WormMine: Gene WBGene00194737

• WormBase Gene ID: WBGene00194737
• Gene Name: Y50D7A.13
• Sequence Name: Y50D7A.13
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable metalloendopeptidase activity. Predicted to be involved in collagen catabolic process and extracellular matrix organization. Predicted to be located in extracellular space. Human ortholog(s) of this gene implicated in several diseases, including Alzheimer's disease; artery disease (multiple); autoimmune disease (multiple); and carcinoma (multiple). Is an ortholog of human MMP2 (matrix metallopeptidase 2); MMP23B (matrix metallopeptidase 23B); and MMP9 (matrix metallopeptidase 9).
• Biotype: SO:0001217
• Genetic Position: :±
• Length (nt): 5164

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00194737

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y50D7A.13a.1	Y50D7A.13a.1	690	III: 289464-294627
Transcript:Y50D7A.13b.1	Y50D7A.13b.1	93	III: 289464-292342

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y50D7A.13a	Y50D7A.13a	585	III: 289464-289539
CDS:Y50D7A.13b	Y50D7A.13b	93	III: 289464-289539

2 RNAi Result

• WBRNAi00001652
• WBRNAi00020835

133 Allele

• gk962532
• gk964281
• WBVar01912583
• otn13014
• WBVar01912579
• WBVar01912580
• WBVar01912581
• WBVar01912582
• WBVar02077464
• otn10973
• WBVar01912578
• WBVar02101266
• WBVar02101265
• WBVar02120257
• WBVar01902854
• WBVar01902855
• otn7412
• WBVar01951039
• WBVar00029733
• WBVar01254524
• otn8456
• WBVar00029738
• otn8457
• WBVar00029743
• WBVar00029748
• WBVar01699770
• WBVar01699772
• WBVar01699771
• WBVar02102093
• WBVar02102092

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00194737
• Start: 289464
• End: 294627
• Strand: -1

3 Data Sets

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

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrIII_289439..289463
• Length (nt): 25
• Chromosome Location: III: 289439-289463
• Organism: Caenorhabditis elegans

