WormMine: Gene WBGene00003482

• WormBase Gene ID: WBGene00003482
• Gene Name: mua-3
• Sequence Name: K08E5.3
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable collagen binding activity and intermediate filament binding activity. Involved in cell-matrix adhesion. Located in hemidesmosome and intermediate filament. Expressed in several structures, including amphid neurons; enteric muscle; excretory system; phasmid sensillum; and rectum. Used to study Marfan syndrome. Human ortholog(s) of this gene implicated in multiple epiphyseal dysplasia 5 and osteoarthritis. Is an ortholog of human MATN3 (matrilin 3).
• Biotype: SO:0001217
• Genetic Position: III :1.97555 ±0.010818
• Length (nt): 22833

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003482

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:K08E5.3a.1	K08E5.3a.1	11573	III: 10160697-10183529
Transcript:K08E5.3b.1	K08E5.3b.1	10213	III: 10167675-10183529

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:K08E5.3a	K08E5.3a	11304	III: 10160697-10160877
CDS:K08E5.3b	K08E5.3b	9552	III: 10168067-10168124

26 RNAi Result

• WBRNAi00063826
• WBRNAi00063822
• WBRNAi00063824
• WBRNAi00089825
• WBRNAi00066968
• WBRNAi00067011
• WBRNAi00067034
• WBRNAi00067069
• WBRNAi00067077
• WBRNAi00067102
• WBRNAi00067240
• WBRNAi00067570
• WBRNAi00067732
• WBRNAi00050300
• WBRNAi00050301
• WBRNAi00026335
• WBRNAi00002605
• WBRNAi00009194
• WBRNAi00016813
• WBRNAi00006172
• WBRNAi00085489
• WBRNAi00063820
• WBRNAi00001994
• WBRNAi00090302
• WBRNAi00089984
• WBRNAi00090143

324 Allele

• gk964518
• gk962701
• gk963887
• rh169
• rh195
• rh222
• gk488135
• WBVar01447900
• gk781757
• WBVar01447901
• gk183533
• WBVar02049776
• gk682656
• gk867325
• WBVar01542223
• WBVar01267508
• WBVar01267509
• WBVar01267515
• WBVar01267511
• gk944526
• gk944525
• WBVar01823314
• WBVar01823313
• WBVar01823315
• h14825
• h10278
• h3997
• h11914
• h17770
• WBVar01827855

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003482
• Start: 10160697
• End: 10183529
• 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_10183530..10183761
• Length (nt): 232
• Chromosome Location: III: 10183530-10183761
• Organism: Caenorhabditis elegans

262 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
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
	Coexpression clique No. 60, 176662_at-Y53F4B.16, on the genome-wide coexpression clique map for the nematode GPL200 platform.	All available microarray datasets for the GPL200 platform (Affymetrix C. elegans Genome Array) were obtained from the GEO repository. This included 2243 individual microarray experiments. These were normalized against each other with the software RMAexpress (Bolstad, 2014). Based on these normalized values, Pearsons correlation coefficients were obtained for each probe-probe pair of the 22,620 probes represented on this array type. The resulting list of correlation coefficients was then ranked to generate the ranked coexpression database with information on each probe represented on the GPL200 platform.	WBPaper00061527:176662_at-Y53F4B.16
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	Transcripts that showed significantly decreased expression at 5-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites.	DESeq2, fold change > 2, FDR < 0.05	WBPaper00065835:Day5_vs_Day1_downregulated
	Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:hypodermis_expressed
	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 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)
	Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_glp-1(e2141)
	Transcripts that showed significantly increased expression in rrf-3(pk1426) comparing to in N2 at embryo stage.	DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01.	WBPaper00056169:rrf-3(pk1426)_upregulated_embryo
	Transcripts that showed significantly increased expression after 24 hours of induction of human beta Amyloid at young adult stage	A 2-fold change in expression level and a false discovery rate analog of p < 0.05.	WBPaper00064130:Beta-Amyloid_24h_upregulated_mRNA
Bacteria infection: Bacillus thuringiensis	Transcripts that showed significantly increased expression in N2 animals infected by bacteria BMB171/Cry5Ba, an acrystalliferous Bt mutant BMB171 transformed with toxin gene cry5Ba on the shuttle vector pHT304, comparing to N2 animals infected by BMB171/pHT304.	N.A.	WBPaper00064229:B.thuringiensis-Cry5Ba_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 10 mix) vs BT407 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_6h
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 after four-day-old young adult worms were placed on NGM plates seeded with OP50 in the presence 5% Agaro-oligosaccharides(AGO) for 24 h, comparing to animals grown in the absence of AGO.	Fold change > 2.	WBPaper00064306:Agaro-oligosaccharides_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 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_6h
	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 hrde-1(tm1200) animals, comparing to in N2, after growing at 25C for five generations (late generation).	CuffDiff2	WBPaper00051265:F4_hrde-1(tm1200)_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
	Genes that showed significantly increased expression in daf-2(e1370);hel-1(gk148684) comparing to in hel-1(gk148684)	To identify DEGs, Students t test and the log2 median ratio test were performed to compute t values and median ratios for all the annotated genes. The adjusted P values from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjusted P values from the individual tests were combined to compute the overall P values using Stouffers method , and genes with overall P < 0.05 and fold change > 1.5 were selected as DEGs.	WBPaper00047131:daf-2(e1370)_upregulated_hel-1(gk148684)-background
	Genes that showed significantly increased expression in daf-2(e1370) comparing to in N2.	To identify DEGs, Students t test and the log2 median ratio test were performed to compute t values and median ratios for all the annotated genes. The adjusted P values from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjusted P values from the individual tests were combined to compute the overall P values using Stouffers method , and genes with overall P < 0.05 and fold change > 1.5 were selected as DEGs.	WBPaper00047131:daf-2(e1370)_upregulated_N2-background
	Transcripts that showed significantly increased expression in daf-2(e1370) comparing to in control animals.	NOIseq(v2.34.0), fold change > = 1.5, Differentially expressed genes (DEGs) were defined as having a probability of differentialexpression > 95%.	WBPaper00064727:daf-2(e1370)_upregulated
	Transcripts enriched in AMso according to single cell RNAseq.	Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched.	WBPaper00061651:AMso_enriched

