WormMine: Gene WBGene00003404

• WormBase Gene ID: WBGene00003404
• Gene Name: mpz-1
• Sequence Name: C52A11.4
• Brief Description: mpz-1 encodes a multi-PDZ domain scaffold protein; mpz-1(RNAi) animals have reduced serotonin (5-HT)-stimulated egg laying unless truncated SER-1 is transgenically expressed in vulval muscle; overexpressed MPZ-1 PDZ domain 10 also reduces SER-1-mediated egg laying; the PDZ domain 10 of MPZ-1 binds the C-terminal PDZ-binding motif (ETFL) of the 5-HT receptor SER-1; MPZ-1 also physically interacts with the RHGF-2 RhoGEF, and may also bind NPR-1 and ZC84.4; MPZ-1 binding enhances SER-1 activity; mpz-1 is expressed in the nerve ring, pharyngeal, body, and tail neurons, as well as body wall and vulval muscles; mpz-1 is coexpressed with ser-1 in three neuron types and vulval muscle; MPZ-1 co-localizes with SNB-1 in neuronal puncta and with RHGF-2 in nerve ring axons; mpz-1 may be translationally regulated by a small upstream open reading frame (uORF).
• Organism: Caenorhabditis elegans
• Automated Description: Enables GTPase activating protein binding activity. Located in axon. Expressed in body wall musculature; nerve ring; neurons; and vulval muscle. Human ortholog(s) of this gene implicated in hydrocephalus. Is an ortholog of human MPDZ (multiple PDZ domain crumbs cell polarity complex component) and PATJ (PATJ crumbs cell polarity complex component).
• Biotype: SO:0001217
• Genetic Position: II :3.12519 ±0.000174
• Length (nt): 39492

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003404

Genomics

10 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C52A11.4a.1	C52A11.4a.1	7856	II: 10738635-10772847
Transcript:C52A11.4f.1	C52A11.4f.1	7834	II: 10738635-10772813
Transcript:C52A11.4j.1	C52A11.4j.1	1413	II: 10739275-10742536
Transcript:C52A11.4i.1	C52A11.4i.1	2943	II: 10739275-10748584
Transcript:C52A11.4h.1	C52A11.4h.1	4230	II: 10739275-10752420
Transcript:C52A11.4c.1	C52A11.4c.1	6609	II: 10739275-10764442
Transcript:C52A11.4e.1	C52A11.4e.1	6555	II: 10739275-10766641
Transcript:C52A11.4g.1	C52A11.4g.1	7050	II: 10739275-10771962
Transcript:C52A11.4d.1	C52A11.4d.1	7269	II: 10739275-10778126
Transcript:C52A11.4b.1	C52A11.4b.1	2549	II: 10757462-10772828

Other

10 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C52A11.4a	C52A11.4a	7182	II: 10739275-10739358
CDS:C52A11.4f	C52A11.4f	7194	II: 10739275-10739358
CDS:C52A11.4h	C52A11.4h	4230	II: 10739275-10739358
CDS:C52A11.4c	C52A11.4c	6609	II: 10739275-10739358
CDS:C52A11.4e	C52A11.4e	6555	II: 10739275-10739358
CDS:C52A11.4g	C52A11.4g	6567	II: 10739275-10739358
CDS:C52A11.4b	C52A11.4b	2517	II: 10757479-10757779
CDS:C52A11.4d	C52A11.4d	7269	II: 10739275-10739358
CDS:C52A11.4i	C52A11.4i	2943	II: 10739275-10739358
CDS:C52A11.4j	C52A11.4j	1413	II: 10739275-10739358

5 RNAi Result

• WBRNAi00043004
• WBRNAi00012288
• WBRNAi00065442
• WBRNAi00077321
• WBRNAi00065441

565 Allele

• gk963801
• gk963053
• otn9580
• gk962682
• gk963356
• WBVar00228610
• gk153631
• WBVar02068206
• WBVar02068205
• WBVar02068204
• WBVar02068207
• WBVar01604912
• WBVar01604900
• WBVar01604905
• WBVar01604906
• WBVar01604907
• WBVar01604908
• WBVar01604901
• WBVar01604902
• WBVar01604903
• WBVar01604904
• WBVar01604909
• WBVar01604910
• WBVar01604911
• WBVar01439648
• WBVar01439650
• WBVar01439657
• WBVar01439656
• WBVar01439655
• WBVar01439654

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003404
• Start: 10738635
• End: 10778126
• 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_10738629..10738634
• Length (nt): 6
• Chromosome Location: II: 10738629-10738634
• Organism: Caenorhabditis elegans

