WormMine: Gene WBGene00002073

• WormBase Gene ID: WBGene00002073
• Gene Name: ima-2
• Sequence Name: F26B1.3
• Brief Description: ima-2 encodes one of three C. elegans importin alpha proteins; IMA-2 is predicted to function as an adaptor protein that regulates import of nuclear proteins; during development, ima-2 activity is required for normal germline and embryonic mitoses, specifically for proper chromosome segregration and nuclear reassembly; IMA-2 expression is detected in germ cells, oocytes, and early embryonic cells in a dynamic pattern that depends upon the stage of the cell cycle: in germ cells and early embryonic cells at interphase, IMA-2 is cytoplasmic and nuclear envelope-associated, while in oocytes, IMA-2 is cytoplasmic and intranuclear; during mitoses (prometaphase until telophase), IMA-2 surrounds condensed chromosomes, but does not associate with the mitotic spindle; early somatic expression of maternal IMA-2 is diluted upon cell division, with appreciable expression subsequently seen only in the germ line.
• Organism: Caenorhabditis elegans
• Automated Description: Enables nuclear import signal receptor activity. Involved in several processes, including meiotic sister chromatid cohesion; mitotic nuclear membrane reassembly; and protein import into nucleus. Located in cytoplasm and nuclear envelope. Expressed in Z2; Z3; and germ line. Is an ortholog of human KPNA2 (karyopherin subunit alpha 2) and KPNA7 (karyopherin subunit alpha 7).
• Biotype: SO:0001217
• Genetic Position: I :0.958776 ±0.01404
• Length (nt): 2030

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00002073

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F26B1.3.1	F26B1.3.1	1803	I: 6315233-6317262

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F26B1.3	F26B1.3	1596	I: 6315247-6315342

15 RNAi Result

• WBRNAi00065352
• WBRNAi00086895
• WBRNAi00000034
• WBRNAi00022655
• WBRNAi00022709
• WBRNAi00022710
• WBRNAi00008002
• WBRNAi00025241
• WBRNAi00025242
• WBRNAi00045598
• WBRNAi00062937
• WBRNAi00062945
• WBRNAi00081298
• WBRNAi00077503
• WBRNAi00062951

33 Allele

• gk962858
• gk962706
• gk963902
• gk796493
• gk797459
• gk581045
• gk615977
• WBVar01283213
• gk590801
• gk112771
• gk866527
• gk112772
• gk723211
• gk112773
• gk662101
• tm1303
• gk728342
• gk537176
• gk681341
• gk417046
• gk694504
• gk336879
• gk593034
• ax545
• gk562796
• gk883626
• gk699157
• gk874518
• gk358152
• ok256

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00002073
• Start: 6315233
• End: 6317262
• 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_chrI_6317263..6317696
• Length (nt): 434
• Chromosome Location: I: 6317263-6317696
• Organism: Caenorhabditis elegans

251 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
	Genes with expression altered >= 3-fold in dpy-10(e128) mutants.	Data across the wild type series was analyzed using the Significance analysis of Microarrays (SAM) algorithm (to calculate the False Discovery Rate (FDR)).	WBPaper00035873:dpy-10_regulated
	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
	Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr reference).	A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.	WBPaper00037950:AVE-neuron_L1-larva_expressed
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
	Genes that were downregulated in lin-15B(n744).	For each gene in each microarray hybridization experiment, the ratio of RNA levels from the two samples was transformed into a log2 value and the mean log2 ratio was calculated. The log2 ratios were normalized by print-tip Loess normalization (Dudoit and Yang, 2002). All genes with a false discovery rate of <= 5% (q <= 0.05) (Storey and Tibshirani, 2003) and a mean fold-change ratio of >= 1.5 were selected for further analysis.	WBPaper00038168:lin-15B(n744)_downregulated
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 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
	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 expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:pharynx_expressed
	Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
	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 that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_glp-1(e2141)
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 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 decreased expression in hsp-6(mg585) comparing to in N2 at L4 larva stage.	EdgeR, fold change > 2, FDR < 0.001.	WBPaper00056290:hsp-6(mg585)_downregulated
Heat Shock: 35C 4 hours at L4 larva stage.	Transcripts that showed significantly decreased expression after L4 larva N2 animals were heat stressed at 35C for 4 hours	DESeq2	WBPaper00057154:HeatShock_downregulated_mRNA

8 Expression Patterns

• Primary Identifier: Expr1031226
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr2436
• Pattern: Affinity-purified antibodies to IMA-2 detected the protein only in germ line cells. In embryos the maternal IMA-2 was diluted during early cell divisions and was expressed at detectable levels only in the germ line precursor cells Z2 and Z3, not in the somatic cells. In the adult hermaphrodite germ line, IMA-2 was present within all germ cells from the distal end of the germ line to the proximal oocyte. IMA-2 was not detected in sperm.
• Subcellular Localization: In distal germ cells, IMA-2 was predominantly cytoplasmic and NE associated. However, in the developing oocytes IMA-2 was predominantly cytoplasmic and intranuclear with no apparent enrichment at the NE. When distal germ cells in prometaphase and metaphase were evident by DAPI staining of the DNA, IMA-2 was enriched at the region immediately surrounding the condensed chromosomes. In the fertilized egg before pronuclear migration, IMA-2 was predominantly cytoplasmic and NE associated in both pronuclei. The intranuclear IMA-2 in the proximal oocyte had dispersed into the oocyte cytoplasm at NE breakdown, but returned to the NE upon NE reformation around the pronuclei. Because sperm do not contain IMA-2, the male pronuclear IMA-2 must have originated in the egg cytoplasm. As the pronuclei became associated, the intensity of IMA-2 staining at the NE decreased. After pronuclear fusion, IMA-2 completely filled the space surrounding the chromosomes but did not seem to be enriched on the surface of the condensed chromosome. This perichromosomal localization persisted during congression of the chromosomes toward the metaphase plate but had decreased by the time of metaphase plate formation. Early in anaphase as chromosome separation first became apparent, IMA-2 staining could still be seen in the region surrounding the chromosome, but was significantly decreased compared with earlier stages. Later in telophase, IMA-2 again became associated with the NE as soon as the structure was detectable around the daughter nuclei. IMA-2 staining persisted at the NE through cytokinesis and into interphase of the next cell cycle. The mitotic IMA-2 staining was not coincident with beta-tubulin staining in the spindle microtubules or the spindle poles. In two-cell embryos: IMA-2 surrounded the chromosomes only in nuclei that were in late prometaphase or later. Nuclei containing fully condensed chromosomes, but in which the microtubules had not penetrated, excluded IMA-2. Note, however, that by this point IMA-2 was only weakly detected at the NE. Nuclei in which peripheral nucleoporin staining could be detected did not accumulate IMA-2 around the chromosomes.

• Primary Identifier: Expr1341
• Pattern: Within the adult germline, IMA-2 was detected in the common cytoplasm of the rachis and in association with the nuclei throughout the germline, regardless of hermaphrodite age. IMA-2 was detected in embryos and in adult germlines, but not in adult somatic tissues, consistent with the expression of the mRNA detected by northern blot analysis.
• Subcellular Localization: cytoplasm and nuclei

• Primary Identifier: Expr2012726
• 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: Expr2030963
• 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: Expr1340
• Pattern: ima-2 expressed weakly during early larval stages of development, but their expression increased dramatically in adult worms when germ cells are continually proliferating.

• Primary Identifier: Expr1015623
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1149508
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

27 GO Annotation

10 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00002073
• Start: 6315233
• End: 6317262
• Strand: 1

27 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 2030

1 Sequence Ontology Term