WormMine: Gene WBGene00006784

• WormBase Gene ID: WBGene00006784
• Gene Name: unc-49
• Sequence Name: T21C12.1
• Brief Description: unc-49 encodes multiple subunits of a heteromeric GABA receptor; unc-49 activity is required for postsynaptic GABA responsiveness and thus for normal regulation of locomotion; UNC-49::GFP reporter fusions for at least two isoforms are expressed in dorsal and ventral head and body wall muscles, with isoform-specific expression also seen in the sphincter muscle; UNC-49::GFP subcellular localization is most prominent at neuromuscular junctions; in Xenopus oocytes and mammalian tissue culture cells, two UNC-49 subunits, UNC-49B and UNC-49C, are able to form a functional heteromeric GABA receptor.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable neurotransmitter receptor activity. Predicted to contribute to chloride channel activity. Involved in gamma-aminobutyric acid signaling pathway; locomotory behavior; and regulation of backward locomotion. Located in neuromuscular junction and postsynaptic membrane. Expressed in AVA; anal sphincter muscle; body wall musculature; and somatic nervous system. Used to study epilepsy.
• Biotype: SO:0001217
• Genetic Position: III :3.35021 ±0.089636
• Length (nt): 11944

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00006784

Genomics

14 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T21C12.1d.1	T21C12.1d.1	2570	III: 10520762-10532705
Transcript:T21C12.1c.1	T21C12.1c.1	2606	III: 10520762-10532705
Transcript:T21C12.1f.1	T21C12.1f.1	1705	III: 10520762-10532705
Transcript:T21C12.1c.2	T21C12.1c.2	1742	III: 10520843-10530739
Transcript:T21C12.1e.1	T21C12.1e.1	2581	III: 10520843-10532704
Transcript:T21C12.1b.1	T21C12.1b.1	1657	III: 10520845-10527870
Transcript:T21C12.1j.1	T21C12.1j.1	564	III: 10520968-10525274
Transcript:T21C12.1k.1	T21C12.1k.1	1467	III: 10520968-10529961
Transcript:T21C12.1l.1	T21C12.1l.1	960	III: 10524268-10527800
Transcript:T21C12.1m.1	T21C12.1m.1	960	III: 10524268-10530586
Transcript:T21C12.1o.1	T21C12.1o.1	843	III: 10524268-10532553
Transcript:T21C12.1n.1	T21C12.1n.1	228	III: 10527421-10527800
Transcript:T21C12.1h.1	T21C12.1h.1	1406	III: 10530116-10532704
Transcript:T21C12.1i.1	T21C12.1i.1	474	III: 10531433-10532553

Other

13 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T21C12.1b	T21C12.1b	1464	III: 10520968-10521041
CDS:T21C12.1c	T21C12.1c	1464	III: 10520968-10521041
CDS:T21C12.1d	T21C12.1d	1428	III: 10520968-10521041
CDS:T21C12.1f	T21C12.1f	1347	III: 10520968-10521041
CDS:T21C12.1j	T21C12.1j	564	III: 10520968-10521041
CDS:T21C12.1l	T21C12.1l	960	III: 10524268-10524325
CDS:T21C12.1m	T21C12.1m	960	III: 10524268-10524325
CDS:T21C12.1o	T21C12.1o	843	III: 10524268-10524325
CDS:T21C12.1n	T21C12.1n	228	III: 10527421-10527466
CDS:T21C12.1h	T21C12.1h	795	III: 10530576-10530738
CDS:T21C12.1i	T21C12.1i	474	III: 10531433-10531664
CDS:T21C12.1e	T21C12.1e	1521	III: 10520968-10521041
CDS:T21C12.1k	T21C12.1k	1467	III: 10520968-10521041

10 RNAi Result

• WBRNAi00000954
• WBRNAi00089728
• WBRNAi00053708
• WBRNAi00018961
• WBRNAi00006214
• WBRNAi00027895
• WBRNAi00066348
• WBRNAi00089939
• WBRNAi00090099
• WBRNAi00090257

220 Allele

• gk964518
• gk963887
• gk963675
• gk963676
• gk963083
• otn9867
• otn9868
• otn9869
• otn12192
• otn12194
• otn12193
• WBVar00240576
• WBVar00240578
• WBVar01267983
• gk184282
• gk944590
• WBVar01542283
• WBVar01542284
• WBVar01542281
• WBVar01267964
• WBVar01267969
• WBVar01267978
• WBVar01267974
• WBVar01267972
• WBVar01267979
• WBVar01267981
• gk944589
• otn496
• otn494
• otn495

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00006784
• Start: 10520762
• End: 10532705
• 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_10532706..10535525
• Length (nt): 2820
• Chromosome Location: III: 10532706-10535525
• Organism: Caenorhabditis elegans

191 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
	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
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
	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 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 that showed significantly decreased expression at 11-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites.	DESeq2, fold change > 2, FDR < 0.05	WBPaper00065835:Day11_vs_Day1_downregulated
	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
	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 that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_downregulated_daf-16(mu86);glp-1(e2141)
	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 expressed in vulva.	FPKM >= 1.	WBPaper00064122:vulva_transcriptome
	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

10 Expression Patterns

• Primary Identifier: Marker19
• Remark: Picture: 4A. Reporter gene fusion type not specified.
• Subcellular Localization: Expressed in postsynaptic terminals in muscle at the NMJs (neuromuscular junctions).

• Primary Identifier: Expr15907
• Pattern: To confirm UNC-49 expression in AVA, we expressed GFP under control of the unc-49 promoter (Punc-49) in a strain with AVA labeled by mStrawberry.

• Primary Identifier: Expr2036017
• 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: Expr1032855
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1283
• Pattern: Fluorescence was detected mainly on head muscles and body wall muscles on both the dorsal and ventral sides. Strong spincter muscle GFP was observed in unc-49B::gfp but not unc-49C::gfp animals. Both constructs produce variable, weak fluorescence in head ganglia.
• Subcellular Localization: Faint GFP was observed in the plasma membrane of the cell soma and muscle arms while intense GFP was observed where the motor neuron and muscles contact.

• Primary Identifier: Marker2
• Remark: Picture: Fig. 1D.
• Reporter Gene: Presynaptic terminals were visualized using unc-47::SNB-CFP. Postsynaptic GABA receptor fields were visualized by unc-49::UNC-49B::YFP.
• Pattern: YFP fluorescence was detected in the nerve ring and along the ventral and dorsal cords with a punctate pattern.
• Subcellular Localization: Presynaptic terminals were visualized using unc-47::SNB-CFP. Postsynaptic GABA receptor fields were visualized by UNC-49B::YFP.

• Primary Identifier: Expr1157259
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2017881
• 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: Expr1027570
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr1200291
• Pattern: Data from the TransgeneOme project

27 GO Annotation

29 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00006784
• Start: 10520762
• End: 10532705
• Strand: 1

27 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 11944

1 Sequence Ontology Term