WormMine: Gene WBGene00004857

• WormBase Gene ID: WBGene00004857
• Gene Name: sma-3
• Sequence Name: R13F6.9
• Brief Description: sma-3 encodes a Smad protein; during development, SMA-3 functions as part of a DBL-1/SMA-6 TGF-beta-related signaling pathway that controls body size and male tail sensory ray and spicule formation; sma-3, through this pathway, also regulates reproductive aging; studies have shown that a reduction of TGF-beta pathway genes extends reproductive span by maintaining oocyte and germline quality; sma-3 is widely expressed at all developmental stages, beginning during embryogenesis, continuing through all larval stages, and seen very strongly in adult hermaphrodites and males; a SMA-3::GFP is detected in the pharynx, intestine, and hypodermis and localizes to the nucleus; sma-3 expression in the hypodermis is necessary and sufficient for normal body size; SMA-3 can physically interact with the LIN-31 forkhead transcription factor and with DAF-16.
• Organism: Caenorhabditis elegans
• Automated Description: Enables transcription coactivator activity. Involved in several processes, including defense response to other organism; male anatomical structure morphogenesis; and regulation of developmental process. Located in cytoplasm and nucleus. Expressed in several structures, including hypodermis; intestine; pharynx; somatic gonad; and tail.
• Biotype: SO:0001217
• Genetic Position: III :-0.9165 ±0.001173
• Length (nt): 2995

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004857

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:R13F6.9.1	R13F6.9.1	1304	III: 6860974-6863968

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:R13F6.9	R13F6.9	1182	III: 6861091-6861156

10 RNAi Result

• WBRNAi00081750
• WBRNAi00051928
• WBRNAi00051929
• WBRNAi00005965
• WBRNAi00027662
• WBRNAi00097937
• WBRNAi00097938
• WBRNAi00009073
• WBRNAi00026120
• WBRNAi00075973

54 Allele

• gk964518
• gk963887
• gk964032
• gk964033
• WBVar02068625
• WBVar01264803
• WBVar01264802
• e958
• e637
• gk177360
• gk177359
• gk177362
• gk177361
• gk177358
• gk177357
• e491
• gk177364
• gk177363
• WBVar01995454
• jj55
• jj63
• jj74
• jj75
• jj3
• jj82
• WBVar01952306
• gk647652
• WBVar01628685
• gk398262
• WBVar01628686

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004857
• Start: 6860974
• End: 6863968
• 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_6860787..6860973
• Length (nt): 187
• Chromosome Location: III: 6860787-6860973
• Organism: Caenorhabditis elegans

118 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
	Transcripts that showed significantly increased expression glp-1(e2141); TU3401 animals comparing to in TU3401 animals.	Fold change > 2, FDR < 0.01.	WBPaper00065993:glp-1(e2141)_upregulated
	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 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 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 increased expression in nhr-114(gk849) comparing to wild type animals at L4 larva.	DESeq2 1.26.0, fold change > 2, FDR < 0.05.	WBPaper00064539:nhr-114(gk849)_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 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 that showed significantly increased expression in xrep-4(lax137).	DESeq2. Genes were selected if their p value < 0.01.	WBPaper00066062:xrep-4(lax137)_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 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 nuo-6(qm200) 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:nuo-6(qm200)_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 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
	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 significantly decreased expression in eat-2(ad1116) comparing to in N2 at 3-days post L4 adult hermaphrodite animals.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:eat-2(ad1116)_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 significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(+), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_P-granule(-)GFP(+)_vs_control_day2-adult
	Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(-), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_P-granule(-)GFP(-)_vs_control_day2-adult
	Transcripts that showed significantly increased expression after N2 animals were exposed to BL21 bacteria carrying pET28a-cry5B, comparing to animals exposed to BL21 control bacteria.	Differentially expressed genes were identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change >= 2.0 and a P value <= 0.05.	WBPaper00065732:Cry5Ba_upregulated_N2
	Transcripts that showed significantly increased expression in pgl-1(ct131) animals (isolated from SS0002[pgl-1(ct131)him-3(e1147)], comparing to in control animals SS1174, at 1-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_pgl-1(ct131)_vs_control_day1-adult
	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
	Transcripts that showed significantly altered expression after 24 hour exposure to nitroguanidine (NQ).	Multivariate permutation tests with random variance model implemented in BRB-Array Tools version 4.5 were performed to infer differentially expressed genes (DEGs). One thousand random permutations were computed per chemical class (i.e., a group of 16 arrays or samples). The confidence level of false discovery rate assessment was set at 80%, and the maximum allowed portion of false-positive genes was 10%.	WBPaper00055899:nitroguanidine_regulated
	Transcripts that showed significantly increased 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)_upregulated
	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
	Transcripts unqiuely expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_enriched

11 Expression Patterns

• Primary Identifier: Expr2034126
• 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: Expr12509
• Pattern: As previously described (Expr2295, Expr3520), expression of the reporter was observed in hypodermis, intestine and pharynx. Within the pharynx, expression was observed in most or all pharyngeal muscles and marginal cells.

