Expression Patterns

• Primary Identifier: Expr4293
• Subcellular Localization: In the body-wall muscles, a rather faint but reproducible pattern reminiscent of the sarcomeric pattern of muscle organization was visible. To determine which sarcomere structures were labelled, transgenic worms were incubated with either anti-vinculin antibodies to mark the dense bodies (corresponding to the vertebrate Z line) or anti-myosin A antibodies to mark the M line. Upon superimposing the gfp and antibody images, the gfp labelling was found to be localized in rows which correspond to the dense bodies and to the M line of the body wall muscles.

• Primary Identifier: Expr2034117
• 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: Expr9103
• Remark: Picture: Figure 2.
• Pattern: Two independent transgenic strains were created that expressed GFP under the control of the ctn-1 promoter (Pctn-1) and slo-1 promoter (Pslo-1), respectively. The expression pattern of ctn-1 largely overlapped with that of slo-1. Specifically, both ctn-1 and slo-1 were expressed in many neurons and several types of muscles, including body-wall muscle, vulval muscle and stomatointestinal muscle. However, slo-1 appeared to be expressed in more neurons in the head than ctn-1, whereas ctn-1 was expressed in pharyngeal muscle cells and some other unidentified cells that did not express slo-1.

• Primary Identifier: Expr11464
• Subcellular Localization: GFP::SLO-1 expression is detected in neuronal cellbodies.

• Primary Identifier: Expr12699
• Pattern: slo-1 and slo-2 are expressed in both AWC neurons in the majority of wild-type animals, both slo-1 and slo-2 are asymmetrically expressed in AWCL or AWCR in a stochastic manner (AWCL>AWCR versus AWCL

• Primary Identifier: Expr12700
• Subcellular Localization: The single copy insertion transgenes showed that GFP::UNC-2, SLO-1::TagRFP, SLO-1::GFP, SLO-2::TagRFP, and GFP::EGL-19 were mainly localized on the plasma membrane of AWC cell bodies and also displayed a punctate pattern along AWC axons.

• Primary Identifier: Expr1032404
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr9897
• Reporter Gene: [Pslo-1::SLO-1::GFP] translational fusion.
• Pattern: When mStrawberry-tagged full-length DYB-1 (DYB-1::mStrawberry) was coexpressed with GFP-tagged full-length SLO-1 (SLO-1::GFP) under the controls of their respective promoters, the two fusion proteins appeared as puncta with colocalization at muscle dense body regions and along the dorsal nerve cord. The two fusion proteins also showed overlapping expression in the nerve ring. We coexpressed mStrawberry-tagged SLO-1 (SLO-1::mStrawberry) and GFP-tagged UNC-2 (UNC-2::GFP) in GABAergic neurons and found that the two fusion proteins colocalized in the ventral nerve cord suggesting that SLO-1 colocalized at presynaptic sites in motoneurons.

• Primary Identifier: Expr1779
• Remark: No GO_term assigned.
• Pattern: Staining of wild-type animals revealed immunoreactivity in synaptic regions of the nervous system including in both the nerve ring and nerve cords, as well as in the body-wall and vulval muscle.
• Subcellular Localization: The staining in the body-wall muscle was restricted and appeared as puncta, which is reminiscent of the localization pattern of ryanodine receptors.

• Primary Identifier: Expr1780
• Pattern: Fluorescence images from live wild-type adult hermaphrodite animals expressing the SLO-1a::GFP fusion as an extrachromosomal array. Lateral view showing bright fluorescence in the nerve ring and punctate fluorescence near the surface of body-wall muscle.

• Primary Identifier: Expr3950
• Pattern: Expression was seen in M4. Expression was also detected in most other pharyngeal neurons.

• Primary Identifier: Expr2015884
• 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: Expr12346
• Subcellular Localization: SLO-1::GFP exhibited bright, tiny punctate structures with weak diffuse fluorescence along the presynaptic regions of DA and DB neurons, but not in the dendrite regions. SLO-1::GFP puncta colocalized with the synaptic vesicle marker RAB-3::mCherry. Therefore, it is most likely that SLO-1::GFP puncta represent presynaptic terminals. Expression in DA and DB cholinergic motor neurons driven by the unc-129 promoter.

• Primary Identifier: Expr1013143
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1160582
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

32 GO Annotation

7 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004830
• Start: 18492261
• End: 18508212
• Strand: 1

32 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 15952

1 Sequence Ontology Term

• Name: gene

19 Strains

• WBStrain00022711
• WBStrain00022712
• WBStrain00022713
• WBStrain00022714
• WBStrain00022719
• WBStrain00022715
• WBStrain00022716
• WBStrain00022717
• WBStrain00022718
• WBStrain00022720
• WBStrain00022729
• WBStrain00022730
• WBStrain00022731
• WBStrain00022732
• WBStrain00029063
• WBStrain00029060
• WBStrain00005259
• WBStrain00005257
• WBStrain00004038

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrV_18487259..18492260
• Length (nt): 5002
• Chromosome Location: V: 18487259-18492260
• Organism: Caenorhabditis elegans