WormMine: Gene WBGene00004951

• WormBase Gene ID: WBGene00004951
• Gene Name: spc-1
• Sequence Name: K10B3.10
• Brief Description: spc-1 encodes the C. elegans alpha spectrin ortholog; during development, spc-1 activity is required for body morphogenesis, formation of body wall muscles, locomotion, and larval development.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable actin filament binding activity. Involved in several processes, including embryonic body morphogenesis; nematode larval development; and regulation of growth. Predicted to be located in several cellular components, including cell junction; cortical actin cytoskeleton; and plasma membrane. Expressed in several structures, including body wall musculature; hermaphrodite gonad; intestine; pharynx; and vulval cell. Human ortholog(s) of this gene implicated in autosomal dominant distal hereditary motor neuronopathy 11; developmental and epileptic encephalopathy 5; and hereditary spherocytosis type 3. Is an ortholog of human SPTAN1 (spectrin alpha, non-erythrocytic 1).
• Biotype: SO:0001217
• Genetic Position: X :-12.1435 ±0.053657
• Length (nt): 9641

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004951

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:K10B3.10b.1	K10B3.10b.1	7804	X: 3117439-3127061
Transcript:K10B3.10a.1	K10B3.10a.1	7807	X: 3117439-3127079

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:K10B3.10a	K10B3.10a	7284	X: 3117944-3118072
CDS:K10B3.10b	K10B3.10b	7299	X: 3117944-3118072

10 RNAi Result

• WBRNAi00008979
• WBRNAi00025934
• WBRNAi00000485
• WBRNAi00050477
• WBRNAi00080495
• WBRNAi00060092
• WBRNAi00060093
• WBRNAi00022774
• WBRNAi00060091
• WBRNAi00060090

143 Allele

• gk963725
• otn9099
• ra409
• WBVar01757912
• WBVar01757911
• WBVar01757913
• WBVar01601324
• WBVar01601325
• WBVar01601326
• WBVar02068007
• WBVar00076897
• WBVar00076898
• WBVar00076899
• WBVar00076900
• WBVar02026877
• WBVar01825029
• gk920480
• gk786887
• gk707927
• gk925105
• gk624899
• gk815572
• gk785710
• gk856072
• gk844013
• gk428672
• gk463131
• gk488353
• gk798263
• gk769339

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004951
• Start: 3117439
• End: 3127079
• 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_chrX_3116590..3117438
• Length (nt): 849
• Chromosome Location: X: 3116590-3117438
• Organism: Caenorhabditis elegans

222 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 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
Osmotic stress	Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_Food
	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
	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
	Transcripts that showed significantly increased expression after animals were treated with 100uM Rapamycin and 50mM Metformin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Metformin_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
	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 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
	Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
	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
	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
	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 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 detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
	Proteins that showed significantly decreased expression after 1-day-old wild type adults were exposed to cisplatin (300ug per mL) for 6 hours.	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:Cisplatin_downregulated_WT
	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

13 Expression Patterns

• Primary Identifier: Expr2034255
• 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: Expr1904
• Remark: No details on expression pattern at other stages. spc-1 = alpha-spectrin
• Pattern: Wild-type embryos were stained with AS1 and examined by immunofluorescence microscopy. In early embryos, alpha-spectrin is found at or near the cell membrane in most if not all cells starting at the earliest stage of embryogenesis, indicating that alpha-spectrin is maternally supplied. After morphogenesis and organogenesis initiates, alpha-spectrin localizes to the body wall muscle, hypodermis, pharynx, intestine, and developing nervous system. In epithelial tissues, alpha-spectrin is found at both the apical and basolateral regions of the membrane. This is unlike the localization pattern observed for beta-spectrin, which is found in only the basolateral region of the membrane. With the exception of the apical regions, the localization of alpha-spectrin overlaps with the distribution of beta-spectrin.
• Subcellular Localization: membrane

• Primary Identifier: Expr1032465
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1200210
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr13841
• Reporter Gene: Strain COP1720 expressing spc-1::degron::mKate2 at the endogenous locus was generated by NemaMatrix (Eugene, OR, USA), characterized by genomic sequencing, and generously provided by the Zaidel-Bar Lab (Tel-Aviv University, Tel-Aviv, Israel).
• Pattern: SPC-1/α is prominently expressed in both the spermatheca and SP-UT valvebeginning in L4 and extending into adulthood. In adults, SPC-1/α is also faintly expressed in the sheath.

• Primary Identifier: Expr16320
• Pattern: SPC-1::GFP outlined all 7 vulval rings and was present near apical (luminal) membranes and also at sites of cell-cell contact (basolateral membranes). In contrast, UNC-70::GFP was present only at basolateral membranes, while SMA-1::GFP was present only at apical membranes. We showed previously that the spectrin-related protein VAB-10a/spectraplakin also localizes apically in the vulva (Cohen et al. 2020)

• Primary Identifier: Expr1154187
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2016020
• 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: Expr14822
• Subcellular Localization: The endogenous SPC-1 and UNC-70 protein in the knock in animals distribute to the cell membrane, which is in agreement with the localization pattern observed using immunofluorescence or GFP transgenesis.

• Primary Identifier: Expr14824
• Subcellular Localization: Endogenous spectrin localized to sensory cilia.

• Primary Identifier: Expr14858
• Subcellular Localization: PAK-1and SPC-1 colocalize with actin filaments.

• Primary Identifier: Expr13843
• Reporter Gene: Strain COP1720 expressing spc-1::degron::mKate2 at the endogenous locus was generated by NemaMatrix (Eugene, OR, USA), characterized by genomic sequencing, and generously provided by the Zaidel-Bar Lab (Tel-Aviv University, Tel-Aviv, Israel).
• Subcellular Localization: In adults, the spectrin cytoskeleton, composed of UNC-70/beta and SPC-1/ is most prominent at lateral cell junctions extending from the apical junction marker, AJM-1, to the basal surface. There is also a thinner layer of spectrin at the basal cell surface that overlaps with the basal, contractile, actomyosin bundles. This localization pattern is observed in young adult animals prior to the first ovulation and is maintained throughout adulthood.

• Primary Identifier: Expr1013781
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

17 GO Annotation

8 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004951
• Start: 3117439
• End: 3127079
• Strand: -1

17 Ontology Annotations

2 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly decreased expression in spc-1(cas971) comparing to in N2 at L1 larva stage.	DESeq2, fold change >= 2, FDR <= 0.05	WBPaper00057041:spc-1(cas971)_downregulated
	Transcripts that showed significantly increased expression in spc-1(cas971) comparing to in N2 at L1 larva stage.	DESeq2, fold change >= 2, FDR <= 0.05	WBPaper00057041:spc-1(cas971)_upregulated

1 Sequence

• Length: 9641

1 Sequence Ontology Term

• Name: gene

6 Strains

• WBStrain00034760
• WBStrain00047274
• WBStrain00047279
• WBStrain00047277
• WBStrain00047278
• WBStrain00005882

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrX_3127080..3129288
• Length (nt): 2209
• Chromosome Location: X: 3127080-3129288
• Organism: Caenorhabditis elegans