WormMine: Gene WBGene00004862

• WormBase Gene ID: WBGene00004862
• Gene Name: sma-9
• Sequence Name: T05A10.1
• Brief Description: sma-9 encodes, by extensive alternative splicing, at least 13 isoforms, a number of which are large (~2000-residue) proteins with at least three N-terminal involucrin domains, seven C-terminal zinc-finger domains, and a glutamine/asparagine-rich domain; SMA-9 is orthologous to the Drosophila Smad cofactor Schnurri (FBgn0003396) and the vertebrate HIVEP proteins (Human Immunodeficiency Virus Type 1 Enhancer-Binding Proteins, OMIM:194540, OMIM:143054, and OMIM:606649); in C. elegans, sma-9 functions in a subset of the TGF-beta-mediated signaling pathways that regulate body size and male tail patterning and morphogenesis; sma-9, 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-9 also functions antagonistically to the TGF-beta signaling pathway, and in parallel to the lin-12/Notch pathway, to effect proper cell fate specification in the postembryonic mesodermal lineage, the M lineage; SMA-9 is widely expressed and localizes to nuclei.
• Organism: Caenorhabditis elegans
• Automated Description: Enables transcription coactivator activity and transcription corepressor activity. Involved in several processes, including determination of adult lifespan; nematode male tail tip morphogenesis; and regulation of gene expression. Acts upstream of or within cellular response to heat. Located in nucleus. Expressed in several structures, including excretory cell; intestine; spermatheca; ventral cord neurons; and vulva. Used to study Alzheimer's disease. Human ortholog(s) of this gene implicated in autosomal dominant intellectual developmental disorder 43. Is an ortholog of human HIVEP1 (HIVEP zinc finger 1); HIVEP2 (HIVEP zinc finger 2); and HIVEP3 (HIVEP zinc finger 3).
• Biotype: SO:0001217
• Genetic Position: X :2.51785 ±0.028298
• Length (nt): 13692

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004862

Genomics

16 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T05A10.1c.1	T05A10.1c.1	7397	X: 10769282-10782973
Transcript:T05A10.1m.1	T05A10.1m.1	6769	X: 10769282-10782972
Transcript:T05A10.1b.1	T05A10.1b.1	2184	X: 10769288-10776524
Transcript:T05A10.1c.2	T05A10.1c.2	6739	X: 10773081-10782386
Transcript:T05A10.1g.1	T05A10.1g.1	6108	X: 10773091-10781481
Transcript:T05A10.1i.1	T05A10.1i.1	5784	X: 10773091-10781481
Transcript:T05A10.1d.1	T05A10.1d.1	6729	X: 10773091-10782386
Transcript:T05A10.1f.1	T05A10.1f.1	6471	X: 10773091-10782386
Transcript:T05A10.1j.4	T05A10.1j.4	6892	X: 10773091-10782921
Transcript:T05A10.1j.3	T05A10.1j.3	6690	X: 10773091-10782927
Transcript:T05A10.1j.2	T05A10.1j.2	6896	X: 10773091-10782928
Transcript:T05A10.1e.1	T05A10.1e.1	7201	X: 10773091-10782957
Transcript:T05A10.1j.1	T05A10.1j.1	7128	X: 10773091-10782969
Transcript:T05A10.1a.1	T05A10.1a.1	6788	X: 10773091-10782973
Transcript:T05A10.1h.1	T05A10.1h.1	5949	X: 10773999-10782972
Transcript:T05A10.1h.2	T05A10.1h.2	3418	X: 10777902-10782693

Other

11 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T05A10.1b	T05A10.1b	2178	X: 10769294-10769401
CDS:T05A10.1m	T05A10.1m	6171	X: 10769294-10769401
CDS:T05A10.1g	T05A10.1g	6108	X: 10773091-10773654
CDS:T05A10.1f	T05A10.1f	6471	X: 10773091-10773654
CDS:T05A10.1e	T05A10.1e	6630	X: 10773091-10773654
CDS:T05A10.1c	T05A10.1c	5079	X: 10775285-10775344
CDS:T05A10.1a	T05A10.1a	6201	X: 10773091-10773654
CDS:T05A10.1d	T05A10.1d	6729	X: 10773091-10773654
CDS:T05A10.1h	T05A10.1h	1614	X: 10778988-10779007
CDS:T05A10.1i	T05A10.1i	5784	X: 10773091-10773654
CDS:T05A10.1j	T05A10.1j	4530	X: 10773091-10773654

21 RNAi Result

• WBRNAi00081748
• WBRNAi00000664
• WBRNAi00052431
• WBRNAi00018170
• WBRNAi00113602
• WBRNAi00062961
• WBRNAi00062962
• WBRNAi00062963
• WBRNAi00107523
• WBRNAi00082715
• WBRNAi00082717
• WBRNAi00082716
• WBRNAi00097944
• WBRNAi00097931
• WBRNAi00097943
• WBRNAi00097942
• WBRNAi00097945
• WBRNAi00107154
• WBRNAi00107105
• WBRNAi00107610
• WBRNAi00107512

216 Allele

• gk964260
• gk962707
• WBVar01928230
• gk962546
• qc3
• qc1
• WBVar01759319
• WBVar01759321
• WBVar01759320
• WBVar02066045
• WBVar02066046
• WBVar02066047
• WBVar02066048
• WBVar01602153
• WBVar01602154
• WBVar02069069
• WBVar01711118
• tm572
• WBVar01820520
• WBVar01889138
• gk953507
• wk77
• gk292676
• gk292675
• WBVar01889137
• WBVar01889133
• WBVar01889134
• WBVar01889135
• WBVar01889136
• WBVar01889129

