WormMine: Gene WBGene00003830

• WormBase Gene ID: WBGene00003830
• Gene Name: num-1
• Sequence Name: T03D8.1
• Brief Description: num-1 encodes two isoforms of an ortholog of Drosophila NUMB that inhibits endocytotic recycling and antagonizes RME-1 in vivo; NUM-1 is required for recycling (but not internalization) of a transmembrane endocytosis marker; num-1(bc365) null mutants, while mostly normal, no longer require RME-1 in endocytotic recycling; NUM-1A is localized to the basolateral surfaces of most polarized epithelial cells, such as those in hypodermis and intestine; NUM-1A and -1C isoforms are expressed in many somatic cells in all stages of development, with notable expression in the embryonic intestinal primordium and differentiating epithelia, and (later, through larval to adult stages) in intestine, pharynx, hypodermis, seam cells, coelomocytes, spermatheca, uterus, and head neurons; NUM-1A and -1C are expressed in nuclei, cytoplasmic granules, and cell membranes, being notably concentrated at cell peripheries at lateral cell-cell junctions in early embryos; NUM-1A and -1C are localized to the cell periphery by highly basic N-terminal domains with predicted phosphorylation sites; NUM-1A and -1C isoforms bind PKC-3 via their PTB domains in two-hybrid assays, and may serve as PKC-3 adaptors in vivo; in addition, the NUM-1A PTB also binds the TAT-1C translocase.
• Organism: Caenorhabditis elegans
• Automated Description: Enables enzyme binding activity and protein domain specific binding activity. Involved in endocytic recycling; phospholipid transport; and protein targeting to membrane. Located in basolateral plasma membrane and cytoplasm. Expressed in several structures, including alimentary muscle; hermaphrodite gonad; nerve ring; pseudocoelom; and rectal valve cell. Is an ortholog of human NUMB (NUMB endocytic adaptor protein) and NUMBL (NUMB like endocytic adaptor protein).
• Biotype: SO:0001217
• Genetic Position: V :25.3151 ±0.008479
• Length (nt): 7809

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003830

Genomics

5 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T03D8.1d.1	T03D8.1d.1	2049	V: 20829811-20837224
Transcript:T03D8.1a.1	T03D8.1a.1	2177	V: 20832379-20837619
Transcript:T03D8.1c.1	T03D8.1c.1	1650	V: 20832511-20837224
Transcript:T03D8.1b.1	T03D8.1b.1	3158	V: 20833087-20837595
Transcript:T03D8.1e.1	T03D8.1e.1	1608	V: 20833112-20837224

Other

5 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T03D8.1d	T03D8.1d	2049	V: 20829811-20829979
CDS:T03D8.1a	T03D8.1a	1782	V: 20832379-20832533
CDS:T03D8.1c	T03D8.1c	1650	V: 20832511-20832533
CDS:T03D8.1b	T03D8.1b	1206	V: 20835615-20836148
CDS:T03D8.1e	T03D8.1e	1608	V: 20833112-20833189

5 RNAi Result

• WBRNAi00052262
• WBRNAi00018067
• WBRNAi00098490
• WBRNAi00114329
• WBRNAi00035081

136 Allele

• gk963271
• gk964176
• gk963489
• gk963304
• gk963809
• WBVar01756820
• WBVar01756821
• WBVar01756822
• WBVar01756823
• WBVar01756824
• WBVar01756825
• WBVar01756826
• WBVar01756827
• WBVar01756828
• WBVar01756829
• WBVar01756831
• WBVar01756832
• WBVar01756833
• WBVar01756834
• WBVar01756835
• WBVar00073961
• WBVar00073960
• WBVar00073965
• WBVar00073964
• WBVar00073963
• WBVar00073962
• WBVar00073969
• WBVar00073968
• WBVar00073967
• WBVar00073966

1 Chromosome

• WormBase ID: V
• Organism: Caenorhabditis elegans
• Length (nt): 20924180

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003830
• Start: 20829811
• End: 20837619
• 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_chrV_20837620..20838079
• Length (nt): 460
• Chromosome Location: V: 20837620-20838079
• Organism: Caenorhabditis elegans

