WormMine: Gene WBGene00004855

• WormBase Gene ID: WBGene00004855
• Gene Name: sma-1
• Sequence Name: R31.1
• Brief Description: sma-1 encodes a beta-H spectrin; during embryonic morphogenesis, SMA-1 activity is required for a normal rate of elongation and thus, for a wild-type body length upon hatching; in addition, SMA-1 is required for proper morphogenesis of the pharynx and the excretory cell; sma-1 mRNA transcripts are first detected in hypodermal cells at the beginning of embryonic morphogenesis with later expression visible in the developing pharynx, intestine, and excretory cell.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable actin filament binding activity. Involved in several processes, including nematode pharyngeal gland morphogenesis; nematode pharynx development; and regulation of anatomical structure size. Located in apical plasma membrane; cytoplasm; and nucleus. Expressed in several structures, including excretory cell; hermaphrodite gonad; neurons; pharynx; and vulval cell. Is an ortholog of human SPTBN5 (spectrin beta, non-erythrocytic 5).
• Biotype: SO:0001217
• Genetic Position: V :3.53974 ±0.002879
• Length (nt): 17175

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004855

Genomics

6 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:R31.1a.1	R31.1a.1	13098	V: 11899449-11916623
Transcript:R31.1e.1	R31.1e.1	12171	V: 11899564-11916141
Transcript:R31.1d.1	R31.1d.1	12570	V: 11901108-11916607
Transcript:R31.1b.1	R31.1b.1	12192	V: 11901350-11916141
Transcript:R31.1c.1	R31.1c.1	11943	V: 11902833-11916141
Transcript:R31.1f.1	R31.1f.1	11613	V: 11902833-11916141

Other

6 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:R31.1b	R31.1b	12192	V: 11901350-11901370
CDS:R31.1f	R31.1f	11613	V: 11902833-11903069
CDS:R31.1a	R31.1a	12501	V: 11899564-11899630
CDS:R31.1c	R31.1c	11943	V: 11902833-11903069
CDS:R31.1d	R31.1d	11862	V: 11901350-11901370
CDS:R31.1e	R31.1e	12171	V: 11899564-11899630

10 RNAi Result

• WBRNAi00083130
• WBRNAi00082909
• WBRNAi00026129
• WBRNAi00009083
• WBRNAi00052022
• WBRNAi00113741
• WBRNAi00064314
• WBRNAi00078483
• WBRNAi00081111
• WBRNAi00113745

240 Allele

• gk963271
• gk963301
• gk964458
• gk964459
• gk963618
• WBVar02061203
• otn8950
• gk964054
• gk964055
• gk625436
• gk662329
• ru3
• ru1
• ru13
• ru7
• ru18
• ru16
• ru19
• gk964109
• WBVar01866419
• WBVar01866421
• WBVar01866420
• WBVar01866425
• WBVar01866424
• WBVar01866423
• WBVar01866422
• WBVar01866429
• WBVar01866428
• WBVar01866427
• WBVar01866426

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004855
• Start: 11899449
• End: 11916623
• 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_11916624..11917088
• Length (nt): 465
• Chromosome Location: V: 11916624-11917088
• Organism: Caenorhabditis elegans

