WormMine: Gene WBGene00001612

• WormBase Gene ID: WBGene00001612
• Gene Name: glr-1
• Sequence Name: C06E1.4
• Brief Description: glr-1 encodes an AMPA-type ionotropic glutamate receptor; GLR-1 activity is required for mediating the behavioral response to light nose touch and the frequency with which animals change locomotory direction in response to sensory cues such as food; GLR-1 is also required for memory formation; GLR-1 and GLR-2, a second AMPA-type ionotropic glutamate receptor, can interact to form functional heteromeric channels; GLR-1 is expressed in motorneurons and interneurons, including four of the five pairs of command interneurons that are required for locomotory control; in the ventral nerve cord and nerve ring, GLR-1 localizes to perinuclear structures in cell bodies and to punctate structures that appear to be glutamatergic postsynaptic specializations; proper GLR-1 localization in the anterior ventral nerve cord of older larvae and adults requires activity of the class I PDZ protein LIN-10; GLR-1 is ubiquitinated in vivo and its abundance at postsynaptic elements, which may influence postsynaptic strength, is regulated by ubiquitination; indeed, GLR-1 trafficking in interneurons has been shown to be regulated by the UEV-1 ubiquitin-conjugating enzyme variant and the UBC-13 ubiquitin-conjugating enzyme; GLR-1 dynamics are also regulated by the alpha-adducin, ADD-1, which may link actin cytoskeleton reorganization with synapse structure and composition.
• Organism: Caenorhabditis elegans
• Automated Description: Enables enzyme binding activity and glutamate-gated receptor activity. Involved in several processes, including forward locomotion; learning or memory; and positive regulation of locomotion. Located in several cellular components, including perinuclear endoplasmic reticulum; postsynapse; and somatodendritic compartment. Part of ionotropic glutamate receptor complex. Expressed in interneuron; neurons; and ventral nerve cord. Used to study neurodegenerative disease. Human ortholog(s) of this gene implicated in several diseases, including Huntington's disease; childhood absence epilepsy; and intellectual disability (multiple). Is an ortholog of human GRIA2 (glutamate ionotropic receptor AMPA type subunit 2) and GRIA3 (glutamate ionotropic receptor AMPA type subunit 3).
• Biotype: SO:0001217
• Genetic Position: III :-0.245417 ±0.001615
• Length (nt): 4480

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001612

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C06E1.4.1	C06E1.4.1	3009	III: 8584163-8588642

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C06E1.4	C06E1.4	2889	III: 8584256-8584342

4 RNAi Result

• WBRNAi00039890
• WBRNAi00010303
• WBRNAi00005523
• WBRNAi00027649

57 Allele

• gk964518
• gk963887
• gk330571
• gk879685
• gk869694
• gk590468
• gk910113
• gk686700
• gk756732
• gk619650
• gk882528
• gk785339
• gk381759
• gk521031
• gk547073
• gk452898
• gk667116
• gk788517
• gk468773
• gk794702
• gk327481
• gk441124
• gk579428
• gk827390
• gk422808
• gk928362
• gk885889
• gk328222
• gk833398
• gk533333

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001612
• Start: 8584163
• End: 8588642
• 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_chrIII_8583911..8584162
• Length (nt): 252
• Chromosome Location: III: 8583911-8584162
• Organism: Caenorhabditis elegans

