WormMine: Gene WBGene00002081

• WormBase Gene ID: WBGene00002081
• Gene Name: ina-1
• Sequence Name: F54G8.3
• Brief Description: ina-1 encodes one of two C. elegans alpha integrin subunits; during development, ina-1 activity is required for migration of a number of cell types, including neurons, coelomocyte precursors, and the distal tip cells of the somatic gonad; in addition, ina-1 is required for axon fasciculation and morphogenesis of structures such as the head, pharynx, egg-laying apparatus, and male tail; INA-1 coimmunoprecipitates with the PAT-3 beta integrin subunit suggesting that, in vivo, INA-1 and PAT-3 function as a heterodimer to regulate cell migration and tissue morphogenesis; INA-1 is expressed in many tissues, including neurons, the gonad, and the pharyngeal basement membrane; expression begins during gastrulation and continues through to adulthood.
• Organism: Caenorhabditis elegans
• Automated Description: Enables transmembrane signaling receptor activity. Involved in several processes, including anatomical structure morphogenesis; cell-cell adhesion mediated by integrin; and generation of neurons. Located in phagocytic cup. Part of integrin complex. Expressed in several structures, including distal tip cell; hermaphrodite gonad; neurons; ventral nerve cord; and vulE. Used to study cancer and epilepsy. Human ortholog(s) of this gene implicated in Duchenne muscular dystrophy; congenital muscular dystrophy due to integrin alpha-7 deficiency; and junctional epidermolysis bullosa with pyloric atresia. Is an ortholog of human ITGA6 (integrin subunit alpha 6).
• Biotype: SO:0001217
• Genetic Position: III :0.28181 ±0.007054
• Length (nt): 4730

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00002081

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F54G8.3.1	F54G8.3.1	3773	III: 9168073-9172802

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F54G8.3	F54G8.3	3420	III: 9168361-9168548

55 RNAi Result

• WBRNAi00089829
• WBRNAi00048388
• WBRNAi00048389
• WBRNAi00048390
• WBRNAi00025641
• WBRNAi00083946
• WBRNAi00032823
• WBRNAi00071703
• WBRNAi00006163
• WBRNAi00006991
• WBRNAi00097218
• WBRNAi00097358
• WBRNAi00097373
• WBRNAi00071344
• WBRNAi00008861
• WBRNAi00075648
• WBRNAi00065727
• WBRNAi00075649
• WBRNAi00092228
• WBRNAi00097800
• WBRNAi00097814
• WBRNAi00097794
• WBRNAi00097797
• WBRNAi00097799
• WBRNAi00097798
• WBRNAi00090424
• WBRNAi00097801
• WBRNAi00097803
• WBRNAi00097802
• WBRNAi00097805

62 Allele

• gk964518
• gk963887
• WBVar00070313
• gk866799
• gk445855
• gk369456
• gk721456
• gk700018
• gk360632
• gk751369
• gk604943
• gk563513
• gk318720
• gk862620
• gk574994
• gk369114
• gk640412
• gk667694
• gk782365
• gk661800
• gk579430
• gk431930
• gk524664
• gk696257
• gk784673
• gk898678
• gk886273
• gk480922
• gk695430
• gk390216

1 Chromosome

• WormBase ID: III
• Organism: Caenorhabditis elegans
• Length (nt): 13783801

1 Chromosome Location

• Feature . Primary Identifier: WBGene00002081
• Start: 9168073
• End: 9172802
• Strand: -1

4 Data Sets

• WormBaseAcedbConverter
• GO Annotation data set
• C. elegans genomic annotations (GFF3 Gene)
• Panther orthologue and paralogue predictions

0 Downstream Intergenic Region

162 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	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
	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:all-neurons_L1-larva_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
Bacteria infection: Enterococcus faecalis	Genes with increased expression after 24 hours of infection by E.faecalis Fold changes shown are pathogen vs OP50.	For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated.	WBPaper00038438:E.faecalis_24hr_upregulated_TilingArray
	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 that showed significantly higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc).	DESeq2, fold change >= 2, FDR <= 0.01.	WBPaper00056826:SGP_biased
	Proteins interacting with NHR-49-GFP according to co-IP and LC-MS.	N.A.	WBPaper00064071:NHR-49_interacting
	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 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
	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
	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 that showed significantly increased expression in hrde-1(tm1200) animals, comparing to in N2, after growing at 25C for five generations (late generation).	CuffDiff2	WBPaper00051265:F4_hrde-1(tm1200)_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 xrep-4(lax137).	DESeq2. Genes were selected if their p value < 0.01.	WBPaper00066062:xrep-4(lax137)_upregulated
	Genes that showed expression levels higher than the corresponding reference sample (L2 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:A-class-motor-neurons_L2-larva_expressed
	Genes that showed expression levels higher than the corresponding reference sample (L2 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:all-neurons_L2-larva_expressed
	Proteins that showed significantly decreased expression after 1-day-old wild type adults were exposed to cisplatin (300ug per mL) for 6 hours.	The differential expression analysis was performed in R. Differentially expressed proteins were identified by using a two-sided t-test on log-transformed data.	WBPaper00065373:Cisplatin_downregulated_WT
	Genes that showed expression levels higher than the corresponding reference sample (L2 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:excretory-cell_L2-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
	Genes that showed expression levels higher than the corresponding reference sample (L2 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:intestine_L2-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:PVD-OLL-neurons_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
	Transcripts that showed significantly altered expression in rnp-6(dh1127) animals comparing to in N2 when fed with live S. aureus.	Differentially expressed genes (DEGs) (q-value <0.05) between different samples were identified using the stringtie version 1.3.0, followed by Cufflinks version 2.2.	WBPaper00059824:rnp-6(dh1127)_regulated_S.aureus
	Transcripts detected in germline isolated from day-1 adult hermaphrodite animals.	All three experiments have CPM >= 1.	WBPaper00067147:germline_expressed
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)
	Genes that were not enriched in either spermatogenic fem-3(q96gf) nor oogenic fog-2(q71) gonads, according to RNAseq analysis.	To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq.	WBPaper00045521:Gender_Neutral
	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

