WormMine: Gene WBGene00004736

• WormBase Gene ID: WBGene00004736
• Gene Name: sca-1
• Sequence Name: K11D9.2
• Brief Description: The sca-1 gene encodes a sarco-endoplasmic reticulum Ca[2+] ATPase homolog that is required for development and muscle function; sca-1 is also a ortholog of human ATP2A1 (OMIM:108730), which when mutated leads to Darier-White disease (OMIM:124200).
• Organism: Caenorhabditis elegans
• Automated Description: Enables P-type calcium transporter activity and chromatin DNA binding activity. Involved in several processes, including chemical homeostasis; determination of adult lifespan; and response to stress. Located in cytoplasmic vesicle and endomembrane system. Expressed in several structures, including egg-laying apparatus; excretory system; intestine; non-striated muscle; and spermatheca. Human ortholog(s) of this gene implicated in Brody myopathy; hypertension (multiple); and keratosis (multiple). Is an ortholog of human ATP2A3 (ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 3).
• Biotype: SO:0001217
• Genetic Position: :±
• Length (nt): 4945

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004736

Genomics

4 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:K11D9.2b.1	K11D9.2b.1	3466	III: 10811906-10816844
Transcript:K11D9.2b.2	K11D9.2b.2	3334	III: 10812044-10816850
Transcript:K11D9.2a.1	K11D9.2a.1	3633	III: 10812532-10816844
Transcript:K11D9.2c.1	K11D9.2c.1	2799	III: 10812951-10815908

Other

3 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:K11D9.2c	K11D9.2c	2799	III: 10812951-10813253
CDS:K11D9.2a	K11D9.2a	3180	III: 10812951-10813253
CDS:K11D9.2b	K11D9.2b	3015	III: 10812323-10812354

43 RNAi Result

• WBRNAi00095683
• WBRNAi00107771
• WBRNAi00107770
• WBRNAi00066907
• WBRNAi00066714
• WBRNAi00085521
• WBRNAi00000344
• WBRNAi00002592
• WBRNAi00008988
• WBRNAi00065134
• WBRNAi00050600
• WBRNAi00001219
• WBRNAi00025952
• WBRNAi00030222
• WBRNAi00091094
• WBRNAi00071362
• WBRNAi00111147
• WBRNAi00063501
• WBRNAi00063502
• WBRNAi00063503
• WBRNAi00092780
• WBRNAi00092797
• WBRNAi00106907
• WBRNAi00092778
• WBRNAi00110093
• WBRNAi00065151
• WBRNAi00065152
• WBRNAi00081159
• WBRNAi00095898
• WBRNAi00095975

61 Allele

• gk964518
• gk963887
• gk963083
• gk184899
• gk962936
• ok3768
• gk958903
• gk337635
• gk932105
• gk838776
• gk717918
• gk3383
• gk962935
• gk184898
• WBVar01268514
• WBVar01268513
• WBVar01268512
• h15912
• gk953296
• gk330588
• gk580649
• gk184900
• gk184901
• gk461384
• gk871463
• gk698109
• gk790189
• gk388141
• gk383965
• gk508981

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004736
• Start: 10811906
• End: 10816850
• 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_chrIII_10811002..10811905
• Length (nt): 904
• Chromosome Location: III: 10811002-10811905
• Organism: Caenorhabditis elegans