48 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts that showed differential expression between 24 and 26 hours post hatching L2d and dauer committed larvae of daf-9(dh6), triggered by the dafachronic acid (DA) growth hormone. Cluster 3 genes increased expression transiently at 26 hour post hatching.	Benjamini Hochberg corrected q-value < 0.01.	WBPaper00053388:dauer_regulated_Cluster3
	Transcripts that showed significantly increased expression in mbl-1(syb4345), referred to as mbl-1long(ex7+), comparing to in N2 at L4 larva stage.	DESeq2, Fold change > 2 and FDR < 0.05	WBPaper00066410:mbl-1(syb4345)_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 daf-2(e1370) comparing to in N2.	Student's t-test, fold change > 2, p-value < 0.05.	WBPaper00055386:daf-2(e1370)_upregulated
	Transcripts that showed significantly decreased expression in nhr-114(gk849) comparing to wild type animals at L4 larva.	DESeq2 1.26.0, fold change > 2, FDR < 0.05.	WBPaper00064539:nhr-114(gk849)_downregulated
	Transcripts that showed significantly decreased expression in pals-17(syb3980) comparing to in N2 animals at young adult stage.	Differential expression analyses were performed using limma-voom in Galaxy, adj p <= 0.05, logFC > 2	WBPaper00065984:pals-17(syb3980)_downregulated
	Transcripts depleted in RIS neurons comparing to in all cells.	edgeR 3.24.3, FDR < 0.01	WBPaper00058969:RIS_depleted
Temprature shift to 28C for 48 hours.	Transcripts that showed significantly increased expression after animals were exposed to 28C temperature for 48 hours.	Differentially expressed genes wereidentified using DESeq (v.1.18.0) by normalizing readsbased on the negative binomial distribution method andcomparing each HS timepoint to the 0-h control.	WBPaper00061341:28C_48h_upregulated
	Genome-wide analysis of developmental and sex-regulated gene expression profile.	self-organizing map	cgc4489_group_14
	Transcripts that showed significantly increased expression in unc-30(ok613) animals at L4 larva stage after 4 hours of Pseudomonas aeruginosa infection, comparing to infected N2 animals.	Genes exhibiting at least two-fold change were considered differentially expressed.	WBPaper00061439:unc-30(ok613)_upregulated_P.aeruginosa-infection
	Transcripts that did not alter expression in smg-1(r910) and smg-1(r910) smg-2(r915) mutants comparing to in N2, but their mRNAs co-purify with SMG-2.	edgeR	WBPaper00053308:SMG-2_associated_NMD(-)_unaltered_ClassII
	Transcripts that interact with 3xFLAG-DLC-1 as identified by immunoprecipitation followed by RNA sequencing.	DESeq2, fold change > 2,, p-value < 0.01	WBPaper00055334:DLC-1_interacting
	Transcripts that showed significantly increased expression in tetraploid N2 comparing to diploid N2 animals at L4 larva stage.	DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05.	WBPaper00066110:tetraploid_vs_diploid_upregulated
	Transcripts that showed significantly increased expression in jmjd-5(zr1234) comparing to in N2 animals.	DESeq2, adjusted p value < 0.01 and absolute log2FC > = 1.	WBPaper00062156:jmjd-5(zr1234)_upregulated
	Transcripts that showed significantly increased expression in hsp-6(mg585) comparing to in N2 at L4 larva stage.	EdgeR, fold change > 2, FDR < 0.001.	WBPaper00056290:hsp-6(mg585)_upregulated
	Transcripts that showed differential expression between 24 and 26 hours post hatching L2d and dauer committed larvae of daf-9(dh6), triggered by the dafachronic acid (DA) growth hormone. Cluster 5 genes decreased expression after dauer commitment.	Benjamini Hochberg corrected q-value < 0.01.	WBPaper00053388:dauer_regulated_Cluster5
	Transcripts that showed significantly decreased 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)_downregulated_neuron
	Transcripts that showed significantly increased expression in eat-2(ad465) comparing to in N2.	Student's t-test, fold change > 2, p-value < 0.05.	WBPaper00055386:eat-2(ad465)_upregulated
	Transcripts that showed significantly increased expression in hpl-2(tm1489) comparing to in N2 animals.	DESeq2, adjusted p-value < 0.05, log2 fold change > 2 or < -2.	WBPaper00054493:hpl-2(tm1489)_upregulated
	Transcripts that showed significantly decreased expression in BAT525 [hmg-3 (tm2539) / dpy-5(e61) unc-13(e1091) I.] comparing to in N2 at 1-day post L4 adult hermaphrodite stage	DESeq 2, fold change > 4, adjusted p-value < 0.05.	WBPaper00055013:hmg-3(bar24)_downregulated
	Genes identified as up-regulated at a 5% false discovery rate through RNAseq experiments with three tatn-1(qd182) and three N2 RNA samples.	ANOVA with FDR <= 0.05.	WBPaper00044656:tatn-1(qd182)_upregulated
Bacteria diet: Chryseobacterium sp. CHNTR56 MYb120	Transcripts that showed significantly increased expression after animals were fed by Chryseobacterium sp. CHNTR56 MYb120, comparing to animals fed by OP50.	edgeR FDR <= 0.05, fold change >= 4.	WBPaper00061424:Diet_MYb120_upregulated
	Transcripts that showed significantly decreased expression in lin-53(RNAi) embryos comparing to control animals.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00067044:lin-53(RNAi)_downregulated
	Transcripts that showed significantly increased expression in bcf-1(ylf1) comparing to in N2 adult animals.	DESeq2	WBPaper00064933:bcf-1(ylf1)_upregulated_transcript
	Transcripts that showed significantly decreased expression in ints-4(RNAi) animals treated with 300uM CdCl2 from L1 to late L3 larva stage, comparing to control RNAi animals with the same Cadmium treatment.	DESeq2, v1.12.0, fold change > 2, FDR < 0.05	WBPaper00057068:ints-4(RNAi)_downregulated_Cadmium
	Transcripts that showed significantly increased expression in nhr-8(hd117) comparing to in N2.	Differentially expressed genes were identified using Sleuth (version 0.30.0).	WBPaper00062446:nhr-8(hd117)_upregulated
	Transcripts that showed significantly decreased 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_downregulated_neural
	Transcripts that showed significantly increased expression in mrps-5(RNAi) comparing to in control animals.	Fold change > 4, p-value < 0.01	WBPaper00056330:mrps-5(RNAi)_upregulated
	Transcripts that showed significantly increased expression in lpd-3(ok2138) comparing to in N2 animals.	DESeq2, fold change > 4, FDR < 0.05.	WBPaper00064661:lpd-3(ok2138)_upregulated

6 Expression Patterns

• Primary Identifier: Expr1160534
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1160533
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2007754
• 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: Expr1040461
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr2025997
• 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: Expr1040462
• Pattern: Tiling arrays expression graphs

13 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00194737
• Start: 289464
• End: 294627
• Strand: -1

13 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 5164

1 Sequence Ontology Term

• Name: gene

0 Strains

0 Upstream Intergenic Region