18 Expression Patterns

• Primary Identifier: Expr4892
• Remark: Picture: Figure 4A, B, D.
• Pattern: INA-1::GFP was present in the DTCs at the L2 stage prior to migration and maintained throughout L4. In wild-type N2 adults, INA-1::GFP was down-regulated with the cessation of migration (2% GFP-positive, n = 49).

• Primary Identifier: Expr1031234
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1998
• Remark: Ubiquitous
• Pattern: Embryonic GFP expression was identical to that seen with anti-INA-1 antisera: ubiquitous expression beginning at gastrulation, with more pronounced expression in the developing pharynx. Because all cells of the embryo expressed moderate levels of GFP during the migrations of the CAN, ALM, and HSN neurons, it is unable to detect any changes in the levels or localization of GFP in these neurons during their migrations. In L1 larvae, however, most cells no longer expressed GFP, making expression of the GFP reporter in the migratory Q neuroblasts and their descendants quite distinct. In L1 larvae, these cells turned on GFP as they began their migrations, and then turned it off when the migrations were completed. In older larvae, some of the Q-derived neurons turned GFP back on. Other migrating cells in larvae also expressed GFP, notably the distal tip cells of the hermaphrodite gonad and the P cells. Cells in organs undergoing morphogenesis, such as the hermaphrodite uterus and vulva and the male tail, also expressed high levels of GFP. Finally, the GFP reporter was also expressed in many nonmigratory neurons, including neurons in the head, tail, and ventral nerve cord, at various times during larval and adult stages.

• Primary Identifier: Expr8767
• Remark: Picture: Fig S2B.
• Pattern: Overexpression of a full-length integrin subunit INA-1::GFP transgene also resulted in intracellular accumulation in the AC and neighboring somatic gonad and vulval cells.

• Primary Identifier: Expr16238
• Pattern: We observed low levels of Pina-1::GFP expression in GABAergic motor neurons of both L1 and L4 animals. At the L1 stage, where only DD GABAergic neurons are present, we noted dim fluorescence in DD cell bodies that was obscured by comparatively high levels of Pina-1::GFP epidermal expression. At the L4 stage, somatic fluorescence in GABAergic motor neurons remained dim, but was more clearly discernible in comparison with L1, likely due to decreased Pina-1::GFP expression in the epidermis of L4 stage animals. We noted consistent low levels of expression across both VD and DD GABAergic neurons. We also noted stronger labeling of additional ventral cord motor neurons that were not labeled by the Punc-47::mCherry reporter, suggesting expression of ina-1 in other motor neuron classes. To address this possibility, we generated a transgenic strain co-expressing the Pina-1::GFP reporter with the cholinergic marker Pacr-2::mCherry. Overall, we noted that Pina-1::GFP fluorescence was stronger in cholinergic motor neurons compared with GABAergic motor neurons, and was expressed in only a subset of cholinergic motor neurons at both L1 and L4 stages. At the L4 stage, Pina-1::GFP fluorescence was most consistently observed labeling the B-class cholinergic motor neurons.

• Primary Identifier: Expr9010
• Remark: Picture: Fig 2A.
• Subcellular Localization: The INA-1::GFP protein was localized to the cell surface of the ABplaapppp cell. When the engulfment process was initiated, INA-1::GFP accumulated at the contact site with C3, even before C3 displayed a characteristic apoptotic morphology under DIC optics.

• Primary Identifier: Expr9009
• Remark: Picture: Figure S2; Table 3.
• Subcellular Localization: INA-1::GFP was localized to the plasma membrane in many cells, including apoptotic cells and their neighboring engulfing cells, and rescued the Ina-1 engulfment defect.