198 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
	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
	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 higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc).	DESeq2, fold change >= 2, FDR <= 0.01.	WBPaper00056826:SGP_biased
	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
	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 seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
	Transcripts expressed in vulva.	FPKM >= 1.	WBPaper00064122:vulva_transcriptome
	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 mrg-1(qa6200) comparing to in control animals in primordial germ cells (PGCs) at L1 larva stage.	DESeq2(v1.32.0), FDR < 0.05.	WBPaper00064315:mrg-1(qa6200)_upregulated_PGCs
	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 changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals.	Sleuth	WBPaper00051558:aging_regulated
	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 decreased expression in dissected female germline comparing to in dissected male germline.	Log2 Fold change > 2 or <-1, p-value < 0.05.	WBPaper00053599:female_vs_male_downregulated
	Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
	Transcripts that showed significantly increased expression in xrep-4(lax137).	DESeq2. Genes were selected if their p value < 0.01.	WBPaper00066062:xrep-4(lax137)_upregulated
	Transcripts that showed significantly increased expression in daf-2(e1370) comparing to in N2.	Differential gene expression analysis was performed using the quasi-likeli-hood framework in edgeR package v. 3.20.1 in R v. 3.4.1.	WBPaper00053810:daf-2(e1370)_upregulated
	Transcripts that showed significantly increased expression in pie-1(ne4443[PIE-1-Degron-GFP])	DESeq2. Differentially expressed genes were defined as twofold change and adjusted p-value less than 0.05.	WBPaper00061478:pie-1(ne4433)_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 pry-1(mu38) animals comparing to in N2 at L1 larva stage.	DESeq, FDR < 0.05	WBPaper00055626:pry-1(mu38)_upregulated
	Transcripts detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed

13 Expression Patterns

• Primary Identifier: Expr4485
• Remark: No detailed description on expression pattern in other life stage.
• Pattern: Expressed in anterior neurons (not individually identified in this study) from L2 to adult, posterior neurons from L2 to adult, intestine from L2 to adult, pharynx from L2 to adult, mid body cell bodies in some L4 animals, head hypodermal cells/muscle from L2 to adult.

• Primary Identifier: Expr4486
• Remark: No detailed description on expression pattern in other life stage.
• Pattern: Expressed in posterior neurons from L2 to adult, intestine from L2 to adult, pharynx from L2 to adult, head hypodermal cells/muscle in some L2/L3 animals.

• Primary Identifier: Expr2034124
• 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: Expr12323
• Pattern: sma-1:: GFP was expressed in all epithelial cells, as expected (hypodermis, excretory canal cell, intestine, pharyngeal muscles, and pharyngeal marginal cells) (McKeown et al. 1998) but was not detected in gland cells. Likewise, use of a nuclear-localized sma-1::GFP::HIS2B reporter did not indicate any expression in gland nuclei.

• Primary Identifier: Expr3918
• Remark: No detailed description on expression pattern in other life stages. The protein localization patterns observed using SMA-1 antisera are consistent with mRNA in situ expression data (see Expr1425), except in the excretory canal cell, where sma-1 mRNA is present during embryogenesis, but SMA-1 protein expression is delayed until the L1 stage. The timing of SMA-1 protein expression precisely correlates with the period when the excretory cell begins to rapidly elongate, during the first larval stage of development.
• Pattern: SMA-1 spectrin first appears in hypodermal cell precursors located on the dorsal surface of the embryo prior to enclosure. SMA-1 is present in the hypodermal cells as they enclose the embryo, and continues to be expressed in the dorsal, lateral, and ventral hypodermal cells throughout embryogenesis. SMA-1 is also expressed in gut and pharynx cells prior to embryonic enclosure, and throughout embryogenesis. In sma-1(ru18) null mutant embryos, both immunoblot and in situ immunofluorescence staining show no signal, demonstrating the antiserum is specific for SMA-1 protein.
• Subcellular Localization: During early morphogenesis, as the hypodermal cells migrate to enclose the embryo, SMA-1 is present at all epithelial cell boundaries, with some protein in the cytoplasm. Once enclosure is complete, SMA-1 protein localizes to the apical membrane of hypodermal, pharyngeal, and gut cells where it remains during embryonic elongation. SMA-1 is found in a speckled pattern at the apical surface of the both dorsal/ventral and seam hypodermis, with increased intensity near cell boundaries. The reorganization of SMA-1 in the hypodermis is concurrent with a change in the organization of actin, from cortical arrays to parallel bundles associated with the apical membrane.