112 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 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
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
	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
	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
	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
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
	Significantly upregulated genes from clk-1(qm30) microarrays using SAM algorithm with an FDR < 0.1 from adult-only chips.	SAM algorithm with an FDR < 0.1.	WBPaper00033065:clk-1(qm30)_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 that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_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
	Transcripts that were regulated by both set-6(ok2195) and baz-2(tm0235) at 2-day post L4 adult hermaphrodite stage.	N.A.	WBPaper00059356:set-6(ok2195)_baz-2(tm0235)_regulated
	Genes that showed expression levels higher than the corresponding reference sample (L3/L4 all cell 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:dopaminergic-neurons_L3-L4-larva_expressed
	Genes that showed expression levels higher than the corresponding reference sample (L3/L4 all cell 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:hypodermis_L3-L4-larva_expressed
	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
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 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

10 Expression Patterns

• Primary Identifier: Expr1031805
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr8115
• Remark: Picture: Figure 1, and S1.
• Pattern: The expression pattern seen was the same in all eight lines. Strong expression of GFP was first detected in the embryo at the E16 stage in the intestine primordium. In later stage embryos, expression was also seen in other epithelial tissues. In larval worms, and throughout the adult stage, expression was seen in the intestine, pharynx, hypodermis, seam cells, spermatheca, and uterus. During postembryonic development, several nonepithelial cells also expressed the transgene, including many neurons in the nerve ring and coelomocytes, scavenger cells situated in the pseudocoelom. Within the nervous system, expression was not uniform but higher in a subset of neurons.
• Subcellular Localization: At the subcellular level, in most cells the protein accumulated in punctate structures within the cytoplasm. Some protein was present very close to the plasma membrane and may be associated with it. In polarized epithelia, expression of the protein was predominantly on the baso-lateral parts of the cell and was largely absent from the apical cell membrane or the apical cytoplasm. In the intestine, seam cells, ventral hypodermis, pharynx, and other polarized epithelial cells, the most apical boundary of expression coincided with the adherens junctions that separate baso-lateral and apical cell membranes. Localization of the GFP fusion protein close to the junctions in the intestine and seam cells was observed.

• Primary Identifier: Expr845
• Remark: T03D8.1 = cka-1 --WS59.
• Pattern: Robust GFP fluorescence was observed in cells comprising the intestine. CKA1 promoter activity was also evident in pharyngeal cells and the anal sphincter and depressor muscles. Robust CKA1 promoter activity was evident in both the large nuclei of (~10) intestinal (gut) cells and smaller nuclei located in anal depressor and sphincter muscle cells and cells of the intestinal-rectal valve. A modest level of CKA1 gene transcription was detected in pharyngeal muscle nuclei. Similar patterns of CKA1 gene transcription were obtained for both adults and larvae in several experiments.

• Primary Identifier: Expr846
• Remark: proliferating embryo (curator) = early embryo (author)
• Pattern: Immunofluorescence microscopy disclosed that CKA1 isoforms concentrate at the cell periphery in early embryos. Fluorescence signals that correspond to CKA1/CKA1S IgG complexes are enriched along segments of the cell periphery that are involved in cell-cell junctions.
• Subcellular Localization: Concentrated at the cell periphery.

• Primary Identifier: Expr2010
• Remark: Other strains-- UL914, UL924
• Pattern: Expression is seen in all somatic cells from early embryonic stages until adulthood. Expression is generally nuclear localised but is also membrane associated, particularly in the intestine where individual cells are clearly delineated. This gene has similarity to the Drosophila gene numb.
• Subcellular Localization: Expression is generally nuclear localised but is also membrane associated.

• Primary Identifier: Expr1155893
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr844
• Remark: T03D8.1 in this article is called cka-1.
• Pattern: IgGs directed against CKA1/CKA1S complexed both adapter protein isoforms in samples of total C. elegans proteins. CKA1 and CKA1S are expressed in vivo at each stage of C. elegans development.

• Primary Identifier: Expr1027478
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2032765
• 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: Expr2014526
• 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).

20 GO Annotation

1 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003830
• Start: 20829811
• End: 20837619
• Strand: 1

20 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 7809

1 Sequence Ontology Term