WormMine: Gene WBGene00002228

• WormBase Gene ID: WBGene00002228
• Gene Name: klp-18
• Sequence Name: C06G3.2
• Brief Description: klp-18 encodes a kinesin motor protein whose motor domain is most similar to that of the Xenopus and human klp2 proteins; loss of klp-18 activity via RNAi indicates that KLP-18 is required for the assembly of a disordered array of acentrosomal (female meiotic) microtubules into an organized, functional, bipolar spindle; in addition, KLP-18 may also play a role in cortex dynamics during post-meiotic development; antibody staining indicates that during meiosis and mitosis (early embryonic) KLP-18 localizes to: 1) spindles, and especially spindle poles, during prometaphase, metaphase, and early anaphase, and 2) the interzone during late anaphase and telophase; in early embryos, KLP-18 is also seen around the nucleus and cell cortex at sites of cell-cell contact; KLP-18 expression in later embryos and larvae is confined to the germ line which, in adults, stains brightly in both distal and proximal regions.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable ATP hydrolysis activity; microtubule binding activity; and microtubule motor activity. Involved in meiotic spindle assembly. Located in cell cortex; microtubule; and spindle pole. Expressed in Z2; Z3; and germ line. Is an ortholog of human KIF15 (kinesin family member 15).
• Biotype: SO:0001217
• Genetic Position: IV :3.2795 ±0.000501
• Length (nt): 3484

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00002228

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C06G3.2.1	C06G3.2.1	3197	IV: 7040211-7043694

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C06G3.2	C06G3.2	2799	IV: 7040212-7040462

23 RNAi Result

• WBRNAi00010338
• WBRNAi00077947
• WBRNAi00063703
• WBRNAi00063704
• WBRNAi00063705
• WBRNAi00039932
• WBRNAi00041817
• WBRNAi00028592
• WBRNAi00007786
• WBRNAi00024719
• WBRNAi00008479
• WBRNAi00114588
• WBRNAi00061728
• WBRNAi00023036
• WBRNAi00023131
• WBRNAi00023643
• WBRNAi00023931
• WBRNAi00086497
• WBRNAi00079243
• WBRNAi00114733
• WBRNAi00063702
• WBRNAi00063706
• WBRNAi00094923

45 Allele

• gk964500
• gk963722
• gk963417
• gk963416
• h14212
• gk928447
• gk401045
• gk527232
• gk899496
• gk735887
• gk841768
• gk720610
• gk544524
• gk804311
• gk366040
• gk608657
• gk595137
• gk692492
• gk652639
• gk524719
• gk353269
• gk608656
• gk920889
• WBVar01452994
• or870
• tm2841
• wig2
• wig3
• ok2519
• WBVar01853442

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00002228
• Start: 7040211
• End: 7043694
• 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_7043695..7044057
• Length (nt): 363
• Chromosome Location: IV: 7043695-7044057
• Organism: Caenorhabditis elegans

178 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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 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
	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
	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
	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 NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:NMDA-neuron_expressed
	Genes with expression level regulated by genotype (N2 vs CB4856) and age at old adults stage (214 hours at 24 centigrade).	For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR).	WBPaper00040858:eQTL_age_regulated_aging
	Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_fem-3(q20)
	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)
	Transcripts that showed significantly increased expression in day 3 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_upregulated_fem-3(q20)
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 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
	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
Transgeneration hypoxia treatment.	Transcripts that are significantly upregulated in F1 animals after P0 parents were exposed to 0.1% oxygen for 16 hours at L4 larva stage.	For calling the significant differentially expressed genes (DEGs),the false discovery rate (FDR) after multiple testing correction was set as 0.05 and analyzed in edgeR.	WBPaper00064871:hypoxia_upregulated_F1
	Transcripts that showed significantly decreased expression in daf-16(mgDf50) comparing to in N2 at L1 larva stage.	DESeq v1.20.0 was used to analyze differential gene expression. Transcripts with adjusted p-value < 0.05 were considered differentialled expressed.	WBPaper00048971:daf-16(mgDf50)_downregulated_L1
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
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_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

7 Expression Patterns

• Primary Identifier: Expr1031305
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr2631
• Pattern: In adult C. elegans, klp-18 mRNA expression is strongest in the female germ line. In glp-4 hermaphrodites, which have a severely under-proliferated germ line, no klp-18 transcript is detectable. In fem-2 hermaphrodites, which produce only oocytes, klp-18 transcript is present at high levels, and in fem-3 gain-of-function hermaphrodites, which produce only sperm, it is present at approximately wild-type levels. Additional northern blot analysis revealed increasing klp-18 transcript levels at progressively later stages of wild-type larval development. This increase is likely due to a growing population of germ cells.

• Primary Identifier: Expr2632
• Remark: A dramatic reduction of staining in embryos after preincubation of the antibody with an excess of KLP-18 fusion protein. Staining was also greatly reduced or eliminated in embryos subjected to RNAi depletion of KLP-18.
• Pattern: During later stages of embryogenesis, KLP-18 levels gradually diminished in somatic cells but increased in the primordial germ cells Z2 and Z3, presumably due to expression in the embryonic germ line. The germ line stained brightly for KLP-18 at all stages of larval development. Adult hermaphrodites contained high levels of cytoplasmic stain in the distal gonad arm. Adults also showed high levels of staining in the proximal gonad arm.
• Subcellular Localization: During the meiotic divisions that occur in the male germ line, anti-KLP-18 staining patterns were similar to those seen in female meiosis and mitosis. KLP-18 was concentrated at the spindle poles, which have centrosomes, and in the anaphase interzone. There was also a significant amount of KLP-18 staining on male meiotic chromosomes. Immunostaining showed KLP-18 colocalized with the disorganized MTs during prometaphase. As the MTs became ordered into a parallel bipolar array, KLP-18 concentrated most at the poles but was also present between the poles and chromosomes. The concentration at poles persisted during metaphase and early anaphase, but then shifted to the interzone between the separating chromosomes during late anaphase/telophase. Similar KLP-18 staining patterns were observed during meiosis II. KLP-18 staining was most concentrated in mitotic spindles toward the poles. During anaphase, KLP-18 staining also concentrated between the separating groups of chromosomes, with a dim zone at the spindle equator. After cytokinesis, KLP-18 accumulated somewhat around the nucleus and at the cortex near sites of cell-cell contact. Adult hermaphrodites contained high levels of cytoplasmic stain in the distal gonad arm.

• Primary Identifier: Expr2012961
• 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: Expr1144008
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2031193
• 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: Expr1010889
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

20 GO Annotation

4 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00002228
• Start: 7040211
• End: 7043694
• Strand: 1

20 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 3484

1 Sequence Ontology Term

• Name: gene

6 Strains

• WBStrain00036968
• WBStrain00049736
• WBStrain00049767
• WBStrain00049796
• WBStrain00049537
• WBStrain00007392

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIV_7039581..7040210
• Length (nt): 630
• Chromosome Location: IV: 7039581-7040210
• Organism: Caenorhabditis elegans