WormMine: Gene WBGene00001980

• WormBase Gene ID: WBGene00001980
• Gene Name: hmr-1
• Sequence Name: W02B9.1
• Brief Description: hmr-1 encodes two isoforms of a classical cadherin that contain extracellular cadherin, EGF-like, and laminin G domains as well as a highly conserved intracellular domain that binds beta-catenin; by homology, the HMR-1 proteins are predicted to function as calcium-dependent, homophilic cell-cell adhesion receptors; in vivo, HMR-1A activity is required for mediating the cell migrations, cell shape changes, and presumably actin cytoskeleton rearrangements that occur during embryonic tissue and body morphogenesis; HMR-1B is required for fasciculation and outgrowth of a subset of motor neuron processes; HMR-1 antibodies detect expression in all embryonic blastomeres at early stages of development but as hypodermal adherens junctions form and morphogenesis begins, HMR-1 becomes highly expressed in the apical junctions of all hypodermal cells; later, HMR-1 is expressed primarily at the apical margins of hypodermal, pharyngeal, and intestinal cells in a pattern consistent with localization to adherens junctions; an HMR-1B reporter fusion is expressed in neurons, including the DD, VD, and AS class of motor neurons; HMR-1 activity is required for proper localization of other junctional components, such as HMP-1/alpha-catenin and HMP-2/beta-catenin, but not for localization of AJM-1, the junctional component recognized by the MH27 antibody.
• Organism: Caenorhabditis elegans
• Automated Description: Enables beta-catenin binding activity and delta-catenin binding activity. Involved in cytoskeleton organization; embryo development; and gastrulation. Located in adherens junction; distal dendrite; and plasma membrane. Part of catenin complex. Expressed in several structures, including germline precursor cell; hypodermis; motor neurons; nerve ring; and neuroblasts.
• Biotype: SO:0001217
• Genetic Position: I :6.60962 ±0.05706
• Length (nt): 58913

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001980

Genomics

5 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:W02B9.1a.2	W02B9.1a.2	4653	I: 11075755-11094526
Transcript:W02B9.1b.1	W02B9.1b.1	9485	I: 11075758-11134667
Transcript:W02B9.1a.1	W02B9.1a.1	4688	I: 11075761-11094526
Transcript:W02B9.1e.1	W02B9.1e.1	2805	I: 11076372-11084053
Transcript:W02B9.1d.1	W02B9.1d.1	3195	I: 11076372-11087832

Other

4 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:W02B9.1b	W02B9.1b	8763	I: 11076372-11076623
CDS:W02B9.1e	W02B9.1e	2805	I: 11076372-11076623
CDS:W02B9.1a	W02B9.1a	3810	I: 11076372-11076623
CDS:W02B9.1d	W02B9.1d	3195	I: 11076372-11076623

61 RNAi Result

• WBRNAi00114289
• WBRNAi00114054
• WBRNAi00114133
• WBRNAi00114212
• WBRNAi00077674
• WBRNAi00077369
• WBRNAi00077362
• WBRNAi00101406
• WBRNAi00093061
• WBRNAi00004369
• WBRNAi00075305
• WBRNAi00054576
• WBRNAi00054577
• WBRNAi00054578
• WBRNAi00078672
• WBRNAi00063122
• WBRNAi00026456
• WBRNAi00004701
• WBRNAi00004929
• WBRNAi00101425
• WBRNAi00071899
• WBRNAi00101422
• WBRNAi00101421
• WBRNAi00101424
• WBRNAi00101423
• WBRNAi00101418
• WBRNAi00101419
• WBRNAi00103824
• WBRNAi00071059
• WBRNAi00101420

936 Allele

• gk962858
• gk962706
• gk963849
• otn10719
• h4433
• h10052
• h3249
• h13380
• h12042
• h3964
• h3965
• h3966
• h3967
• h6931
• h6497
• h14117
• h7145
• gk963906
• otn12816
• otn11835
• otn11834
• WBVar02066409
• WBVar02066412
• WBVar02066413
• WBVar02066410
• WBVar02066411
• WBVar02066416
• WBVar02066417
• WBVar02066414
• WBVar02066415

1 Chromosome

• WormBase ID: I
• Organism: Caenorhabditis elegans
• Length (nt): 15072434

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001980
• Start: 11075755
• End: 11134667
• 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_chrI_11070013..11075754
• Length (nt): 5742
• Chromosome Location: I: 11070013-11075754
• Organism: Caenorhabditis elegans

