WormMine: Gene WBGene00006839

• WormBase Gene ID: WBGene00006839
• Gene Name: unc-115
• Sequence Name: F09B9.2
• Brief Description: unc-115 encodes a protein that binds actin filaments and that is required for RAS signalling and UNC-40/netrin activity during axon pathfinding.
• Organism: Caenorhabditis elegans
• Automated Description: Enables actin filament binding activity. Involved in neuron projection morphogenesis; regulation of filopodium assembly; and regulation of lamellipodium assembly. Located in basal plasma membrane and cytoplasm. Expressed in several structures, including PDE; excretory cell; pharynx; somatic nervous system; and vulva. Is an ortholog of human ABLIM2 (actin binding LIM protein family member 2).
• Biotype: SO:0001217
• Genetic Position: X :1.86244 ±0.006291
• Length (nt): 6251

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00006839

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F09B9.2a.1	F09B9.2a.1	3002	X: 10146892-10153142
Transcript:F09B9.2b.1	F09B9.2b.1	1920	X: 10147492-10152116

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F09B9.2b	F09B9.2b	1920	X: 10147492-10147630
CDS:F09B9.2a	F09B9.2a	1878	X: 10146990-10146993

17 RNAi Result

• WBRNAi00089800
• WBRNAi00001237
• WBRNAi00001945
• WBRNAi00044080
• WBRNAi00025039
• WBRNAi00027261
• WBRNAi00012950
• WBRNAi00084964
• WBRNAi00027790
• WBRNAi00060119
• WBRNAi00060121
• WBRNAi00060118
• WBRNAi00060120
• WBRNAi00086122
• WBRNAi00090010
• WBRNAi00090169
• WBRNAi00090328

111 Allele

• WBVar01928050
• gk964260
• gk962707
• WBVar01759026
• WBVar01759025
• WBVar01759028
• WBVar01759027
• WBVar00082195
• WBVar01551664
• WBVar02065873
• WBVar02065874
• h8227
• e2225
• WBVar01620203
• WBVar01620204
• WBVar01620205
• WBVar01620206
• WBVar01620207
• WBVar01620208
• WBVar01981208
• ky274
• WBVar02116623
• WBVar02001165
• WBVar00082196
• gk457887
• WBVar00062234
• gk565479
• WBVar01888410
• gk704289
• WBVar01888411

1 Chromosome

• WormBase ID: X
• Organism: Caenorhabditis elegans
• Length (nt): 17718942

1 Chromosome Location

• Feature . Primary Identifier: WBGene00006839
• Start: 10146892
• End: 10153142
• 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_chrX_10153143..10154816
• Length (nt): 1674
• Chromosome Location: X: 10153143-10154816
• Organism: Caenorhabditis elegans

190 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 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
	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
	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
	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:bodywall-muscle_L1-larva_expressed
	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
	Genes significantly enriched in NSM neurons (isolated by FACS) versus the reference, according to RNAseq analysis towards total RNA.	Gene expression quantification and differential expression was analyzed using cufflinks v2.2.1. Enriched contains only genes significantly enriched (differentially expressed >= 2.4 fold in total RNA or >= 3.2 fold in DSN treated total RNA) in the NSM neurons versus the reference.	WBPaper00045974:NSM_enriched_totalRNA_RNAseq
	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 that showed significantly decreased expression in atfs-1(cmh15) (null allele) animals comparing to in N2 animals at L4 larva stage.	edgeR, fold change > 2, FDR < 0.05	WBPaper00060909:atfs-1(cmh15)_downregulated
	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
	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
	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
Dietary restriction	Transcripts that showed significantly decreased expression after N2 animals were under dietary restriction (DR, OP50 OD = 0.1) from 3-day post L4 till 6-day post L4 adult hermaphrodite stage, comparing to under ad libtum (AL, OP50 OD = 3) condition.	Bioconductor package edgeR, p < 0.05.	WBPaper00056443:DietaryRestriction_downregulated
	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 increased expression in alg-1(gk214), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-1(gk214)_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
	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

11 Expression Patterns

• Primary Identifier: Expr2035975
• 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: Expr1396
• Pattern: The earliest detectable expression of UNC-115::GFP was in neurons and epidermis at about 300 min postfertilization, when the embryo begins to elongate, and axons begin to grow. UNC-115::GFP and the shorter fusion GFPS was expressed in most or all neurons throughout development. UNC-115::GFP expression was also observed in non neuronal cells, including the epidermal syncytium hyp7, the head and tail epidermal cells, the excretory canal cell, the pharynx, and the developing vulva, but not in the lateral epidermal seam cells or the ventral epidermal P cells. The earliest detectable expression of UNC-115::GFP was in neurons and epidermis at about 300 min postfertilization, when the embryo begins to elongate, and axons begin to grow. UNC-115::GFP and the shorter fusion GFPS was expressed in most or all neurons throughout development. UNC-115::GFP expression was also observed in nonneuronal cells, including the epidermal syncytium hyp7, the head and tail epidermal cells, the excretory canal cell, the pharynx, and the developing vulva, but not in the lateral epidermal seam cells or the ventral epidermal P cells.
• Subcellular Localization: UNC-115::GFP protein was present uniformly in neuronal cell bodies and processes and was excluded from nuclei. The protein was also present at high levels in the growth cones of developing axons as they extended to their targets and in cell-cortex-associated plaques along the excretory canals as well as plaques at the junctions of epidermal cells.

• Primary Identifier: Expr1032898
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr814
• Remark: Both wild-type SAD-1 and this GFP fusion caused paralysis and other phenotypes when expressed at high concentrations, but at the lower concentrations examined in this experiment punc-115SAD-1::GFP did not cause locomotion defects.
• Pattern: SAD-1::GFP fluorescence was most prominent in the nerve ring and the ventral and dorsal cords, regions of the axon where the majority of synapses are made. Little or no staining was observed in the sensory dendrites or the axonal commissures, which are devoid of synapses. Weaker fluorescence was also visible in the neuronal cell bodies excluded from the nucleus.
• Subcellular Localization: Little or no staining was observed in the sensory dendrites or the axonal commissures, which are devoid of synapses. Weaker fluorescence was also visible in the neuronal cell bodies excluded from the nucleus. Fluorescence appeared as a combination of punctate and diffuse staining within the axon.

• Primary Identifier: Expr12404
• Pattern: The 1.5-kb unc-115 promoter used to construct the unc-115 mini- gene is expressed in the PDEs.
• Subcellular Localization: UNC-115::GFP was distributed uniformly in the cytoplasm of embryonic blastomeres.

• Primary Identifier: Chronogram699
• Remark: Original chronogram file: chronogram.1729.xml
• Reporter Gene: [F09B9.2:gfp] transcriptional fusion.

• Primary Identifier: Expr12403
• Subcellular Localization: UNC-115::GFP was distributed uniformly in the cytoplasm of embryonic blastomeres.

• Primary Identifier: Expr1022839
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2017839
• 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: Expr11604
• Subcellular Localization: AC-specific expression of GFP-tagged UNC-115 showed that UNC-115 was first localized to the basal invasive membrane, approximately 5 hours prior to invasion and its polarity increased throughout AC invasion.

• Primary Identifier: Expr1148046
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

16 GO Annotation

14 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00006839
• Start: 10146892
• End: 10153142
• Strand: 1

16 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 6251

1 Sequence Ontology Term