WormMine: Gene WBGene00003787

• WormBase Gene ID: WBGene00003787
• Gene Name: npp-1
• Sequence Name: K07F5.13
• Brief Description: npp-1 encodes a nucleoporin that is most closely related to the vertebrate nucleoporin Nup54 and Saccharomyces cerevisiae nucleoporin Nup57p; during embryonic development, npp-1 activity is essential for some aspects of nuclear structure and function, as well as for proper mitotic spindle orientation, asymmetric cell division, cell fate specification, and mitotic cell cycle timing; npp-1 is also required for normal oogenesis and levels of fertility and for effective RNA interference (RNAi); an NPP-1::GFP reporter is expressed at all stages of development and localizes to the nuclear envelope; the NPP-1C isoform interacts with itself and with nucleoporins NPP-3, NPP-4, NPP-11, and NPP-13B in yeast two-hybrid assays; NPP-1 also binds bovine calmodulin in vitro in a calcium-dependent manner.
• Organism: Caenorhabditis elegans
• Automated Description: Enables calmodulin binding activity. Involved in several processes, including establishment of mitotic spindle orientation; nuclear pore organization; and positive regulation of mitotic cell cycle, embryonic. Located in nuclear envelope. Expressed in several structures, including hypodermis. Human ortholog(s) of this gene implicated in dystonia. Is an ortholog of human NUP54 (nucleoporin 54).
• Biotype: SO:0001217
• Genetic Position: IV :4.43529 ±0.000395
• Length (nt): 3632

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003787

Genomics

3 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:K07F5.13c.1	K07F5.13c.1	2295	IV: 9858488-9862116
Transcript:K07F5.13b.1	K07F5.13b.1	2021	IV: 9858488-9862112
Transcript:K07F5.13a.1	K07F5.13a.1	2963	IV: 9858494-9862119

Other

3 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:K07F5.13c	K07F5.13c	1920	IV: 9858492-9858589
CDS:K07F5.13a	K07F5.13a	1839	IV: 9859372-9859867
CDS:K07F5.13b	K07F5.13b	1650	IV: 9858492-9858589

13 RNAi Result

• WBRNAi00077885
• WBRNAi00016746
• WBRNAi00076554
• WBRNAi00071445
• WBRNAi00078406
• WBRNAi00050184
• WBRNAi00007708
• WBRNAi00008967
• WBRNAi00025909
• WBRNAi00065348
• WBRNAi00069332
• WBRNAi00069331
• WBRNAi00110873

56 Allele

• gk964278
• gk964078
• gk964500
• gk962765
• gk963883
• gk964226
• gk964227
• WBVar01856367
• WBVar01856366
• WBVar02058544
• WBVar01856365
• WBVar02058543
• WBVar01856364
• WBVar02037040
• gk710558
• syb207
• gk525272
• gk861680
• gk621964
• gk881967
• gk902133
• gk841048
• gk609795
• gk704799
• gk515472
• gk752644
• gk902671
• gk552149
• gk833459
• gk604329

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003787
• Start: 9858488
• End: 9862119
• 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_9862120..9862220
• Length (nt): 101
• Chromosome Location: IV: 9862120-9862220
• Organism: Caenorhabditis elegans

137 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 of coding genes that showed significantly decreased 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_depleted_coding-RNA
	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
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly decreased expression in N2 after animals were exposed to E. faecalis OG1RF for 16 hours comparing to exposure to E. Coli OP50.	Cuffcompare and Cuffdiff	WBPaper00056090:E.faecalis_downregulated_N2
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	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
	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
	Genes with expression level regulated by genotype (N2 vs CB4856) at Late reproduction stage (96 hours at 24 centigrade).	Authors permuted transcript values and used a genome-wide threshold of log10 P-value = 2, which resembles a false discovery rate (FDR) of 0.0118.	WBPaper00040858:eQTL_regulated_reproductive
Bacteria diet: Escherichia coli HB101. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria E. coli HB101 for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:HB101_downregulated
	Strictly maternal class (SM): genes that are the subset of maternal genes that are not also classified as embryonic.	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_SM
Bacteria diet: Sphingomonas aquatilis Yellow. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria Sphingomonas aquatilis (Yellow) for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:S.aquatilis_downregulated
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 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
	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
	Significantly differentially expressed genes as determined by microarray analysis of wild-type and cde-1 mutant germlines.	RNAs that changed at least 2-fold with a probability of p < 0.05 were considered differentially regulated between wildtype and cde-1.	WBPaper00035269:cde-1_regulated
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
	Genes down regulated by mir-243(n4759).	RNAs that changed at least 2-fold with a probability of p > 0.05 in three biological replicates were considered differentially regulated between wild-type and mir-243.	WBPaper00036130:mir-243_down_regulated
25C vs. 20C	Transcripts that showed significantly increased expression in 1-day post L4 adult hermaphrodite N2 grown at 25C, comparing to in N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:25C_vs_20C_upregulated
	Transcripts that showed significantly increased expression in 10-days post L4 adult hermaphrodite N2 grown at 20C, comparing to in 1-day post L4 adult hermaphrodite N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:Day10_vs_Day1_upregulated
	Transcripts that showed significantly decreased 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_downregulated
	Proteins interacting with HA-PPM-1.D.	N.A.	WBPaper00062498:PPM-1.D_interacting
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
	Transcripts that showed significantly decreased expression in the neurons of bcat-1(RNAi) animals at 5-days post L4 adult hermaphrodite stage, comparing to animals injected with empty vector.	DESeq2. FDR < 0.05.	WBPaper00060459:bcat-1(RNAi)_downregulated
	Proteins identified in extracellular vesicle.	N.A.	WBPaper00062669:extracellular-vesicle_protein
	Transcripts that showed significantly decreased expression in nhl-2(ok818) comparing to in N2 at 25C.	EdgeR, FDR < 0.05, fold change < 0.5.	WBPaper00055971:nhl-2(ok818)_25C_upregulated

7 Expression Patterns

• Primary Identifier: Expr1031773
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr139
• Remark: Other strain-- UL712
• Pattern: Expression is seen from precomma stage embryos to young larval stages. In young embryos expression is generally weak and diffuse. In older embryos and larvae expression is nuclear localised in hypodermis. Expression in the strains generated is intermittent and sporadic. In young embryos expression is generally weak and diffuse. In older embryos and larvae expression is nuclear localised in hypodermis.

• Primary Identifier: Expr1153878
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr3978
• Remark: Five stable lines were produced, all of which show identical expression patterns.
• Pattern: Expressed in most, if not all cells.
• Subcellular Localization: NPP-1::GFP is localized to the nuclear envelope of most, if not all cells of transgenic animals. This is consistent with the expected localization of a nucleoporin. There is no evidence for developmental regulation of npp-1 because all cells in all stages of development express NPP-1::GFP. Signal is detected at pronuclear formation and is found on the nuclear envelope of both the maternal and paternal pronucleus. Signal disappears at pronuclear breakdown, but returns to the nuclear envelope as the envelope reforms during telophase. There is also some punctate cytoplasmic GFP signal that can be observed moving in the cytoplasm. These punctuate cytoplasmic signals may be an artifact of expressing GFP because similar patterns are seen with negative control constructs. There are also frequently punctate GFP signals inside the nucleus which are not apparent in the GFP-only control lines.

• Primary Identifier: Expr1025320
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2014379
• 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: Expr2032620
• 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).

25 GO Annotation

5 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003787
• Start: 9858488
• End: 9862119
• Strand: 1

25 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 3632

1 Sequence Ontology Term