• Primary Identifier: Expr1425
• Pattern: sma-1 transcripts are present in the embryonic epidermis at the start of morphogenesis. In a population of mixed-stage embryos hybridized with a sma-1 antisense probe, sma-1 RNA was not observed in pre-morphogenesis embryos. In particular, there was no sign of sma-1 transcripts in early cleavage-stage embryos (2-8 cells). In embryos just beginning morphogenesis, sma-1 RNA was present in cells along the dorsal surface of the embryo, corresponding to the location of the epidermis at this point in development. Examining embryos at successive stages of morphogenesis, it was found that sma-1 RNA changed in a pattern that exactly matched the movements of the migrating epidermal cells. During early morphogenesis, when the epidermal cell sheet spreads over the lateral surfaces of the embryo, sma-1-expressing cells were observed on the dorsal and lateral surfaces of the embryo, but not on the ventral surface or in the head region, which at this stage are not yet covered by the spreading epidermis. In cross-section, it can be seen that the sma-1 RNA is located in the outermost cell layer of the embryo. As morphogenesis progresses, the spreading epidermis encloses first the ventral surface of the embryo and then the head as the embryo bends ventrally and begins to elongate. In embryos at this stage of morphogenesis, there was a corresponding pattern in which sma-1 RNA was seen first on the ventral surface and then on the anterior (head) surface of the embryo. At the same time, the overall level of sma-1 RNA rapidly decreased as the embryo began to elongate. sma-1 RNA in the epidermis was not observed in embryos past the 2-fold stage. In addition to sma-1 expression in the cells of the epidermis, a line of sma-1 RNA was observed in the interior of the embryo, oriented along the anterior-posterior axis. Based on its location, this sma-1 RNA seems located in the developing digestive tract of the embryo, consisting of the pharynx and intestine. During early morphogenesis, it is difficult to determine the anterior extent of sma-1 staining in the interior of the embryo, but as the embryo begins to elongate, the level of sma-1 RNA increases and at the 1.5-fold stage sma-1 RNA is clearly present in both the pharynx and intestine. A lower level of pharyngeal/intestinal RNA was observed in 2- to 3-fold stage embryos. In these older embryos, sma-1 RNA was also found in the excretory cell and in an unidentified cell near the anus. Expression of sma-1 RNA was observed in several epithelial tissues: epidermis, pharynx, intestine and excretory cell. sma-1 RNA was not seen in the body wall muscle cells, which are arranged in four stripes underlying the epidermis. The highest level of sma-1 RNA was observed in the epidermis during the early stages of morphogenesis, prior to when differences are observed between development of wild-type and sma-1 embryos.

• Primary Identifier: Expr1032407
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr16294
• Subcellular Localization: Using CRISPR-Cas9, we inserted a fluorescent tag at the endogenous locus encoding VAB-10B, PAR-1, SMA-1, EPS-8A, and H24G06.1, an uncharacterized protein. We found that, like PTRN-1, all five proteins localized to the apical membranes of the embryonic intestine.

• Primary Identifier: Expr13842
• Pattern: Beginning in L4, SMA-1/βH is seen in both the spermathecal bag and SP-UTvalve with the strongest expression in the 4 cells most proximal to the SP-UT valve. Interestingly, this expression pattern changes during spermathecal development, and by adulthood, SMA-1/βH becomes restricted to a ring connecting the spermathecal bag and SP-UT valve.

• Primary Identifier: Expr1155661
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr16322
• 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: Expr2015891
• 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: Expr1010810
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

31 GO Annotation

4 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004855
• Start: 11899449
• End: 11916623
• Strand: 1

31 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 17175

1 Sequence Ontology Term

• Name: gene

18 Strains

• WBStrain00022629
• WBStrain00022738
• WBStrain00022476
• WBStrain00029024
• WBStrain00034370
• WBStrain00003945
• WBStrain00003984
• WBStrain00000353
• WBStrain00000354
• WBStrain00000327
• WBStrain00004402
• WBStrain00004083
• WBStrain00003958
• WBStrain00004364
• WBStrain00006194
• WBStrain00006251
• WBStrain00004526
• WBStrain00004217

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrV_11899146..11899448
• Length (nt): 303
• Chromosome Location: V: 11899146-11899448
• Organism: Caenorhabditis elegans