WormMine: Gene WBGene00003914

• WormBase Gene ID: WBGene00003914
• Gene Name: pam-1
• Sequence Name: F49E8.3
• Brief Description: pam-1 encodes a metalloprotease that is the C. elegans puromycin-sensitive aminopeptidase (PSA) ortholog; in the one-cell embryo, PAM-1 is required for timely exit from meiosis II proper centrosome positioning, proper localization of polarity and cell fate determinants, and formation of the anteroposterior axis; genetic studies indicate that cyb-3, which encodes a B-type cyclin, is required for pam-1(lf) meiotic exit defects, suggesting that CYB-3 activity is regulated by PAM-1, directly or indirectly, in the early embryo; a pam-1::gfp reporter fusion is expressed in embryos, larvae, and adults; in larvae and adults, expression is particularly notable in the posterior intestine and amphid sensory neurons; in males, expression is also seen in neurons in the developing and mature male tail; in vitro, PAM-1 exhibits metal-dependent aminopeptidase activity, hydrolyzing the N-terminal amino acid from various peptide substrates.
• Organism: Caenorhabditis elegans
• Automated Description: Enables metalloaminopeptidase activity. Involved in several processes, including exit from meiosis; first cell cycle pseudocleavage; and regulation of reproductive process. Located in condensed chromosome; cytoplasm; and mitotic spindle pole. Expressed in amphid process; intestine; male-specific anatomical entity; nerve ring; and tail neurons. Is an ortholog of human NPEPPS (aminopeptidase puromycin sensitive).
• Biotype: SO:0001217
• Genetic Position: IV :3.34579 ±0.001269
• Length (nt): 6837

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003914

Genomics

4 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F49E8.3a.3	F49E8.3a.3	2967	IV: 7543976-7550191
Transcript:F49E8.3a.1	F49E8.3a.1	2812	IV: 7543984-7547117
Transcript:F49E8.3a.2	F49E8.3a.2	3008	IV: 7543987-7550812
Transcript:F49E8.3b.1	F49E8.3b.1	2847	IV: 7544140-7550804

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F49E8.3b	F49E8.3b	2847	IV: 7544140-7544226
CDS:F49E8.3a	F49E8.3a	2655	IV: 7544140-7544226

7 RNAi Result

• WBRNAi00062566
• WBRNAi00047869
• WBRNAi00047870
• WBRNAi00076453
• WBRNAi00032551
• WBRNAi00089085
• WBRNAi00008824

89 Allele

• gk964278
• gk964500
• gk963722
• gk963417
• gk963416
• WBVar02122959
• tm742
• WBVar02020892
• otn637
• gk395928
• gk566956
• WBVar01453122
• gk573368
• gk361536
• gk832907
• gk844907
• WBVar01453124
• WBVar01453123
• ok477
• gk205693
• or347
• WBVar00190725
• WBVar00190726
• WBVar02003868
• or370
• WBVar01668787
• WBVar01966609
• or403
• ttTi11613
• WBVar01966608

1 Chromosome

• WormBase ID: IV
• Organism: Caenorhabditis elegans
• Length (nt): 17493829

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003914
• Start: 7543976
• End: 7550812
• 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_chrIV_7542536..7543975
• Length (nt): 1440
• Chromosome Location: IV: 7542536-7543975
• Organism: Caenorhabditis elegans

131 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
	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
	mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis.	Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05.	WBPaper00045420:fertilization_downregulated_transcript
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
Osmotic stress	Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when no food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_NoFood
	Transcripts that showed significantly higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc).	DESeq2, fold change >= 2, FDR <= 0.01.	WBPaper00056826:SGP_biased
	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
	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
	Maternal class (M): genes that are called present in at least one of the three PC6 replicates.	A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing.	[cgc5767]:expression_class_M
	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 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 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_6h
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
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
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
	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 changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals.	Sleuth	WBPaper00051558:aging_regulated
	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 detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome
Skin Wounding: skin wounding using femtosecond or Micropoint UV laser or with single stabs of a microinjection needle to the anterior or posterior body 24 h after the L4 stage.	Transcripts that showed significantly decreased expression after skin wounding using femtosecond or Micropoint UV laser or with single stabs of a microinjection needle to the anterior or posterior body 24 h after the L4 stage of N2 animals.	The cutoff for differential expressed genes (DEGs) were: Benjamini-Hochberg adjusted p-value less than 0.05 and fold change larger than 1.5.	WBPaper00059895:wounding_downregulated
	Transcripts that showed significantly increased expression in pry-1(mu38) animals comparing to in N2 at L1 larva stage.	DESeq, FDR < 0.05	WBPaper00055626:pry-1(mu38)_upregulated
Bacteria: B.thuringiensis	Transcripts in elt-2(RNAi) animals that were significantly differentially expressed at least for one time point and one pathogenic strain Bt247 and Bt679 compared to the non pathogenic strain Bt407.	Cuffdiff	WBPaper00060358:B.thuringiensis_pathogen_regulated_elt-2(RNAi)
Bacteria: B.thuringiensis	Transcripts in N2 animals that were significantly differentially expressed at least for one time point and one pathogenic strain Bt247 and Bt679 compared to the non pathogenic strain Bt407.	Cuffdiff	WBPaper00060358:B.thuringiensis_pathogen_regulated_N2
	Genes that were not enriched in either spermatogenic fem-3(q96gf) nor oogenic fog-2(q71) gonads, according to RNAseq analysis.	To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq.	WBPaper00045521:Gender_Neutral
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
	Proteins identified in extracellular vesicle.	N.A.	WBPaper00062669:extracellular-vesicle_protein

10 Expression Patterns

• Primary Identifier: Expr1031847
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1151700
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2635
• Pattern: In addition to the components described above, adult males showed transgene neuronal expression in the developing and mature male tail. Independent lines of transgenic C. elegans expressing the reporter transgene showed fluorescence in embryo, larval and adult stages. Embryonic reporter gene activity was observed around the time of gastrulation and continued throughout development. Strong fluorescence was observed in the intestinal cells of larvae and adults, and this was particularly enhanced in the cells of the posterior gut. Larval and adult fluorescence was also observed in neuronal cell bodies around the nerve ring and in processes extending towards the tip of the nose, indicative of them being the amphid sensory neurons.
• Subcellular Localization: Expressed in neuronal cell bodies and processes.

• Primary Identifier: Expr9077
• Remark: Picture: Fig. 1A.
• Subcellular Localization: PAM-1 is a cytoplasmic aminopeptidase present throughout the cell during early development. During meiosis I, PAM-1 localizes to the cytoplasm just under the cell cortex. By meiosis II, this subcortical localization extends to the entire cytoplasm where it is seen throughout early development. During the first cell division and beyond, PAM-1 is enriched around mitotic chromosomes, clearly seen in metaphase and anaphase, and near the spindle poles.

• Primary Identifier: Chronogram872
• Remark: Original chronogram file: chronogram.1914.xml
• Reporter Gene: [F49E8.3:gfp] transcriptional fusion.

• Primary Identifier: Chronogram871
• Remark: Original chronogram file: chronogram.1913.xml
• Reporter Gene: [F49E8.3:gfp] transcriptional fusion.

• Primary Identifier: Expr2032950
• 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: Chronogram1758
• Remark: Original chronogram file: chronogram.674.xml
• Reporter Gene: [F49E8.3:gfp] transcriptional fusion.

• Primary Identifier: Expr2014716
• 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: Expr1016847
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

47 GO Annotation

40 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003914
• Start: 7543976
• End: 7550812
• Strand: -1

47 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 6837

1 Sequence Ontology Term