172 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 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
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
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
	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 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
	Genes with expression level regulated by genotype (N2 vs CB4856) at Late reproduction stage (96 hours at 24 centigrade).	Authors permuted transcript values and used a genome-wide threshold of log10 P-value = 2, which resembles a false discovery rate (FDR) of 0.0118.	WBPaper00040858:eQTL_regulated_reproductive
	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)
	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 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
	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
Reduced humidity (98% relative humidity).	Genes that were down-regulated after one day exposure to reduced humidity (98% relative humidity) according to microarray analysis.	Multiple hypothesis testing with the Benjamini-Hochberg correction was applied on calculated p-values. A change in the expression level was considered to be significant if the adjusted p-value was less than 0.001.	WBPaper00044578:reduced-humidity_downregulated_microarray
	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
	Transcripts that showed significantly increased expression in hpk-1(pk1393) comparing to in N2 at adult day 2.	DESeq 2, fold change > 2, FDR < 0.05.	WBPaper00065581:hpk-1(pk1393)_upregulated
	Transcripts that showed significantly increased expression in hda-1(ne4752[3xFLAG-Degron-HDA-1]) in gonads dissected from 1-day old adult animals.	Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R.	WBPaper00061479:hda-1(ne4752)_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:glr-1(+)-neurons_L2-larva_expressed
	Transcripts that showed significantly increased expression in wdr-23(mac32) embryos from parents fed with E. coliHB101, comparing to N2 embryos parents fed with E. coli HB101.	DESeq2, Fold Change > 2 or < 0.5.	WBPaper00059566:wdr-23(mac32)_upregulated
	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 increased expression in hda-2(ok1479) comparing to in N2 animals.	DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2.	WBPaper00062159:hda-2(ok1479)_upregulated
	Transcripts that showed significantly increased expression in srbc-48(ac23);kyIs262;fer-1(b232ts) comparing to in kyIs262;fer-1(b232ts), 24h after infection with P.aeruginosa.	DESeq2, FDR <0.05, fold change > 2.	WBPaper00059664:srbc-48(ac23)_upregulated
	Transcripts that showed significantly increased expression in daf-2(e1370) comparing to in N2.	Student's t-test, fold change > 2, p-value < 0.05.	WBPaper00055386:daf-2(e1370)_upregulated
	Transcripts that showed significantly decreased expression in set-2(tm1630) animals at embryo stage, comparing to in N2 animals.	DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction.	WBPaper00060014:set-2(tm1630)_downregulated
	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
	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
	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
	Genes found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014.	N.A.	WBPaper00026929:sir-2.1_overexpression_regulated

25 Expression Patterns

• Primary Identifier: Expr4407
• Remark: No detailed description on cellular expression patterns in other tissues.
• Subcellular Localization: GLR-1::GFP puncta in the ventral nerve cord colocalize with presynaptic markers (synaptobrevin and a vesicular glutamate transporter).

• Primary Identifier: Expr1030969
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Marker94
• Remark: Picture: N.A.
• Pattern: Marker for RMD, SMDD, SMDV neurons.

• Primary Identifier: Marker95
• Remark: Picture: N.A.
• Pattern: Marker for RMD, SMDD, SMDV neurons.

• Primary Identifier: Marker60
• Remark: Picture: N.A. Reporter gene fusion type not specified.
• Pattern: RIS cell fate marker.

• Primary Identifier: Expr10951
• Subcellular Localization: GLR-1::CFP and GLR-2::YFP colocalize in neuronal cell bodies and at puncta in neuronal processes.

• Primary Identifier: Expr249
• Pattern: AVG AVJ DVC PVC PVQ RIG RIS RMD RMEL/R SMD URY [Nature 378:82]

• Primary Identifier: Expr16502
• Pattern: GLR-1 & NMR-1 in AVA are mostly localized to the anterior process.

• Primary Identifier: Expr816
• Pattern: AVA, AVB, AVD, AVE, PVC, AIB, RMD, RIM, SMD, AVG, PVQ, URY.

• Primary Identifier: Expr247
• Remark: Data modified according to Shawn Lockery's expression pattern curations.
• Reporter Gene: [glr-1::gfp] and [glr-1::lacZ]. Both transcriptional and translational fusions were generated.
• Pattern: Expression was limited to a subset of inter- and motor neurons, including the interneurons AVA, AVB, AVD, AVE and PVC. Polyclonal antibody also recognized neuronal processes. Expression also seen in AIB, RMD, RIM, SMD. AVG, PVQ, URY stained faintly.