• Primary Identifier: Expr16239
• Pattern: To investigate the subcellular localization of α integrin/INA-1, we expressed a rescuing fluorescently tagged INA-1 (Pina-1::INA-1::GFP) together with transcriptional reporters labeling either GABAergic or cholinergic motor neurons (Punc-47::mCherry or Pacr-2::mCherry, respectively). Similar to previous studies, we noted that INA-1::GFP is present in many tissues in both L1 and L4 stage animals, in particular in neurons of the head, tail, and ventral nerve cord. We found that INA-1 is expressed at low levels in DD GABAergic motor neuron somas of L1 stage animals, and INA-1::GFP fluorescence was occasionally visible within GABAergic DD commissures. At the L4 stage, we also noted low levels of INA-1::GFP expression in GABAergic neuronal cell bodies, consistent with our above expression analysis. Notably, we also observed clear INA-1::GFP fluorescence in neurites that overlapped with Punc-47::mCherry expression, indicating significant levels of integrin in GABAergic processes. As noted above for the Pina-1::GFP transcriptional reporter, we found that INA-1::GFP fluorescence in the ventral nerve cord is not limited to GABAergic motor neurons. To define the identities of these additional neurons with α integrin/INA-1 expression, we examined co-expression of INA-1::GFP with the Pacr-2::mCherry cholinergic marker. At the L1 stage, we found that INA-1::GFP is localized to a subset of cholinergic motor neurons. In contrast, by the L4 stage, INA-1::GFP is present in virtually all cholinergic motor neurons. As noted for the Pina-1::GFP transcriptional reporter, average INA-1::GFP fluorescence intensity in cholinergic cell bodies was brighter in comparison to GABAergic cell bodies but is somewhat variable across cholinergic motor neurons, perhaps pointing to cell-type-specific regulation of integrin. Notably however, neurites labeled by the cholinergic marker showed less robust INA-1::GFP fluorescence compared with GABAergic processes, suggesting less efficient distribution of integrin to the processes of cholinergic neurons.

• Primary Identifier: Expr12292
• Remark: To cite this work: Ghosh, Srimoyee; Inoue, Takao; Sternberg, Paul (2015): ina-1::gfp expression. WormBase. Dataset. DOI: http://dx.doi.org/10.17912/W2159J . Reviewed by Bhagwati Gupta. Funding: National Institutes of Health USPHS training grant GM07616.
• Pattern: ina-1 is expressed throughout uterine toroids. At mid L4, expression is seen in uterine toroid 1 and 4 (ut1, ut4) and in the anterior uterine toroids 2 and 3 (ut2, ut3). In addition, ina-1::GFP is detected in the spermathecal-uterine junction and spermatheca. At the L4 lethargus stage, bright expression is observed in uterine toroids 1 and 4, the spermathecal-uterine junction, and spermatheca. Dimmer expression is present in uterine toroid 2 and posterior toroid 3. Fluorescence is also detected in vulE.

• Primary Identifier: Expr1021632
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1152181
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr12349
• Pattern: A 400 bp region of the ina-1 promoter is sufficient for DTC expression of ina-1.

• Primary Identifier: Expr2012740
• 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: Expr1467
• Remark: Antisera from both mice and rabbits gave the same staining pattern.
• Pattern: Embryos began to stain with anti-INA-1 antisera during gastrulation, with all cells expressing low levels of INA-1. In older, comma-stage embryos, there was an increased level of INA-1 in the basement membrane of the developing pharynx. Pharyngeal staining persisted in older embryos and larvae.

• Primary Identifier: Expr2030977
• 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: Expr1170037
• Pattern: Time-lapse fluorescence microscopy was performed, including DIC for morphology. Gene expression patterns were summarized in 4 manners: Average over time, Average over time and at different positions along the anterior-posterior (AP) axis, a voxelized representation over time, and on individual cells overlaid from a reference coordinate dataset (https://doi.org/10.1016/j.ydbio.2009.06.014). The analysis was done with a pipeline based on the multi-purpose image analysis software Endrov (https://doi.org/10.1038/nmeth.2478), which further is needed to browse the raw recording data. Thumbnail movies were also generated, using maximum Z projection for the 3D fluorescence channel. Raw recordings available in the Endrov OST-file format are available at https://www.ebi.ac.uk/biostudies/studies/S-BIAD191?query=S-BIAD191

• Primary Identifier: Expr14842
• Subcellular Localization: Endogenously tagged INA-1:: mNG, PAT-2::2XmNG, and PAT-3::mNG were expressed in the gonad and pharyngeal cells and localized to the cell-BM interface.

• Primary Identifier: Expr13137
• Subcellular Localization: In the absence of axon injury, INA-1::GFP was distributed uniformly throughout D-type motor axons.

35 GO Annotation

15 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00002081
• Start: 9168073
• End: 9172802
• Strand: -1

35 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 4730

1 Sequence Ontology Term

• Name: gene

6 Strains

• WBStrain00022227
• WBStrain00028732
• WBStrain00028742
• WBStrain00028746
• WBStrain00047388
• WBStrain00050783

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrIII_9172803..9175076
• Length (nt): 2274
• Chromosome Location: III: 9172803-9175076
• Organism: Caenorhabditis elegans