6 Expression Patterns

• Primary Identifier: Expr1031597
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1627
• Remark: Probably also expressed at postembryonic stages, but actual stages was not mentioned clearly in the paper.
• Pattern: MUA-3 also localizes to sites where other striated muscles make adhesive contact and transmit force across the hypodermis. These include the vulval muscles, the anal depressor muscle, and the junctions between anal sphincter muscle and rectal cuticle that cross the intestinal/rectal epithelium. MUA-3 localizes to several sites where non-muscle cells make tight transhypodermal contacts to the cuticle. It is present in thin longitudinal stripes where the touch neurons (ALM and PLM) compress the hypodermis to make close contact with the cuticle, and where the sensory dendrites of the amphid, phasmid, and IL neurons penetrate the hypodermis and cuticle to form externally exposed sensilla. MUA-3 also localizes to the excretory duct and pore cells, both of which contain a cuticle lined lumen. MUA-3 localizes to several sites where nonmuscle cells make tight transhypodermal contacts to the cuticle. It is present in thin longitudinal stripes where the touch neurons (ALM and PLM) compress the hypodermis to make close contact with the cuticle, and where the sensory dendrites of the amphid, phasmid, and IL neurons penetrate the hypodermis and cuticle to form externally exposed sensilla. MUA-3 also localizes to the excretory duct and pore cells, both of which contain a cuticle lined lumen. MUA-3 was not detected at the uterine seam, where the uterus makes indirect IF mediated contact to the cuticle via the seam cells, or in the pharynx, where IF bundles link the basal lamina to the lumenal cuticle. The major site of MUA-3 localization is the hypodermis at the sites of muscle contact. The immunofluorescence coincides with the extent of the body wall muscle bands and shows a repeating pattern of closely spaced circumferential stripes (~0.4 um periodicity) separated by an unstained gap (~0.2 um) in adults. Individual stripes are not uniformly stained, but rather composed of many individual spots and frequently contain a narrow central nonstaining region. Where neuronal processes interpose between hypodermis and basal lamina, MUA-3 is absent, resulting in stereotypical gaps. The MUA-3 localization pattern is virtually identical with those reported for MH4 and p70 (IF proteins) and MH46 (myotactin). During embryogenesis, MUA-3 is observed in 2-fold and older embryos.

• Primary Identifier: Expr2013822
• 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: Expr1154001
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2032062
• 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: Expr1015401
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

11 GO Annotation

4 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003482
• Start: 10160697
• End: 10183529
• Strand: 1

11 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 22833

1 Sequence Ontology Term

• Name: gene

2 Strains

• WBStrain00030527
• WBStrain00007983

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIII_10160486..10160696
• Length (nt): 211
• Chromosome Location: III: 10160486-10160696
• Organism: Caenorhabditis elegans