• Primary Identifier: Expr15366

• Primary Identifier: Expr8363
• Remark: Picture: Figure 3C.
• Subcellular Localization: In transgenic worms that coexpressed functional full-length STG-1::mCherry and GLR-1::GFP both under the regulation of the glr-1 promoter, the fusion proteins colocalized at punctate structures in the ventral cord that are thought to represent postsynaptic sites.

• Primary Identifier: Expr12237
• Subcellular Localization: GLR-1::GFP is localized in punctate structures in the ventral nerve cord. 80% of these puncta were closely apposed to presynaptic markers (synaptobrevin or a VGLUT), suggesting that a large fraction of GLR-1::GFP puncta correspond to postsynaptic elements.

• Primary Identifier: Expr10535
• Subcellular Localization: GLR-1::GFP, expressed under the glr-1 promoter, localizes to puncta in the VNC. Greater than 80% of these puncta are closely apposed to presynaptic markers, indicating that the majority of GLR-1::GFP puncta in the VNC represent postsynaptic sites.

• Primary Identifier: Expr1198
• Remark: Expression was not detected in transgenic worms injected with a promoterless construct.
• Pattern: Expression of the GLR-1::GFP fusion protein was limited to a subset of neurons, including the command interneurons. Transgenic strains that expressed glr-1::GLR-1(A/T)::GFP exhibited green fluorescent protein (GFP) fluorescence in the same neurons.

• Primary Identifier: Expr3934
• Remark: The topological arrangement of vertebrate stargazin has the N- and C-terminal regions intracellular and the loop between the first and second transmembrane domains (TMD) extracellular. By tagging STG-1 with GFP at the loop between TMD1 and TMD2 (GFP::STG-1), or near the C terminus (STG-1::GFP), and using antibody detection of GFP at the cell surface, it was shown that the topology of C. elegans STG-1 is consistent with that of vertebrate transmembrane AMPAR regulatory proteins.
• Subcellular Localization: Coexpression of CFP-tagged GLR-1 and YFP-tagged STG-1 showed that the two molecules colocalized at the tips of muscle arms.

• Primary Identifier: Expr3422
• Subcellular Localization: In wild-type animals, both endogenous GLR-1 and GLR-1::GFP can be found throughout the cell body cytosol in punctate structures as well as at punctate structures throughout the neurites previously shown to correspond to synaptic inputs. Mutant nematodes that lack glr-1 show no fluorescence, indicating the specificity of the antibody. To determine whether the punctate structures in the cell body corresponded to Golgi-localized receptor, GLR-1::CFP and mannosidase-YFP (MAN::YFP) were coexpressedand and they colocalized to punctate structures within the cell bodies.

• Primary Identifier: Chronogram1350
• Remark: Original chronogram file: chronogram.2596.xml
• Reporter Gene: [C06E1.4:gfp] transcriptional fusion.

• Primary Identifier: Expr1022802
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr11529
• Subcellular Localization: The abundance of GLR-1 was analyzed at synapses by examining the distribution of a green fluorescent protein-tagged version of GLR-1 (GLR-1::GFP), which localizes in a punctate pattern in VNC interneurons. More than 80% of these GLR-1::GFP puncta are closely apposed to presynaptic markers, indicating that the majority of puncta correspond to postsynaptic sites.

• Primary Identifier: Expr11273
• Subcellular Localization: CNI-1 and GLR-1 colocalized in discrete regions of the ER/Golgi. Surface Expressed CNI-1 colocalizes with synaptic GLR-1.

• Primary Identifier: Expr12900
• Subcellular Localization: GFP-tagged GLR-1 is localized to the proximal dendritic segment.

• Primary Identifier: Expr2030348
• 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: Expr2012112
• 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: Expr1143970
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

63 GO Annotation

23 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001612
• Start: 8584163
• End: 8588642
• Strand: -1

63 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 4480

1 Sequence Ontology Term