WormMine: Gene WBGene00006780

• WormBase Gene ID: WBGene00006780
• Gene Name: unc-44
• Sequence Name: B0350.2
• Organism: Caenorhabditis elegans
• Automated Description: Enables cell adhesion molecule binding activity. Involved in several processes, including axon guidance; establishment or maintenance of cytoskeleton polarity; and regulation of cellular component organization. Located in lateral plasma membrane. Expressed in hermaphrodite gonad; hypodermis; intestinal cell; and vulval cell. Human ortholog(s) of this gene implicated in several diseases, including ankyrin-B-related cardiac arrhythmia; autosomal recessive intellectual developmental disorder 37; and heart conduction disease (multiple). Is an ortholog of human ANK2 (ankyrin 2) and ANK3 (ankyrin 3).
• Biotype: SO:0001217
• Genetic Position: IV :2.88585±
• Length (nt): 29301

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00006780

Genomics

9 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:B0350.2c.1	B0350.2c.1	5844	IV: 5975557-5987485
Transcript:B0350.2e.1	B0350.2e.1	5754	IV: 5975560-5987476
Transcript:B0350.2h.1	B0350.2h.1	5648	IV: 5975571-5985376
Transcript:B0350.2f.1	B0350.2f.1	21716	IV: 5975576-6004857
Transcript:B0350.2j.1	B0350.2j.1	2949	IV: 5980012-5985181
Transcript:B0350.2i.1	B0350.2i.1	3105	IV: 5980012-5987264
Transcript:B0350.2b.1	B0350.2b.1	2918	IV: 5981133-5985381
Transcript:B0350.2d.1	B0350.2d.1	2388	IV: 5982475-5985181
Transcript:B0350.2a.1	B0350.2a.1	1173	IV: 5985585-5987481

Other

9 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:B0350.2c	B0350.2c	5604	IV: 5975576-5975866
CDS:B0350.2j	B0350.2j	2949	IV: 5980012-5980161
CDS:B0350.2i	B0350.2i	3105	IV: 5980012-5980161
CDS:B0350.2b	B0350.2b	2718	IV: 5981133-5981422
CDS:B0350.2a	B0350.2a	954	IV: 5985587-5986355
CDS:B0350.2d	B0350.2d	2388	IV: 5982475-5982567
CDS:B0350.2e	B0350.2e	5526	IV: 5975576-5975866
CDS:B0350.2f	B0350.2f	20985	IV: 5975576-5975866
CDS:B0350.2h	B0350.2h	5448	IV: 5975576-5975866

17 RNAi Result

• WBRNAi00024387
• WBRNAi00024388
• WBRNAi00027144
• WBRNAi00089724
• WBRNAi00000577
• WBRNAi00038963
• WBRNAi00038964
• WBRNAi00080497
• WBRNAi00008300
• WBRNAi00009722
• WBRNAi00084965
• WBRNAi00028102
• WBRNAi00086090
• WBRNAi00086119
• WBRNAi00090000
• WBRNAi00090159
• WBRNAi00090318

348 Allele

• otn10001
• gk964500
• gk963722
• gk963417
• gk963375
• gk963416
• gk964474
• gk964495
• gk964496
• gk964473
• q331
• rf1042
• rh86
• gk202868
• WBVar01727775
• rh1013
• rh1042
• gk202873
• otn11281
• gk202889
• gk202890
• h5565
• gk569428
• gk589997
• gk569429
• tm11129
• st200
• tm349
• gk567780
• gk202878

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00006780
• Start: 5975557
• End: 6004857
• 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_6004858..6004999
• Length (nt): 142
• Chromosome Location: IV: 6004858-6004999
• Organism: Caenorhabditis elegans

