WormMine: Gene WBGene00004887

• WormBase Gene ID: WBGene00004887
• Gene Name: smn-1
• Sequence Name: C41G7.1
• Brief Description: smn-1 encodes a homolog of human SMN, which when mutated leads to spinal muscular atrophy (OMIM:253300).
• Organism: Caenorhabditis elegans
• Automated Description: Involved in several processes, including determination of adult lifespan; nematode pharyngeal pumping; and vulval development. Located in nucleus. Expressed in several structures, including body wall musculature; excretory cell; hypodermis; intestine; and vulval muscle. Used to study spinal muscular atrophy. Human ortholog(s) of this gene implicated in spinal muscular atrophy (multiple). Is an ortholog of human SMN1 (survival of motor neuron 1, telomeric) and SMN2 (survival of motor neuron 2, centromeric).
• Biotype: SO:0001217
• Genetic Position: I :3.78179 ±0.001059
• Length (nt): 1063

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004887

Genomics

3 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C41G7.1a.2	C41G7.1a.2	711	I: 9511174-9512022
Transcript:C41G7.1a.1	C41G7.1a.1	871	I: 9511174-9512236
Transcript:C41G7.1b.1	C41G7.1b.1	624	I: 9511283-9512098

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C41G7.1a	C41G7.1a	594	I: 9511283-9511497
CDS:C41G7.1b	C41G7.1b	624	I: 9511283-9511497

22 RNAi Result

• WBRNAi00070476
• WBRNAi00094308
• WBRNAi00042315
• WBRNAi00024793
• WBRNAi00024794
• WBRNAi00030287
• WBRNAi00103034
• WBRNAi00090763
• WBRNAi00094034
• WBRNAi00113515
• WBRNAi00116744
• WBRNAi00002092
• WBRNAi00003132
• WBRNAi00108107
• WBRNAi00094424
• WBRNAi00081094
• WBRNAi00070474
• WBRNAi00070473
• WBRNAi00070475
• WBRNAi00110410
• WBRNAi00110411
• WBRNAi00108101

16 Allele

• gk962858
• gk962706
• gk963902
• gk963849
• gk964316
• h7343
• ok355
• gk118916
• gk118917
• WBVar00155843
• gk318080
• gk844639
• gk534530
• gk589230
• rt248
• cb131

1 Chromosome

• WormBase ID: I
• Organism: Caenorhabditis elegans
• Length (nt): 15072434

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004887
• Start: 9511174
• End: 9512236
• Strand: -1

4 Data Sets

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

0 Downstream Intergenic Region

111 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly decreased expression in N2 after animals were exposed to E. faecalis OG1RF for 16 hours comparing to exposure to E. Coli OP50.	Cuffcompare and Cuffdiff	WBPaper00056090:E.faecalis_downregulated_N2
	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 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 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)
Bacteria diet: Escherichia coli HB101. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria E. coli HB101 for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:HB101_downregulated
Bacteria diet: Sphingomonas aquatilis Yellow. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria Sphingomonas aquatilis (Yellow) for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:S.aquatilis_downregulated
	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
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
25C vs. 20C	Transcripts that showed significantly increased expression in 1-day post L4 adult hermaphrodite N2 grown at 25C, comparing to in N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:25C_vs_20C_upregulated
	Transcripts that showed significantly increased expression in 10-days post L4 adult hermaphrodite N2 grown at 20C, comparing to in 1-day post L4 adult hermaphrodite N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:Day10_vs_Day1_upregulated
	Genes with increased RNA expression after 24 hours rotenone treatment	EdgeR provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting p-values were adjusted using the Benjamini and Hochbergs approach for controlling the false discovery rate (FDR). Transcripts with an adjusted p-value smaller 0.05 were assigned as differentially expressed.	WBPaper00044426:rotenone_24h_upregulated
	Transcripts that showed significantly decreased expression in tetraploid N2 comparing to diploid N2 animals at L4 larva stage.	DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05.	WBPaper00066110:tetraploid_vs_diploid_downregulated
	Transcripts that showed significantly decreased expression in hpl-2(tm1489) comparing to in N2 animals.	DESeq2, adjusted p-value < 0.05, log2 fold change > 2 or < -2.	WBPaper00054493:hpl-2(tm1489)_downregulated
	Transcripts detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
	Genes that were not enriched in either spermatogenic fem-3(q96gf) nor oogenic fog-2(q71) gonads, according to RNAseq analysis.	To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq.	WBPaper00045521:Gender_Neutral
	Transcripts that showed decreased expression in hlh-11(ko1) knockout strain comparing to in wild type background.	DESeq2, FDR < 0.05	WBPaper00060683:hlh-11(ko1)_downregulated
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly decreased expression in hpx-2(dg047) after animals were exposed to E. faecalis OG1RF for 16 hours comparing to exposure to E. Coli OP50.	Cuffcompare and Cuffdiff	WBPaper00056090:E.faecalis_downregulated_hpx-2(dg047)
	Genes found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014.	N.A.	WBPaper00026929:sir-2.1_overexpression_regulated
	Germline-intrinsic transcripts.	Comparisons were made between genotypes by subtracting the mean log value of one ratio from another, and the significance of the difference was evaluated using Student t-test for two populations. For the fem-3(gf) versus fem-1(lf) direct comparison, authors performed the same analysis, except they used a Students t-test for one population. Author chose a combination of a twofold difference with a t value exceeding 99% confidence (P < 0.01), because these criteria allowed the inclusion of essentially all genes that had previously been identified as germline-enriched in a wt/glp-4 hermaphrodite comparison. Additionally, requiring a twofold difference reduced false positives, as the number of genes with two-fold difference and a P<0.01 only included ~100 genes more than with P < 0.001, and almost all genes showed germline expression by in situ hybridization.	[cgc6390]:intrinsic
	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_downregulated
	Genes expressed in N2.	Expressed transcripts were identified on the basis of a Present call in 3 out of 4 N2 experiments as determined by Affymetrix MAS 5.0.	WBPaper00025141:N2_Expressed_Genes
	Embryonic class (E): genes that significantly increase in abundance at some point during embryogenesis.	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_E
	Transcripts that showed significantly decreased 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)_downregulated
	Transcripts that showed significantly decreased expression in hsf-1(RNAi) animals comparing to in control animals, without heat shock.	Transcripts that were differentially expressed in different conditions, compared to the hsf-1(+);-HS control, were determined with CuffDiff, which uses the Benjamini-Hochberg correction for multiple testing to obtain the q-value (the FDR-adjusted the p-value).	WBPaper00049942:hsf-1(RNAi)_downregulated

