WormMine: Gene WBGene00014569

• WormBase Gene ID: WBGene00014569
• Gene Name: bkip-1
• Sequence Name: Y39G8C.3
• Brief Description: bkip-1 encodes a novel transmembrane protein conserved amongst nematodes; genetic studies indicate that BKIP-1 functions to regulate the activity of the SLO-1 Ca2+- and voltage-gated potassium channel; BKIP-1 and SLO-1 interact in vitro; a BKIP-1::GFP fusion protein is expressed in most neurons, body wall muscles cells, and the head mesodermal cell, and localizes to the nerve ring and the dense body.
• Organism: Caenorhabditis elegans
• Automated Description: Enables transmembrane transporter binding activity. Located in neuron projection and striated muscle dense body. Expressed in body wall musculature; head mesodermal cell; muscle cell; neurons; and somatic nervous system.
• Biotype: SO:0001217
• Genetic Position: II :22.4196 ±0.004206
• Length (nt): 1699

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00014569

Genomics

3 Transcripts

Class	WormMine ID	Sequence Name	Length (nt)	Chromosome Location
NcPrimaryTranscript	Transcript:Y39G8C.3c	Y39G8C.3c	327	II: 14101263-14102866
MRNA	Transcript:Y39G8C.3b.1	Y39G8C.3b.1	210	II: 14101263-14102664
MRNA	Transcript:Y39G8C.3a.1	Y39G8C.3a.1	314	II: 14102360-14102961

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y39G8C.3a	Y39G8C.3a	183	II: 14102396-14102437
CDS:Y39G8C.3b	Y39G8C.3b	210	II: 14101263-14101393

1 RNAi Result

• WBRNAi00020427

43 Allele

• gk963801
• gk963053
• gk962684
• gk756649
• gk718381
• gk901106
• gk450575
• gk871417
• gk377116
• gk799130
• gk632626
• gk551627
• gk468707
• gk418764
• WBVar01540105
• WBVar01606410
• WBVar01767379
• WBVar01721470
• WBVar01721469
• WBVar00106835
• WBVar00106836
• WBVar00106834
• WBVar00231938
• WBVar00231937
• zw10
• WBVar00231936
• WBVar01562838
• WBVar01562837
• WBVar00012878
• WBVar01252419

1 Chromosome

• WormBase ID: II
• Organism: Caenorhabditis elegans
• Length (nt): 15279421

1 Chromosome Location

• Feature . Primary Identifier: WBGene00014569
• Start: 14101263
• End: 14102961
• Strand: 1

3 Data Sets

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

1 Downstream Intergenic Region

• WormBase ID: intergenic_region_chrII_14102962..14104769
• Length (nt): 1808
• Chromosome Location: II: 14102962-14104769
• Organism: Caenorhabditis elegans

61 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
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
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
	Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology.	DESEQ2, fold change > 2 and FDR < 0.01.	WBPaper00062103:neuron_enriched
	Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin-Allantoin_upregulated
	Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rifampicin_upregulated
	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 that showed significantly increased expression in rrf-3(pk1426) comparing to in N2 at embryo stage.	DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01.	WBPaper00056169:rrf-3(pk1426)_upregulated_embryo
	Transcripts that showed significantly increased expression in sin-3(tm1276) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:sin-3(tm1276)_upregulated
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
	Transcripts that showed significantly decreased expression in sin-3(tm1276) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult.	DESeq2, fold change > 2, adjusted p-value < 0.01	WBPaper00058598:sin-3(tm1276)_downregulated
	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
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)
	Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(+), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_P-granule(-)GFP(+)_vs_control_day2-adult
	Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(-), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage.	DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2.	WBPaper00050859:upregulated_P-granule(-)GFP(-)_vs_control_day2-adult
	Transcripts of coding genes that showed significantly increased 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_enriched_coding-RNA
	Transcripts that showed significantly increased expression in spr-1(ok2144) comparing to in N2.	DESeq2, fold change > 2, p-value < 0.01.	WBPaper00061203:spr-1(ok2144)_upregulated
	Transcripts that showed significantly increased exression in animals exposed to 100uM cadmium for 24 hours.	DESeq2 v1.20.0, fold change > 2, FDR < 0.05.	WBPaper00065029:cadmium_upregulated
Bacteria infection: Pseudomonas aeruginosa PA14. 24 hours of exposure at 25C.	Transcripts that showed significantly decreased expression in N2 animals with 24 hours of exposure to P. aeruginosa PA14 for 24 hrs at 25C, comparing to N2 animals without exposure to PA14.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00058948:PA14_downregulated
	Transcripts that showed significantly decreased expression in whole animal day 1 N2 adults comparing to in whole animal day 8 N2 adults.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00066978:Day1Adult_vs_Day8Adult_downregulated_neuron
Bacteria: S.maltophilia	Transcriptions that showed signigicantly alted expression in animals treated with pathogenic S.maltophilia strains for 12 hours, comparing to animals treated with non-pathogenic	Transcripts were considered significantly differentially expressed between treatments if the fold change > 2 and the false discovery rate (FDR) - adjusted p-value < 0.05.	WBPaper00059839:S.maltophilia_regulated
	Transcripts that showed significantly lower expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc).	DESeq2, fold change >= 2, FDR <= 0.01.	WBPaper00056826:hmc_biased
	Transcripts that showed significantly increased expression in unc-30(ok613) animals at L4 larva stage, comparing to N2 animals.	Genes exhibiting at least two-fold change were considered differentially expressed.	WBPaper00061439:unc-30(ok613)_upregulated
	Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin_downregulated
	siRNAs that showed significantly lower expression (log2fold > 2, padj < 0.01) in hermaphrodite gonad (somatic gonad plus germine) than in male gonad (somatic gonad plus germine).	DESeq2 v1.13.8, fold change > 2, FDR < 0.01.	WBPaper00056161:male_enriched_siRNA
	Transcripts that showed significantly decreased expression in mter-4(syb3662 syb3403) comparing to in N2.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00061995:mter-4(syb3662syb3403)_downregulated
	Genes up-regulated after 24 hour exposure to colistin.	Gene lists were created using a cutoff P-value of < 0.05, 2-fold change.	WBPaper00045673:colistin_upregulated
	Transcripts that showed significantly increased expression in alg-1(gk204) comparing to in N2 at 5-days post L4 adult hermaphrodites.	DESeq, fold change > 2, adjusted p-value < 0.05.	WBPaper00054758:alg-1(gk204)_upregulated

4 Expression Patterns

• Primary Identifier: Expr2009627
• 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: Expr9177
• Pattern: Strong expression was observed in head neurons, nerve ring, ventral cord, tail neurons, body-wall muscle, head muscle, vulval muscle, anal depressor muscle, and stomatointestinal muscle. bkip-1 was also expressed in head mesodermal cell.
• Subcellular Localization: BKIP-1 was enriched in the nerve ring and in body-wall muscle dense bodies.

• Primary Identifier: Expr2027865
• 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: Expr1159776
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

4 GO Annotation

0 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00014569
• Start: 14101263
• End: 14102961
• Strand: 1

4 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 1699

1 Sequence Ontology Term

• Name: gene

1 Strains

• WBStrain00040907

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrII_14098645..14101262
• Length (nt): 2618
• Chromosome Location: II: 14098645-14101262
• Organism: Caenorhabditis elegans