WormMine: Gene WBGene00006825

• WormBase Gene ID: WBGene00006825
• Gene Name: unc-96
• Sequence Name: F13C5.6
• Brief Description: unc-96 encodes a novel protein with no recognizable domains; unc-96 was identified in screens for mutations that disrupt body wall muscle cell structure and is required for muscle thick filament assembly, maintenance of muscle organization in response to muscle contraction, and normal locomotion; mutations in unc-96 interact genetically with mutations in unc-54, unc-98, unc-15, and unc-105, which encode a muscle-specific myosin heavy chain, zinc finger protein, paramyosin, and degenerin, respectively; in addition, UNC-96 physically interacts with UNC-98 and UNC-15, the latter of which is required for proper UNC-96 localization in body wall muscle; UNC-96 is found in body wall, pharyngeal, and anal depressor muscles; UNC-96 copurifies with thick filaments; antibody staining indicates that UNC-96 localizes to M-lines, while GFP tagging indicates that UNC-96 localizes to both M-lines and dense bodies.
• Organism: Caenorhabditis elegans
• Automated Description: Enables myosin binding activity. Involved in locomotion; regulation of cytoskeleton organization; and striated muscle myosin thick filament assembly. Located in M band and striated muscle myosin thick filament. Expressed in anal depressor muscle; body wall musculature; and pharyngeal muscle cell.
• Biotype: SO:0001217
• Genetic Position: X :-19.557 ±0.643684
• Length (nt): 10171

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00006825

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F13C5.6a.1	F13C5.6a.1	1656	X: 611120-621290
Transcript:F13C5.6b.1	F13C5.6b.1	1686	X: 611120-621290

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F13C5.6a	F13C5.6a	1227	X: 611537-611615
CDS:F13C5.6b	F13C5.6b	1257	X: 611537-611615

15 RNAi Result

• WBRNAi00089766
• WBRNAi00044494
• WBRNAi00102785
• WBRNAi00013207
• WBRNAi00013208
• WBRNAi00024285
• WBRNAi00030880
• WBRNAi00089970
• WBRNAi00090130
• WBRNAi00090288
• WBRNAi00090398
• WBRNAi00090445
• WBRNAi00090492
• WBRNAi00090539
• WBRNAi00102258

153 Allele

• gk963652
• gk963725
• r291
• WBVar01690002
• WBVar01690001
• WBVar01690003
• WBVar02124920
• sf18
• WBVar02124921
• WBVar02122051
• WBVar01600331
• WBVar01600332
• WBVar01600333
• WBVar00074357
• WBVar00074356
• su151
• WBVar01979034
• WBVar01979033
• WBVar01979032
• WBVar01823964
• gk639496
• gk714978
• gk889199
• gk584681
• gk441481
• gk857690
• gk760282
• gk694994
• gk700391
• gk736111

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00006825
• Start: 611120
• End: 621290
• Strand: -1

3 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrX_608493..611119
• Length (nt): 2627
• Chromosome Location: X: 608493-611119
• Organism: Caenorhabditis elegans

149 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 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
	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 increased 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_upregulated
	Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin_upregulated
	Transcripts that showed significantly increased expression after animals were treated with 100uM Psora and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Psora-Allantoin_upregulated
	Transcripts that showed significantly increased 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_upregulated
	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 expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:pharynx_expressed
	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 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
	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 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
	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 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 whole oocytes.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00065975:P-body_vs_oocyte_depleted
	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 animals with germline-specific inx-14(RNAi) comparing to in aniamls fed with control vector, both exposed to PA14 infection.	DESeq2. Differentially-expressed genes (DEG) were identified based on two criteria: FDR (False discovery rateusing Benjamini-Hochberg adjusted p-values) < 0.01 and absolute value of log2(Fold Change) > 1.	WBPaper00066146:germline-inx-14(RNAi)_upregulated_PA14

8 Expression Patterns

• Primary Identifier: Expr7861
• Remark: Picture: Figure 8.
• Pattern: UNC-96 is first detectable at the 1.5-fold stage, in which UNC-96, like MHC A, is diffusely localized in the cytoplasm of body wall muscle cells. It has been established that at the 1.5-fold stage, nascent linear structures containing MHC A, MHC B, and paramyosin are present, but myofibrils have not yet formed. By the 3-fold stage, UNC-96, with the use of antibody, is undetectable in body wall muscle, but it can be seen very prominently in embryonic pharyngeal muscle.
• Subcellular Localization: UNC-96 is first detectable at the 1.5-fold stage, in which UNC-96, like MHC A, is diffusely localized in the cytoplasm of body wall muscle cells.

• Primary Identifier: Expr7860
• Remark: Picture: Figure 7B.
• Pattern: unc-96::gfp is expressed in body wall and pharyngeal and anal depressor muscles.
• Subcellular Localization: In the single sarcomere muscles, UNC-96::GFP is located in the middle of A-bands. In body wall muscle, UNC-96::GFP is specifically located at M-lines, and in addition, at dense bodies. UNC-96::GFP could be seen as early as the 1.5-fold embryonic stage.

• Primary Identifier: Expr7859
• Remark: Picture: Figure 7A.
• Subcellular Localization: In body wall muscle, UNC-96 is located in M-lines, identified by use of antibodies to the M-line marker UNC-89. UNC-96 and UNC-89 are also similarly expressed in pharyngeal and anal depressor muscles. In such single sarcomere muscles, UNC-96 is found in the middle of the A-bands, a location similar to that found in body wall muscles.

• Primary Identifier: Expr2036058
• 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: Expr1032889
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1021808
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2017922
• 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: Expr1148443
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

14 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00006825
• Start: 611120
• End: 621290
• Strand: -1

14 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 10171

1 Sequence Ontology Term

• Name: gene

2 Strains

• WBStrain00007703
• WBStrain00008393

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrX_621291..622314
• Length (nt): 1024
• Chromosome Location: X: 621291-622314
• Organism: Caenorhabditis elegans