10 Expression Patterns

• Primary Identifier: Expr2034153
• 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: Expr1231
• Remark: Germline expression confirmed by immunofluorescence. The actual sequence mentioned in the paper is C41G7.1b, which was called CeSMN, also believed to be egl-32 by authors.
• Pattern: Intense fluorescence in the nuclei of many somatic cells including neurons, body wall muscle and vulval muscle cells, hypodermal and and gut cells and the excretory cell.
• Subcellular Localization: The excretory cell canals and neuronal processes were clearly fluorescent, whereas no significant cytoplasmic signal was apparent for other cell types. Also detected strong fluorescence in the nuclei of the germ cells.

• Primary Identifier: Expr1032426
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1229
• Remark: Germline expression confirmed by immunofluorescence. The actual sequence mentioned in the paper is C41G7.1b, which was called CeSMN, also believed to be egl-32 by authors.
• Pattern: Expressed from the zygotic stage in both pronuclei and in all the blastomeres throughout embryonic development. In mitotic stages, the CeSMN protein disappears from the nucleoplasm, and is re-incorporated into the newly formed nuclei. CeSMNB is present in virtually all the cell nuclei of the young nematodes.
• Subcellular Localization: A strong homogeneous staining is present in all of the interphasic nuclei, although some diffusive signal is also visible in the cytoplasm.

• Primary Identifier: Expr2015920
• 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: Expr1146303
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr12328
• Subcellular Localization: The SMN-1::GFP fusion protein is localized in the body-wall muscle nuclei. smn-1 driven by the myo-3 promoter.

• Primary Identifier: Expr13407
• Subcellular Localization: SMN-1 expressed from the rescuing smn-1::mCherry transgene is seen in the nucleus and cytoplasm. In the cytoplasm, most SMN-1::mCherry is found at myofilaments in regularly spaced puncta. These puncta appear more ordered in adult muscle as compared with younger muscle. The SMN-1 expression pattern at muscle myofilaments resembles that of ARX-2::mCherry. To test whether ARX-2 and SMN-1 colocalize, we generated transgenic animals expressing both smn-1::GFP and arx-2::mCherry in muscle. SMN-1::GFP colocalizes with ARX-2::mCherry at the thin filaments. However, only SMN-1 is observed in the nucleus. We occasionally observed SMN-1::GFP and ARX-2::mCherry in peri-nuclear puncta. We conclude that SMN-1 and ARX-2 colocalize at muscle myofilaments adjacent to elongated mitochondrial tubules.

• Primary Identifier: Expr1230
• Remark: Germline expression confirmed by immunofluorescence. The actual sequence mentioned in the paper is C41G7.1b, which was called CeSMN, also believed to be egl-32 by authors.
• Pattern: A single CeSMN transcript was present from the embryonic stage. Semiquantitative PCR on cDNA samples obtained at 2 hour intervals from early L1 to adult do not appear to vary significantly throughout larval development.

• Primary Identifier: Expr1018011
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

12 GO Annotation

1 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004887
• Start: 9511174
• End: 9512236
• Strand: -1

12 Ontology Annotations

2 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increased expression in smn-1(ok355) heterozygots using balancer hT2 comparing to in N2.	DESeq v1.14.0, log2FC > 1, q <= 0.05.	WBPaper00056809:smn-1(ok355)_upregulated
	Transcripts that showed significantly decreased expression in smn-1(ok355) heterozygots using balancer hT2 comparing to in N2.	DESeq v1.14.0, log2FC > 1, q <= 0.05.	WBPaper00056809:smn-1(ok355)_downregulated

1 Sequence

• Length: 1063

1 Sequence Ontology Term

• Name: gene

4 Strains

• WBStrain00024207
• WBStrain00024206
• WBStrain00047286
• WBStrain00008302

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrI_9512237..9512306
• Length (nt): 70
• Chromosome Location: I: 9512237-9512306
• Organism: Caenorhabditis elegans