WormMine: Gene WBGene00003497

• WormBase Gene ID: WBGene00003497
• Gene Name: mup-4
• Sequence Name: K07D8.1
• Brief Description: The mup-4 gene encodes a novel transmembrane protein required for junctional attachments between hypodermis and muscle, and between the apical epithelial surface and the cuticular matrix.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable calcium ion binding activity. Predicted to be involved in cell adhesion. Located in hemidesmosome. Part of hemidesmosome associated protein complex. Expressed in body wall musculature; hypodermis; pharynx; touch receptor neurons; and vulval cell. Human ortholog(s) of this gene implicated in multiple epiphyseal dysplasia 5 and osteoarthritis. Is an ortholog of human MATN2 (matrilin 2) and MATN3 (matrilin 3).
• Biotype: SO:0001217
• Genetic Position: III :-0.729766 ±0.000597
• Length (nt): 9426

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003497

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:K07D8.1.1	K07D8.1.1	6752	III: 7479680-7489105

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:K07D8.1	K07D8.1	6315	III: 7480074-7480175

41 RNAi Result

• WBRNAi00063825
• WBRNAi00063823
• WBRNAi00089822
• WBRNAi00066934
• WBRNAi00067019
• WBRNAi00067078
• WBRNAi00067133
• WBRNAi00067317
• WBRNAi00067437
• WBRNAi00067474
• WBRNAi00067511
• WBRNAi00067593
• WBRNAi00050162
• WBRNAi00008921
• WBRNAi00008966
• WBRNAi00066802
• WBRNAi00085812
• WBRNAi00068483
• WBRNAi00068485
• WBRNAi00068484
• WBRNAi00068929
• WBRNAi00068931
• WBRNAi00068930
• WBRNAi00025800
• WBRNAi00025907
• WBRNAi00071743
• WBRNAi00071315
• WBRNAi00063819
• WBRNAi00063821
• WBRNAi00002439

135 Allele

• gk964518
• gk963887
• s2426
• s2433
• s2440
• s2574
• WBVar01607114
• h9941
• h11476
• gk812502
• gk569891
• gk646700
• gk759136
• gk368461
• WBVar00060415
• gk903580
• gk814002
• gk642025
• gk514566
• gk737163
• gk818058
• WBVar00060420
• gk835029
• gk418527
• gk413957
• gk383281
• WBVar00065288
• gk334191
• WBVar00060425
• gk309790

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003497
• Start: 7479680
• End: 7489105
• 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_7478428..7479679
• Length (nt): 1252
• Chromosome Location: III: 7478428-7479679
• Organism: Caenorhabditis elegans

268 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	oocyte proteins identified by two or more unique peptides during proteomics study.	In the pooled data set, 1453 C. elegans proteins were identified with a probability >= 0.9 according to ProteinProphet, of which 1165 proteins were identified by more than one unique peptide.	WBPaper00038289:oocyte_protein
	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
	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 that showed significantly increased expression in ogt-1(ok1474) neuronal cells isolated by FACs comparing to in FACs isolated neuronal cells from wild type.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00066485:ogt-1(ok1474)_upregulated_neuron
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
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	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 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 GABAergic neuron, according to PAT-Seq analysis using Punc-47-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:GABAergic-neuron_expressed
	Transcripts that showed significantly decreased expression at 11-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites.	DESeq2, fold change > 2, FDR < 0.05	WBPaper00065835:Day11_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
mitochondrial sulfide delivery molecule (mtH2S) AP39	Transcripts that showed significantly increased expression in N2 animals treated with mitochondrial sulfide delivery molecule (mtH2S) AP39 starting from 1-day-post L4 until 11 days post L4.	DESeq2, fold change > 2, FDR < 0.05	WBPaper00065835:mtH2S-AP39-D0-treatment_upregulated_Day11
	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
	Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_daf-16(mu86);glp-1(e2141)
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
Dietary restriction	Transcripts that showed significantly decreased expression after N2 animals were under dietary restriction (DR, OP50 OD = 0.1) from 3-day post L4 till 6-day post L4 adult hermaphrodite stage, comparing to under ad libtum (AL, OP50 OD = 3) condition.	Bioconductor package edgeR, p < 0.05.	WBPaper00056443:DietaryRestriction_downregulated
	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 alg-1(gk214), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-1(gk214)_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 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 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

7 Expression Patterns

• Primary Identifier: Expr1031600
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1626
• Pattern: GFP fluorescence was abundant in circumferential annular rings overlying muscle of 3 fold embryos. The antipeptide antibody raised to the intracellular domain showed similar staining. In contrast, this pattern was never observed in mutants; although mutant and wild-type (WT) embryos also exhibit diffuse patterns of antibody reactivity. MUP-4 continues to localize to circumferential rings over body wall muscle in larvae and adults. MUP-4:: GFP and MUP-4 antibodies also localize to other regions where cells show mechanical attachments to the hypodermis including the inner surface of the pharynx where the radial pharyngeal muscle cells attach to the marginal hypodermal cells, which secrete a cuticle; overlying anal and intestinal muscles; overlying vulval and uterine sex muscles; male tail muscle attachment zones; and the six mechanosensory neurons that mediate touch sensitivity through their attachment to the hypodermis. Examination of WT animals also labeled with mAb MH27, which recognizes adherens junctions, shows that MUP-4 staining can extend beyond the muscle to the seam cell boundary. In some mup-4::gfp-expressing lines, high concentrations of protein was often seen around the hypodermal or touch neuron nuclei. MUP-4 continues to localize to circumferential rings over body wall muscle in larvae and adults. MUP-4::GFP and MUP-4 antibodies also localize to other regions where cells show mechanical attachments to the hypodermis including the inner surface of the pharynx where the radial pharyngeal muscle cells attach to the marginal hypodermal cells, which secrete a cuticle; overlying anal and intestinal muscles; overlying vulval and uterine sex muscles; male tail muscle attachment zones; and the six mechanosensory neurons that mediate touch sensitivity through their attachment to the hypodermis. Examination of WT animals also labeled with mAb MH27, which recognizes adherens junctions, shows that MUP-4 staining can extend beyond the muscle to the seam cell boundary. In some mup-4::gfp-expressing lines, high concentrations of protein was often seen around the hypodermal or touch neuron nuclei.
• Subcellular Localization: The observed pattern of MUP-4 is reminiscent of the pattern of the MH4 mAb, which recognizes IFs of hemidesmosomes. The relationship between MUP-4 and IF localization was further examined by overlay of confocal images of double-labeled animals. This analysis demonstrated that their patterns largely coincide. In addition to the annular localization, MUP-4 and IF proteins are sometimes seen diffusely throughout the hypodermal syncytial cell cytoplasm, possibly reflecting protein not yet recruited to the regions overlying muscle. MUP-4 also shows coincident localization with the MH4 IF in other structures such as the touch neuron channels, further supporting that MUP-4 associates with IFs.

• Primary Identifier: Expr1153857
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr15945
• Pattern: MUP-4::GFP appeared at the L4.6-L4.7 stage, and was enriched over vulC and vulD, where the vm1 sex muscles attach. By L4.9 and adult, when cuticle is present, MUP-4::GFP lined all vulva apical membranes, but it was expressed most prominently in the vulA toroid, which links the vulva to the surrounding epidermis and body muscle.

• Primary Identifier: Expr2013826
• 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: Expr1023788
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2032066
• 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).

12 GO Annotation

4 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003497
• Start: 7479680
• End: 7489105
• Strand: -1

12 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 9426

1 Sequence Ontology Term