WormMine: Gene WBGene00004860

• WormBase Gene ID: WBGene00004860
• Gene Name: sma-6
• Sequence Name: C32D5.2
• Brief Description: sma-6 encodes a serine/threonine protein kinase that is orthologous to type I TGF-beta receptors; sma-6 activity is required for regulating body length and for proper development of the male tail; sma-6, along with other genes in the TGF-beta Sma/Mab pathway, also regulates reproductive aging; a reduction of TGF-beta pathway genes extends reproductive span by maintaining oocyte and germline quality; sma-6 expression first begins at the 1.5-fold stage of embryogenesis and continues through adulthood; sma-6 is expressed in dorsal and ventral hypodermis, pharyngeal muscle, and the intestine; expression in the hypodermis is necessary and sufficient for body length regulation.
• Organism: Caenorhabditis elegans
• Automated Description: Enables BMP binding activity. Involved in several processes, including defense response to other organism; nematode male tail tip morphogenesis; and positive regulation of macromolecule metabolic process. Predicted to be located in plasma membrane. Predicted to be part of receptor complex. Expressed in ASI; hypodermis; intestinal cell; pharynx; and tail. Human ortholog(s) of this gene implicated in several diseases, including bone development disease (multiple); carcinoma (multiple); and glaucoma (multiple). Is an ortholog of human BMPR1B (bone morphogenetic protein receptor type 1B).
• Biotype: SO:0001217
• Genetic Position: II :-0.382096 ±0.000481
• Length (nt): 2872

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004860

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C32D5.2.1	C32D5.2.1	2131	II: 6324484-6327355

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C32D5.2	C32D5.2	1911	II: 6324489-6324628

11 RNAi Result

• WBRNAi00024693
• WBRNAi00067749
• WBRNAi00068065
• WBRNAi00041667
• WBRNAi00011477
• WBRNAi00027866
• WBRNAi00114409
• WBRNAi00097941
• WBRNAi00027202
• WBRNAi00075914
• WBRNAi00090572

41 Allele

• gk963801
• gk963053
• WBVar01604042
• gk144720
• wk11
• gk911643
• gk144719
• gk479255
• gk449256
• gk418740
• gk144716
• wk7
• wk8
• gk144718
• wk9
• gk720308
• gk144717
• wk10
• bx110
• e1482
• jj76
• gk333622
• ok2894
• WBVar01240437
• jj1
• gk365618
• gk599663
• gk617734
• gk727190
• gk662609

1 Chromosome

• WormBase ID: II
• Organism: Caenorhabditis elegans
• Length (nt): 15279421

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004860
• Start: 6324484
• End: 6327355
• 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_chrII_6327356..6328701
• Length (nt): 1346
• Chromosome Location: II: 6327356-6328701
• Organism: Caenorhabditis elegans

115 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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 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
	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_upregulated
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
Osmotic stress	Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when no food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_NoFood
	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
Bacteria infection: Enterococcus faecalis	Genes with increased expression after 24 hours of infection by E.faecalis Fold changes shown are pathogen vs OP50.	For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated.	WBPaper00038438:E.faecalis_24hr_upregulated_TilingArray
	Transcripts that showed significantly decreased expression in atfs-1(cmh15) (null allele) animals comparing to in N2 animals at L4 larva stage.	edgeR, fold change > 2, FDR < 0.05	WBPaper00060909:atfs-1(cmh15)_downregulated
	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 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 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 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 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
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 0hr 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:germline-precursors_blastula-embryo_expressed
	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 npr-15(tm12539) comparing to in N2 at L4 larva stage.	Fold change > 2, FDR < 0.05.	WBPaper00066608:npr-15(tm12539)_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
	Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Allantoin_downregulated
	Transcripts that showed significantly decreased 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_downregulated
	Transcripts that showed significantly decreased expression after animals were treated with 50uM Rifampicin and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin-Allantoin_downregulated
	Transcripts detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
	Transcripts that showed altered expression from P0 to F2 generation animals after N2 parental generation were treated with antimycin, but not in damt-1(gk961032) P0 to F2 animals after the parenal generaton were treated with antimycin.	N.A.	WBPaper00055862:antimycin_damt-1(gk961032)_regulated
	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
	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

10 Expression Patterns

• Primary Identifier: Expr2034129
• 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: Expr1297
• Pattern: sma-6 is expressed during embryonic, larval and adult stages. During the early larval stages (L1-L2), sma-6 is extensively expressed in the anterior pharyngeal and distal posterior regions of the animal. Soon afterwards, expression begins in the posterior intestinal nuclei and advances more anteriorly. Expression is seen in the pairs of intestinal nuclei as they divide. Strong expression is seen in the pharyngeal muscles of the anterior and posterior bulbs of the pharynx. Once the intestinal cell divisions are complete, one can see continued expression in the intestinal cells during L2-L3, and later disappearing in these cells. In adults, the staining pattern disappears from the midsections of the animal and persists in the pharyngeal muscles. In males, expression is seen in the tail, as predicted, but the identity of the cells is unclear. sma-6 expression is also observed in late-stage embryos.
• Subcellular Localization: intestinal nuclei

• Primary Identifier: Expr10559
• Pattern: Expression of sma-6 in the pharynx, intestine, and hypodermis was confirmed. In addition sma-6 expression was observed in the ASI sensory neurons.

• Primary Identifier: Expr1032412
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr998
• Remark: clone: yk53f5
• Pattern: Head, posterior and intestine.

• Primary Identifier: Expr1781
• Pattern: The worms harboring the GFP reporter gene were fluorescent throughout the pharyngeal muscle, intestine, and hypodermis. The fluorescence was observed from around the 1.5-fold stage and continued to the adult stage. The expression in the hypodermis was detected in the dorsal (hyp-7) and ventral hypodermal cells (P cells) in the main body region, but not in the lateral hypodermal H, V, and T cells (seam cells). The expression was also detected in a part of the hypodermal cells of the head (hyp-6), but not in the hypodermal cells of the anterior (hyp-1, -2, -3) and posterior end (hyp-10). Expression not observed in the nervous system.

• Primary Identifier: Expr1024381
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2015896
• 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: Expr1145692
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Chronogram1858
• Remark: Original chronogram file: chronogram.777.xml
• Reporter Gene: [C32D5.2:gfp] transcriptional fusion.

54 GO Annotation

11 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004860
• Start: 6324484
• End: 6327355
• Strand: 1

54 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 2872

1 Sequence Ontology Term

• Name: gene

7 Strains

• WBStrain00023046
• WBStrain00026327
• WBStrain00026347
• WBStrain00030738
• WBStrain00037158
• WBStrain00003052
• WBStrain00004344

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrII_6324351..6324483
• Length (nt): 133
• Chromosome Location: II: 6324351-6324483
• Organism: Caenorhabditis elegans