218 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
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 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
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	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
	Genes significantly enriched in NSM neurons (isolated by FACS) versus the reference, according to RNAseq analysis towards total RNA.	Gene expression quantification and differential expression was analyzed using cufflinks v2.2.1. Enriched contains only genes significantly enriched (differentially expressed >= 2.4 fold in total RNA or >= 3.2 fold in DSN treated total RNA) in the NSM neurons versus the reference.	WBPaper00045974:NSM_enriched_totalRNA_RNAseq
	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 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 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 expressed in vulva.	FPKM >= 1.	WBPaper00064122:vulva_transcriptome
	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
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 changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals.	Sleuth	WBPaper00051558:aging_regulated
	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
	Expression Pattern Group C, enriched for genes involved in metabolic processes.	The significance (P 0.0001) of the relative age (time) was used to determine if a gene was differentially expressed between the three age (time) groups. The effect of this factor explaining gene expression differences was used to determine if the expression went up or down during the two age/time periods (t1 - t2 and t2 -t3). Authors used a permutation approach to determine the thresholds for the different mapping strategies. For each of the used models for eQTL mapping, authors used 23,000 permutations. For each permutation, authors randomly picked a spot; each spot could only be picked once. The gene expression and relative lifespan values were than randomly distributed over the RILs (and time points) and used for mapping. In this way, authors obtained a threshold for each of the explaining factors. For the single time points, authors used a FDR of 0.01 to adjust for multiple testing. The genome-wide threshold for this FDR is -log10 P = 3.8 for each of the three time points. For the combined models (t1 to t2 and t2 to t3), authors used a genome-wide threshold of -log10 P = 4, which resembles an FDR of 0.006, 0.001, and 0.006 for marker, age, and the interaction between marker and age, respectively. To determine the threshold for the single gene examples, authors used 1000 permutations as in the genome-wide threshold. The difference is that they use the gene under study in all of the permutations. The P-values for the gene specific thresholds were determined at FDR = 0.05.	WBPaper00036286:Pattern_C
	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 detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome

11 Expression Patterns

• Primary Identifier: Expr1031573
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr14243
• Pattern: mpz-1 was identified as being expressed in the pharyngeal neurones (including M4 and NSM based on their size and relative position), extrapharyngeal neurones, body wall muscle and vulval muscle. Co-expression of mpz-1::mRFP-1 with mgl-1::GFP was identified in neurones of the nerve ring and the pharyngeal nervous system in the desheathed pharynx preparation.

• Primary Identifier: Expr3959
• Pattern: GFP fluorescence from promoter 2 was exclusively neuronal and included about 40 neurons in the nerve ring, pharyngeal neurons (M4, NSM, MCs), 6 neurons in the body (AVM, SDQR/L, PVM, HSNR/L) and 8 neurons in the tail (ALNL/R, PVCL/R, PVQL/R, PVNL/R).

• Primary Identifier: Expr3960
• Pattern: GFP fluorescence from promoter 3 was observed in all of the muscles and neurons identified in Expr3958 and Expr3959.

• Primary Identifier: Expr3958
• Pattern: GFP fluorescence driven by promoter 1 was robust in body wall and vulval muscles and faint and variable in a small group of neurons around the nerve ring.

• Primary Identifier: Expr11638
• Pattern: As predicted from expression driven by the individual promoters, only 3 pairs of ring motorneurons (RMHs, RMFs, RMDs) expressed both ser-1::yfp and mpz-1::cfp. Unfortunately, attempts to colocalize the full length proteins were unsuccessful using this approach as SER-1::YFP and SER-1::CFP aggregated significantly when expressed in vulval muscle.

• Primary Identifier: Expr2013679
• 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: Expr3961
• Remark: To confirm the synaptic localization of these neuronal puncta, MPZ-1/CFP and synaptobrevin/YFP (vesicle associated membrane protein, VAMP), a presynaptic marker, were coexpressed under the control of mpz-1 promoter 2 to direct neuronal expression. As predicted, YFP::CFP colocalization was observed in most puncta; however, a few exhibited YFP fluorescence alone.
• Subcellular Localization: The expression of full length MPZ-1 from the individual mpz-1 promoters exhibited discrete subcellular localizations. Fluorescence in body wall muscle exhibited faint striations marked with puncta. In vulval muscle GFP fluorescence was concentrated at cell membranes around the vulval opening. This vulval localization was quite similar to that observed for SER-1::GFP. In neurons, MPZ-1::GFP fluorescence was concentrated in cell bodies and was punctate in the sublateral processes and ventral cord, suggesting a synaptic localization. At lower expression levels discrete puncta were also observed in neuron cell bodies.

• Primary Identifier: Expr1146968
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2031913
• 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: Expr1028664
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

5 GO Annotation

19 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003404
• Start: 10738635
• End: 10778126
• Strand: -1

5 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 39492

1 Sequence Ontology Term

• Name: gene

1 Strains

• WBStrain00035872

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrII_10778127..10778386
• Length (nt): 260
• Chromosome Location: II: 10778127-10778386
• Organism: Caenorhabditis elegans