WormMine: Gene WBGene00011345

• WormBase Gene ID: WBGene00011345
• Gene Name: dma-1
• Sequence Name: T01G9.3
• Organism: Caenorhabditis elegans
• Automated Description: Enables protease binding activity. Involved in neuron development and regulation of cell morphogenesis. Located in dendrite membrane. Expressed in head neurons; sensory neurons; somatic nervous system; and vulva.
• Biotype: SO:0001217
• Genetic Position: I :2.70477±
• Length (nt): 2509

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00011345

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T01G9.3.1	T01G9.3.1	2088	I: 8281969-8284477

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T01G9.3	T01G9.3	1812	I: 8282066-8282269

6 RNAi Result

• WBRNAi00052159
• WBRNAi00052160
• WBRNAi00004097
• WBRNAi00091267
• WBRNAi00035031
• WBRNAi00035032

50 Allele

• gk962858
• gk962706
• gk963902
• gk963849
• gk964316
• gk963044
• gk963043
• tm5159
• gk956357
• wy908
• cbc1
• gk116600
• gk116601
• gk116602
• gk116603
• gk116604
• yan51
• wy686
• gk637691
• gk424367
• yan126
• gk735675
• gk564992
• gk464512
• wy1041
• gk667471
• gk519332
• WBVar01957343
• gk523173
• WBVar01909946

1 Chromosome

• WormBase ID: I
• Organism: Caenorhabditis elegans
• Length (nt): 15072434

1 Chromosome Location

• Feature . Primary Identifier: WBGene00011345
• Start: 8281969
• End: 8284477
• Strand: 1

3 Data Sets

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

0 Downstream Intergenic Region

195 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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
	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
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
	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 intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_expressed
	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 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
	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 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 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
	Transcripts that showed significantly increased expression in hpk-1(pk1393) comparing to in N2 at adult day 2.	DESeq 2, fold change > 2, FDR < 0.05.	WBPaper00065581:hpk-1(pk1393)_upregulated
	Transcripts that showed significantly increased expression in hda-1(ne4752[3xFLAG-Degron-HDA-1]) in gonads dissected from 1-day old adult animals.	Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R.	WBPaper00061479:hda-1(ne4752)_upregulated
	Transcripts that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00066594:ilc-17.1(syb5296)_upregulated
	Transcripts that showed significantly increased expression in hda-2(ok1479) comparing to in N2 animals.	DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2.	WBPaper00062159:hda-2(ok1479)_upregulated
	Transcripts that showed significantly increased expression in srbc-48(ac23);kyIs262;fer-1(b232ts) comparing to in kyIs262;fer-1(b232ts), 24h after infection with P.aeruginosa.	DESeq2, FDR <0.05, fold change > 2.	WBPaper00059664:srbc-48(ac23)_upregulated
	Transcripts that showed significantly increased expression in dpy-21(e428) comparing to in N2 during L3 stage.	DESeq v1.6.3. Fold change > 1.5.	WBPaper00050370:dpy-21(e428)_L3_upregulated
	Transcripts that showed significantly decreased expression in set-2(tm1630) animals at embryo stage, comparing to in N2 animals.	DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction.	WBPaper00060014:set-2(tm1630)_downregulated
Starvation	Transcripts that showed significantly altered expression by starvation with 100 mM salt (NaCl)	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:starvation_regulated_LowSalt
	Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(+), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_P-granule(-)GFP(+)_vs_control_day2-adult
	Transcripts of coding genes that showed significantly increased 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_enriched_coding-RNA

15 Expression Patterns

• Primary Identifier: Expr13955
• Pattern: dma-1, bicd-1, and flp-4 were expressed in FLP and PVD neurons.