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004862
• Start: 10769282
• End: 10782973
• 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

165 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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
	mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis.	Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05.	WBPaper00045420:fertilization_downregulated_transcript
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 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 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
	Genes with expression level regulated by genotype (N2 vs CB4856) and age at old adults stage (214 hours at 24 centigrade).	For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR).	WBPaper00040858:eQTL_age_regulated_aging
	Genes with expression level regulated by genotype (N2 vs CB4856) and age at L3 larva and Late reproduction stage (96 hours at 24 centigrade).	For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR).	WBPaper00040858:eQTL_age_regulated_developing
	Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
	Genes with expression level regulated by genotype (N2 vs CB4856) at L3 larva and Late reproduction stage (96 hours at 24 centigrade).	For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR).	WBPaper00040858:eQTL_regulated_developing
	Transcripts expressed in vulva.	FPKM >= 1.	WBPaper00064122:vulva_transcriptome
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h
	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
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
	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 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 that showed significantly increased expression in sftb-1(cer6) deletion homozygous comparing to to in N2 animals at L4 larva stage.	DESeq2, fold change > 2	WBPaper00058725:sftb-1(cer6)_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

10 Expression Patterns

• Primary Identifier: Expr2034130
• 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: Expr2782
• Remark: Different promoter regions do not give rise to the same expression pattern. The 2.8 kb, 5.5 kb and 8.0 kb constructs (upstream of predicted exon 1) show strong fluorescence in all detected tissues except the seam cells. The 1.5 kb construct (5500 bp to 4000 bp relative to predicted exon 1) displays expression in the seam cells, ventral nerve cord and excretory canal only. The 4.0 kb construct (8000 bp to 4000 bp) generates the complete expression pattern, indicating the presence of redundant transcriptional elements. The 5.5 kb and 8.0 kb fragments are identical to the 1.5 kb and 4.0 kb fragments, respectively, except for the addition of sequences from 4000 bp to 1 bp that include the alternative exon 1. The addition of these sequences abolishes expression in the seam cells in these reporters. These results could be due to the presence of a seam-cell specific repressor element between 4000 bp and 1 bp. Alternatively, transcription and splicing in the seam cells might specifically generate the Class B variant that initiates translation in alternative exon 1, which would render the GFP sequences in the 5.5 kb and 8.0 kb constructs out of frame.
• Pattern: sma-9 promoter-driven GFP was expressed in the ventral nerve cord, pharynx and intestine, seam cells, excretory canal, vulva and spermatheca. Expression was observed from L1 to adult stages but not during embryonic development. sma-9 promoter-driven GFP was detected in the lateral seam only from the L1 to the L3 stages, and not in the L4 stage or in the adult.

• Primary Identifier: Expr1032413
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1200018
• Pattern: Data from the TransgeneOme project

• Primary Identifier: Expr10436
• Pattern: Inferred Expression. EPIC dataset. http://epic.gs.washington.edu/ Large-scale cellular resolution compendium of gene expression dynamics throughout development. This reporter was inferred to be expressing in this cell or one of its embryonic progenitor cells as described below. To generate a compact description of which cells express a particular reporter irrespective of time, the authors defined a metric "peak expression" for each of the 671 terminal ("leaf") cells born during embryogenesis. For each of these cells, the peak expression is the maximal reporter intensity observed in that cell or any of its ancestors; this has the effect of transposing earlier expression forward in time to the terminal set of cells. This metric allows straightforward comparisons of genes' cellular and lineal expression overlap, even when the expression occurs with different timing and despite differences in the precise time point that curation ended in different movies, at the cost of ignoring the temporal dynamics of expression, a topic that requires separate treatment. For simplicity, the authors use the term "expressing cells" to mean the number of leaf cells (of 671) with peak expression greater than background (2000 intensity units) and at least 10% of the maximum expression in that embryo. Quantitative expression data for all cells are located here: ftp://caltech.wormbase.org/pub/wormbase/datasets-published/murray2012/

• Primary Identifier: Expr2783
• Pattern: Antibody staining detects SMA-9 protein in most, if not all, somatic nuclei of wild-type animals, but not in sma-9(wk55) animals. Furthermore, the immunolocalization confirms SMA-9 expression in the pharynx, intestine, hypodermis and ventral nerve cord.

• Primary Identifier: Expr1156052
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1011744
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2015897
• 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: Expr3995
• Subcellular Localization: In the wild-type background, all three constructs showed similar GFP expression pattern and subcellular localization: GFP was localized in nuclei of a wide variety of cell types, similar to what was reported using C2 isoform-specific anti-SMA-9 antibodies (see Expr2783).

36 GO Annotation

11 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004862
• Start: 10769282
• End: 10782973
• Strand: 1

36 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 13692

1 Sequence Ontology Term

• Name: gene

18 Strains

• WBStrain00026336
• WBStrain00026350
• WBStrain00036394
• WBStrain00005155
• WBStrain00005156
• WBStrain00005153
• WBStrain00005154
• WBStrain00005160
• WBStrain00005161
• WBStrain00005157
• WBStrain00005158
• WBStrain00005143
• WBStrain00005144
• WBStrain00005148
• WBStrain00005151
• WBStrain00005152
• WBStrain00005149
• WBStrain00005150

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrX_10769075..10769281
• Length (nt): 207
• Chromosome Location: X: 10769075-10769281
• Organism: Caenorhabditis elegans