• Primary Identifier: Expr3520
• Subcellular Localization: When a GFP tag is attached to the N terminus of SMA-3, the fusion protein is still functional and accumulates in the nucleus. SMA-3 mutant forms were tagged with N-terminal GFP. All of these mutated proteins were expressed normally and were nuclear localized.

• Primary Identifier: Expr2295
• Pattern: C-terminal construct: Expression begins late in embryogenesis, and continues through larval stages into adulthood. In larvae, expression is strong in the hypodermis, pharynx and intestine. sma-3 expression in the hypodermis is seen throughout the large hypodermal syncytium hyp7, but not in the lateral hypodermal blast cells (the seam cell). Expression of the N-terminal construct is similar, although much weaker, even after integration. Again, the nuclear fluorescence is prominent in the pharynx, intestine and hypodermis.
• Subcellular Localization: C-terminal construct: Nuclear accumulation in all of these tissues is strong. This nuclear localization does not depend on the activity of sma-6, however. When the integrated N-terminal construct array (qcIs6) was crossed into sma-4(e729) or sma-2(e502) mutant backgrounds, the nuclear localization did not change significantly. When the array is crossed into sma-6(wk7) mutants, the protein became evenly distributed between the cytoplasm and the nucleus in many but not all animals. Thus, the nuclear accumulation of SMA-3::GFP is enhanced by but not dependent on activation by the type I receptor. Determining whether this extensive nuclear localization is characteristic of the endogenous SMA-3 protein must await the development of SMA-3 antibodies.

• Primary Identifier: Expr1032409
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr13381
• Pattern: sma-3 is expressed in the somatic gonad.

• Primary Identifier: Expr11049
• Pattern: The sma-3::mCherry reporter shows expression at low levels in the cytoplasm of the tail tip of both sexes at the beginning of the L4 stage. In males, the SMA-3::mCherry fusion protein enters the nuclei of hyp8-11 prior to tail tip morphogenesis and remains in both the cytoplasm and nuclei during morphogenesis. In hermaphrodites, SMA-3::mCherry remains cytoplasmic throughout L4 and never enters the nuclei.

• Primary Identifier: Expr1155577
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2015893
• 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: Expr1016921
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1061
• Pattern: This construct is expressed widely at all developmental stages. Expression begins during embryogenesis, continues through all larval stages, and is very strong in adult hermaphrodites and males.

41 GO Annotation

13 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004857
• Start: 6860974
• End: 6863968
• Strand: -1

41 Ontology Annotations

2 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed significantly increaseded expression in sma-3(wk30) comparing to in N2 at L2 larva stage.	Differentiallyexpressed genes between the different genotypes were identified using limma-voom. Fold change > 2.	WBPaper00062491:sma-3(wk30)_upregulated
	Transcripts that showed significantly decreaseded expression in sma-3(wk30) comparing to in N2 at L2 larva stage.	Differentiallyexpressed genes between the different genotypes were identified using limma-voom. Fold change > 2.	WBPaper00062491:sma-3(wk30)_downregulated

1 Sequence

• Length: 2995

1 Sequence Ontology Term

• Name: gene

23 Strains

• WBStrain00022570
• WBStrain00026324
• WBStrain00026326
• WBStrain00026338
• WBStrain00027029
• WBStrain00027027
• WBStrain00027030
• WBStrain00027285
• WBStrain00027288
• WBStrain00027159
• WBStrain00028769
• WBStrain00028773
• WBStrain00030747
• WBStrain00034476
• WBStrain00042531
• WBStrain00052428
• WBStrain00005145
• WBStrain00005146
• WBStrain00005147
• WBStrain00007117
• WBStrain00005165
• WBStrain00004173
• WBStrain00005162

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIII_6863969..6865205
• Length (nt): 1237
• Chromosome Location: III: 6863969-6865205
• Organism: Caenorhabditis elegans