175 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
	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
	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
	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:AVE-neuron_L1-larva_expressed
	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
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
	Genome-wide analysis of developmental and sex-regulated gene expression profile.	self-organizing map	cgc4489_group_18
	Coexpression clique No. 60, 176662_at-Y53F4B.16, on the genome-wide coexpression clique map for the nematode GPL200 platform.	All available microarray datasets for the GPL200 platform (Affymetrix C. elegans Genome Array) were obtained from the GEO repository. This included 2243 individual microarray experiments. These were normalized against each other with the software RMAexpress (Bolstad, 2014). Based on these normalized values, Pearsons correlation coefficients were obtained for each probe-probe pair of the 22,620 probes represented on this array type. The resulting list of correlation coefficients was then ranked to generate the ranked coexpression database with information on each probe represented on the GPL200 platform.	WBPaper00061527:176662_at-Y53F4B.16
	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 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
	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 that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_glp-1(e2141)
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
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
	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
Bacteria infection: Staphylococcus aureus MW2. 4 hours of exposure.	Transcripts that showed significantly increased expression after N2 animals had 4 hours of infection by Staphylococcus aureus (MW2).	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:S.aureus-4h_upregulated_N2
	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 differential expression between 24 and 26 hours post hatching L2d and dauer committed larvae of daf-9(dh6), triggered by the dafachronic acid (DA) growth hormone. Cluster 3 genes increased expression transiently at 26 hour post hatching.	Benjamini Hochberg corrected q-value < 0.01.	WBPaper00053388:dauer_regulated_Cluster3
	Transcripts enriched in PHso according to single cell RNAseq.	Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched.	WBPaper00061651:PHso_enriched
	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 detected in body muscle nuclei according to a nuclear FACS-based strategy.	Cufflinks	WBPaper00065120:body-muscle-transcriptome

17 Expression Patterns

• Primary Identifier: Expr1031150
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr13990
• Pattern: In the posterior pharyngeal bulb gfp::hum-7 is expressed throughout, including the pm6 and pm7 cells that help the grinder contract during feeding (Worm Atlas), while hmr-1::mKate2 is enriched only in apical regions, as expected. hmr-1::mKate2 is expressed all through the nerve ring axons, while gfp::hum-7 is expressed in adjacent cells, perhaps glia. Viewing this same strain on the surface shows that while hmr- 1::mKate2 is highly expressed in the seam cells, gfp::hum-7 shows no obvious overlap in the seam cells.

• Primary Identifier: Expr16123
• Subcellular Localization: We found that endogenously tagged HMR-1::GFP protein localized to the distal segment of the emerging AQR dendrite in wild-type larvae, similar to its localization pattern at the distal tips of dendrites in embryonic amphid sensory neurons (Fan et al., 2019). Like DYF-19 and GRDN-1, HMR-1::GFP remained associated with the distal dendritic segment, as the AQR dendrite extended anteriorly.

• Primary Identifier: Expr12332
• Pattern: A full-length hmr-1::gfp transgene driven by the endogenous promoter localizes to epidermal adherens junctions and was able to rescue hmr-1(zu389) homozygotes to viability.

• Primary Identifier: Expr1788
• Pattern: Expression was confined to the nervous system in all developmental stages, including the DD, VD, and AS class of motor neurons.

• Primary Identifier: Expr1435
• Remark: Independent expression patterns described together (hmp-2, hmr-1). No detailed description on cellular expression patterns.
• Subcellular Localization: HMP-2 and HMR-1 expression: the HMP-2 and HMR-1 antisera gave staining patterns very similar to HMP-1 at all stages of embryogenesis.

• Primary Identifier: Expr1158123
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr14676
• Subcellular Localization: A functional, endogenously GFP-tagged hmr-1 allele encoding HMR-1::GFP was expressed in the DTC and germ cells and was enriched at the sites of germ cell-germ cell and DTC-germ cell contact.

• Primary Identifier: Expr2030770
• 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: Expr2012531
• 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: Expr14681
• Subcellular Localization: HMR-1::GFP was enriched in the leading edges of muscle protrusions compared to the same muscle farther from the site of germ cell contact (an average of 1.6-fold brighter fluorescence at the leading edge; n = 10 animals; one-tailed Wilcoxon signed rank test is significant at p % 0.05).

• Primary Identifier: Expr15892
• Subcellular Localization: The CCC (HMP-2 and HMR-1) and SAX-7 localize to regions of cell-cell contact.

• Primary Identifier: Expr1011574
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr13048
• Subcellular Localization: HMR-1 localizes to adhesion junctions in epidermal cells as expected, but also strongly accumulates to neuroblast cell boundaries.

• Primary Identifier: Expr13693
• Pattern: At the four-cell stage, HMR-1 accumulation was asymmetric as there was less HMR-1::GFP intensity at the EMS-P2 contact in HMR-1::GFP-expressing embryos.

• Primary Identifier: Expr10149
• Pattern: HMR-1 is expressed in both primordial germ cells and endoderm.

• Primary Identifier: Expr15803
• Pattern: A HMR-1::GFP reporter which shows comparable localization patterns to the endogenous HMR-1 is strongly enriched at the interface between the basal pharyngeal surface and neuroectoderm during involution in a supracellular patch. This signal is distinct from the known localization at the apical side of the pharynx, which is dorsal to this patch.

38 GO Annotation

11 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001980
• Start: 11075755
• End: 11134667
• Strand: -1

38 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 58913

1 Sequence Ontology Term

• Name: gene

7 Strains

• WBStrain00037750
• WBStrain00022484
• WBStrain00022481
• WBStrain00024209
• WBStrain00024233
• WBStrain00033419
• WBStrain00034583

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrI_11134668..11142109
• Length (nt): 7442
• Chromosome Location: I: 11134668-11142109
• Organism: Caenorhabditis elegans