276 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 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
	TGF- Dauer pathway adult transcriptional targets. Results obtained by comparing the microarray results of the dauer-constitutive mutants daf-7(e1372), daf-7(m62), and daf-1(m40) with dauer-defective mutants daf-3(mgDf90), daf-5(e1386), and daf-7(e1372);daf-3(mgDf90) double mutants at the permissive temperature, 20C, on the first day of adulthood.	SAM	WBPaper00031040:TGF-beta_adult_upregulated
	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 glp-1(e2141); TU3401 animals comparing to in TU3401 animals.	Fold change > 2, FDR < 0.01.	WBPaper00065993:glp-1(e2141)_upregulated
	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 body muscle, according to PAT-Seq analysis using Pmyo-3-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:body-muscle_expressed
	Transcripts that showed significantly decreased expression at 5-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites.	DESeq2, fold change > 2, FDR < 0.05	WBPaper00065835:Day5_vs_Day1_downregulated
	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 up regulated in alg-1(gk214) comparing to in N2.	Differential expression was assessed using an empirical Bayes statistics using the eBayes function.	WBPaper00040823:alg-1(gk214)_upregulated
	Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:pharynx_expressed
	Genes with expression level regulated by genotype (N2 vs CB4856) and age at L3 larva and Late reproduction stage (96 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_developing
	Transcripts expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
	Genes with expression level regulated by genotype (N2 vs CB4856) at L3 larva and Late reproduction stage (96 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_regulated_developing
	Transcripts expressed in vulva.	FPKM >= 1.	WBPaper00064122:vulva_transcriptome
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
	Transcripts that showed significantly increased expression after four-day-old young adult worms were placed on NGM plates seeded with OP50 in the presence 5% Agaro-oligosaccharides(AGO) for 24 h, comparing to animals grown in the absence of AGO.	Fold change > 2.	WBPaper00064306:Agaro-oligosaccharides_upregulated
	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 increased expression in mrg-1(qa6200) comparing to in control animals in primordial germ cells (PGCs) at L1 larva stage.	DESeq2(v1.32.0), FDR < 0.05.	WBPaper00064315:mrg-1(qa6200)_upregulated_PGCs
	Transcripts that showed significantly increased expression in aak-1(tm1944);aak-2(ok524) animals comparing to in N2.	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:aak-1(tm1944);aak-2(ok524)_upregulated
	Transcripts that showed significantly decreased expression in N2 animals exposed to 0.1mM Paraquat from hatching to reaching adult stage.	DESeq2 version 1.22.2, p < 0.05	WBPaper00064716:paraquat_downregulated
	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

11 Expression Patterns

• Primary Identifier: Expr5058
• Remark: Strain: BC14133
• Reporter Gene: [unc-44::gfp] transcriptional fusion. PCR products were amplified using primer A: 5' [CGCTGAGCGGAAATCTGT] 3' and primer B 5' [TCGTTCGAGATGGTCGGT] 3'.
• Pattern: Adult Expression: intestine; anal depressor muscle; body wall muscle; Nervous System; nerve ring; ventral nerve cord; head neurons; pharyngeal neurons; tail neurons; Larval Expression: intestine; anal depressor muscle; body wall muscle; Nervous System; nerve ring; ventral nerve cord; head neurons; pharyngeal neurons; tail neurons

• Primary Identifier: Expr13240
• Pattern: In adults the pattern of UNC-44C::GFP(ju1413) fluorescence was generally consistent with that described for UNC-44 common isoforms by immunostaining (Otsuka et al., 2002); however we also observed strong expression in muscles and in gonadal spermathecal/sheath cells. UNC-44C::GFP(ju1413) expression was detected from early embryos to late larvae. Immediately before the bean stage of embryogenesis, UNC- 44C::GFP proteins were expressed in epidermal cells, within which they localized to the cell periphery. At postnatal L1 stage, UNC-44C::GFP was evident at the peripheries of epidermal seam cells and gut cells. In late larvae and adults, UNC-44C::GFP was seen in cells undergoing morphogenesis or fusion, such as vulval and seam cells.

• Primary Identifier: Expr15035
• Pattern: Although expression is mainly neuronal, low levels are also present in the hypodermal seam cells.
• Subcellular Localization: UNC-44::GFP mainly localizes to axons and dendrites and its expression pattern is nearly indistinguishable from the UNC-119::GFP knock-in. We observed that UNC-44::GFP clearly localizes to the cortex.

• Primary Identifier: Expr2036013
• 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: Expr1032852
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr13241
• Pattern: In contrast to UNC-44C::GFP, we did not detect expression of UNC-44L::GFP(ju1412) before the bean stage of embryogenesis. By the 1.5-fold stage of embryogenesis, we observed expression of UNC-44L::GFP mainly in the developing nervous system. UNC-44L::GFP became progressively more concentrated in the nervous system, predominantly localizing to neuronal processes and to the peripheries of neuronal cell bodies. UNC-44L has been previously thought to be exclusively neuronal, based on immunostaining experiments. However, we observed faint expression of UNC-44L::GFP in epidermal seam cells at the L4 stage, and in the gonadal anchor cell at L3 stage, as well as in neighboring vulval cells at L4. Thus the regulation of UNC-44L is temporally and spatially distinct from the more widely expressed UNC-44 isoforms, and is predominantly but not exclusively confined to neurons.

• Primary Identifier: Expr12913
• Pattern: UNC-44(L) is present in the nerve ring and neuronal processes.

• Primary Identifier: Expr1143138
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1010989
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2017877
• 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: Chronogram1815
• Remark: Original chronogram file: chronogram.726.xml
• Reporter Gene: [B0350.2:gfp] transcriptional fusion.

17 GO Annotation

13 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00006780
• Start: 5975557
• End: 6004857
• Strand: 1

17 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 29301

1 Sequence Ontology Term