• Primary Identifier: Expr1020964
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2029191
• 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: Expr2010952
• 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: Expr15284
• Pattern: We observed prominent dma-1p::dma-1::gfp expression in the IL2 dendrites during dauer. Expression of dma- 1p::dma-1::gfp was not detectable in adult IL2s. dma-1p::dma-1::gfp translational reporter is prominently expressed in the FLPs and PVDs during dauer. We observed prominent dma-1p::dma-1::gfp expression in the IL2 dendrites during dauer. Expression of dma- 1p::dma-1::gfp was not detectable in adult IL2s.

• Primary Identifier: Expr15285
• Subcellular Localization: dma-1p::dma-1::gfp localizes to the IL2 dendrites during dauer.

• Primary Identifier: Expr15286
• Subcellular Localization: During dauer, dma-1p::dma-1::gfp localizes to the FLP cell body and dendrite in the head and the PVD cell body and dendrites in the midbody.

• Primary Identifier: Expr1155793
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr12876
• Subcellular Localization: In wild-type animals, diffuse DMA-1-GFP fluorescence was localized to all dendritic compartments including the higher order branches. Discrete GFP puncta could also be found in the cell body and 1 order dendrites, which were likely secretory or endocytic vesicles that carry DMA-1. Many DMA-1-GFP puncta co-localized with late endosomes/lysosomes labeled by mCherry-RAB-7 in wild-type PVD. DMA-1 localized to the plasma membrane. Monitoring endogenous DMA-1 by engineering a YFP into the dma-1 genomic locus using CRISPR showed a DMA-1 localization pattern similar to the high copy transgenes, with both membrane and vesicular distribution of the protein.

• Primary Identifier: Expr1034994
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr9910
• Pattern: While DMA-1::GFP is dominantly expressed in PVD and FLP, especially by the adult stage, DMA-1::GFP expression in additional head and ventral cord neurons was detected during larval and early adult stages. DMA-1 expression was detected in the PVD cell body shortly after PVD are born (L2 larval stage) before any dendrite outgrowth or branching has occurred. Weaker DMA-1::GFP expression can be seen in ventral cord motorneurons and in the sub-lateral cords.Expression was variable from animal to animal, seen in both commissural and non-commissural motorneurons, and was mostly undetectable by the early adult stage. In the head, expression of DMA-1::GFP was detected during development in additional head neurons besides FLP. Of these neurons, the strongest expression was detected in neurons that run around the nerve ring and extend processes along the sub-lateral cords (likely some combinationof the SIA, SIB, SMB and/or SMD classes of neurons). A number of additional head neurons displayed inconsistent DMA-1::GFP expression from animal to animal. Again, expression in these additional neurons was transient and mostly undetectable by the early adult stage. d, Strong expression DMA-1::GFP was detected in vulva cells during the L3-L4 larval stages.
• Subcellular Localization: Bright DMA-1::GFP localization can be seen in intracellular membrane structures that are likely to be golgi/ER. The plasma membrane is also clearly visible, indicating that DMA-1::GFP is a cell-surface protein.

• Primary Identifier: Expr14556
• Subcellular Localization: The DMA-1::GFP reporter is localized in a punctate fashion in the cell body and along the dendritic tree as well as on the membrane, visible as diffuse membrane staining throughout the whole dendritic tree.

• Primary Identifier: Expr14264
• Subcellular Localization: In wild-type animals, DMA-1::GFP was largely localized to secretory vesicle-like structures in the soma and showed a diffuse plasma membrane-like pattern in the dendrites.

• Primary Identifier: Expr14265
• Subcellular Localization: In wild-type animals, DMA-1::GFP was largely localized to secretory vesicle-like structures in the soma and showed a diffuse plasma membrane-like pattern in the dendrites.

• Primary Identifier: Expr12470
• Subcellular Localization: DMA- 1::GFP localized in the dendritic membranes, and in some intracellular vesicles in wild-type animals. DMA-1::GFP containing vesicles mainly localized to the primary dendrites.

15 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00011345
• Start: 8281969
• End: 8284477
• Strand: 1

15 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 2509

1 Sequence Ontology Term