206 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	oocyte proteins identified by two or more unique peptides during proteomics study.	In the pooled data set, 1453 C. elegans proteins were identified with a probability >= 0.9 according to ProteinProphet, of which 1165 proteins were identified by more than one unique peptide.	WBPaper00038289:oocyte_protein
	Genes with expression altered >= 3-fold in dpy-10(e128) mutants.	Data across the wild type series was analyzed using the Significance analysis of Microarrays (SAM) algorithm (to calculate the False Discovery Rate (FDR)).	WBPaper00035873:dpy-10_regulated
	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
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:bodywall-muscle_L1-larva_expressed
Bacteria: E.faecalis strain OG1RF	Transcripts that showed significantly increased expression after infection by E. faecalis OG1RF.	Ballgown was used to calculate differential expression of genes using FPKM data and to generate tables with fold change and P values. Genes were shortlisted with a cutoff of 2-fold change and P values of less than 0.05.	WBPaper00059754:E.faecalis_OG1RF_upregulated
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	Transcripts expressed in the epithelial tissues surrounding the pharynx that includes the arcade and intestinal valve (AIV) cells, according to PAT-Seq analysis using Pbath-15-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:arcade_intestinal-valve_expressed
	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 expressed in NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:NMDA-neuron_expressed
	Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:pharynx_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 expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h
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
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
	Maternal class (M): genes that are called present in at least one of the three PC6 replicates.	A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing.	[cgc5767]:expression_class_M
	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
Bacteria infection: Staphylococcus aureus MW2. 4 hours of exposure.	Transcripts that showed significantly increased expression after N2 animals had 4 hours of infection by Staphylococcus aureus (MW2).	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:S.aureus-4h_upregulated_N2
	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
	Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
	Proteins that showed significantly decreased expression in 1-day-old sek-1(km4) adults comparing to in wild type animals, both with 6 hours of cisplatin treatment.	The differential expression analysis was performed in R. Differentially expressed proteins were identified by using a two-sided t-test on log-transformed data.	WBPaper00065373:sek-1(km4)_downregulated_cisplatin
	Genes that showed expression levels higher than the corresponding reference sample (L3/L4 all cell reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:dopaminergic-neurons_L3-L4-larva_expressed
	Genes that showed expression levels higher than the corresponding reference sample (L3/L4 all cell reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:PVD-OLL-neurons_L3-L4-larva_expressed
	Transcriptions that showed significantly increased expression in skn-1(RNAi) comparing to empty vector injection into rrf-3(pk1426);daf-2(e1368) animals.	Genes with an absolute fold changeof at least 2 and standard p-values below 0.05 were considered as differentially expressed.	WBPaper00062193:skn-1(RNAi)_upregulated
	Transcripts that showed altered expression in cat-1(RNAi) animals comparing to control animals injected with empty vector.	p-value <= 0.05	WBPaper00066902:cat-1(RNAi)_regulated

9 Expression Patterns

• Primary Identifier: Expr1032336
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1816
• Pattern: All three reporter constructs were expressed in all major contractile tissues, starting during embryogenesis and continuing until adulthood. Fluorescence was particularly pronounced in striated muscle (body wall muscles used for locomotion), non-striated muscle (pharyngeal muscles used for pharyngeal pumping, vulval and uterine muscles used for egg laying, the sphincter muscle and anal depressor used for defecation), and in myoepithelial cells (gonadal sheath cells used for ovulation). Furthermore, all three constructs showed expression in the intestine. Some cells expressed CeSERCAb::GFP but not CeSERCAa::GFP. These include the somatic cells of the spermatheca and the excretory canal and the uterine sheath cells. No cells were found that expressed CeSERCAa::GFP but not CeSERCAb::GFP.
• Subcellular Localization: Fluorescence from Psca-1::GFP was evenly distributed over the cytosol. However, both CeSERCAa::GFP and CeSERCAb::GFP showed specific subcellular localization. Both fusion proteins were found in a tubular meshwork that was most distinct in the body wall muscle cells. This staining was continuous with staining at or near the dense bodies, structures functionally analogous to vertebrate Z-lines. In body wall muscle cells and other cells, staining was also often localized in internal vesicles and membrane-like structures, including the nuclear envelope.

• Primary Identifier: Expr831
• Remark: pRF4 was used as injection marker. See Expr831 for Expr_pattern for the same locus. sca-1 is called ser-2 in this paper.
• Pattern: Expression was seen in various tissues during all developmental stages. GFP expressed throughout the body, but more strongly in body wall muscles from early embryonic stages and persisted through adult stages. Fluorescence was also detected in several neuronal cells. The ventral nerve cord with distinct cell bodies, and excretory cells extending antero-posteriorly along the body also showed strong GFP expression.

• Primary Identifier: Expr832
• Remark: See Expr831 for Expr_pattern for the same locus.
• Pattern: Distinct staining was observed in pharyngeal muscles and vulva epithelial cells. Reduced but prominent signals were also observed in excretory cells extending antero-posteriorly along the whole body. However, no body wall muscle or vulva muscle were stained.

• Primary Identifier: Expr1154308
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1011984
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2015613
• 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: Chronogram1740
• Remark: Original chronogram file: chronogram.657.xml
• Reporter Gene: [K11D9.2:gfp] transcriptional fusion.

• Primary Identifier: Expr2033848
• 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).

37 GO Annotation

12 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004736
• Start: 10811906
• End: 10816850
• Strand: -1

37 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 4945

1 Sequence Ontology Term

• Name: gene

3 Strains

• WBStrain00037790
• WBStrain00037715
• WBStrain00001157

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIII_10816851..10816924
• Length (nt): 74
• Chromosome Location: III: 10816851-10816924
• Organism: Caenorhabditis elegans