WormMine: Gene WBGene00004777

• WormBase Gene ID: WBGene00004777
• Gene Name: ser-2
• Sequence Name: C02D4.2
• Brief Description: ser-2 encodes at least four tyramine 7-transmembrane domain receptors (GPCRs), by alternative splicing from three different promoters, that have distinct but partially overlapping expression patterns; ser-2 has at least three alternative promoters that drive SER-2 expression in a set of sensory, inter- and motor neurons (e.g., AIY, AIZ, and RIA) adding up to ~10% of all neurons in the nervous system, as well as pharyngeal cells and head muscles; the deletion ser-2(pk1397) has no obvious mutant phenotype; LIM-4 is required for SER-2 expression, and MAB-23 is required for SER-2 expression at normally high levels.
• Organism: Caenorhabditis elegans
• Automated Description: Enables tyramine receptor activity. Involved in octopamine or tyramine signaling pathway. Located in plasma membrane. Expressed in body wall musculature; excretory gland cell; neurons; non-striated muscle; and uterine toroidal epithelial cell.
• Biotype: SO:0001217
• Genetic Position: X :22.3622 ±0.014705
• Length (nt): 16431

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004777

Genomics

7 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C02D4.2b.1	C02D4.2b.1	2087	X: 15286533-15298708
Transcript:C02D4.2a.1	C02D4.2a.1	1609	X: 15286535-15294871
Transcript:C02D4.2g.1	C02D4.2g.1	1309	X: 15286799-15294871
Transcript:C02D4.2f.1	C02D4.2f.1	1384	X: 15286845-15292060
Transcript:C02D4.2e.1	C02D4.2e.1	1368	X: 15286845-15294871
Transcript:C02D4.2c.1	C02D4.2c.1	600	X: 15289954-15298223
Transcript:C02D4.2d.1	C02D4.2d.1	591	X: 15289954-15302963

Other

7 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C02D4.2a	C02D4.2a	1299	X: 15286845-15287003
CDS:C02D4.2g	C02D4.2g	1263	X: 15286845-15287003
CDS:C02D4.2f	C02D4.2f	1266	X: 15286845-15287003
CDS:C02D4.2e	C02D4.2e	1368	X: 15286845-15287003
CDS:C02D4.2d	C02D4.2d	591	X: 15289954-15290019
CDS:C02D4.2b	C02D4.2b	1290	X: 15286845-15287003
CDS:C02D4.2c	C02D4.2c	600	X: 15289954-15290019

5 RNAi Result

• WBRNAi00107774
• WBRNAi00039411
• WBRNAi00072191
• WBRNAi00009985
• WBRNAi00028340

286 Allele

• gk964260
• gk962707
• gk963810
• gk963581
• WBVar01928890
• WBVar01928891
• WBVar01928892
• WBVar01928893
• WBVar01928894
• WBVar01928895
• WBVar02123436
• WBVar02123488
• gk450785
• tm10835
• gk393867
• gk360063
• gk731216
• gk867079
• gk544155
• gk354096
• gk571757
• gk303057
• ok2103
• gk303066
• gk303065
• WBVar00221766
• gk716671
• WBVar00221767
• gk952500
• gk303068

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004777
• Start: 15286533
• End: 15302963
• 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_15286485..15286532
• Length (nt): 48
• Chromosome Location: X: 15286485-15286532
• Organism: Caenorhabditis elegans

111 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
Osmotic stress	Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when no food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_NoFood
	Transcripts that showed significantly increased expression in csr-1a(tor159) comparing to in N2 at 25C.	DESeq2, fold change > 2, p-value < 0.05.	WBPaper00061753:csr-1(tor159)_upregulated_25C
	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
	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 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 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
	Significantly upregulated genes from clk-1(qm30) microarrays using SAM algorithm with an FDR < 0.1 from adult-only chips.	SAM algorithm with an FDR < 0.1.	WBPaper00033065:clk-1(qm30)_upregulated
	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
	Genes with increased RNA expression after 24 hours rotenone treatment	EdgeR provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting p-values were adjusted using the Benjamini and Hochbergs approach for controlling the false discovery rate (FDR). Transcripts with an adjusted p-value smaller 0.05 were assigned as differentially expressed.	WBPaper00044426:rotenone_24h_upregulated
	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 altered expression at URX, AQR, and PQR neurons in camt-1(ok515) animals comparing to in wild type AX1888-1 strain.	RNA-seq data were mapped using PRAGUI - a Python 3-based pipeline for RNA-seq data analysis.	WBPaper00061902:camt-1(ok515)_regulated_URX-AQR-PQR
	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 npr-15(tm12539) comparing to in N2 at L4 larva stage.	Fold change > 2, FDR < 0.05.	WBPaper00066608:npr-15(tm12539)_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 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 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 significantly enriched in NSM neurons (isolated by FACS) versus the reference, according to tiling array analysis towards total RNA.	A linear model and moderated t-statistic were used to determine differentially expressed genes as implemented by the limma package (v3.21.4). Enriched list contains only genes significantly enriched in the NSM neurons versus the reference <=1.5X and <= 5% FDR.	WBPaper00045974:NSM_enriched_totalRNA_tiling
	Genes upregulated in sma-2 L4 (3 arrays) or sma-4 L4 (1 array) vs. N2 L4.	FDR = 0%, SAM.	WBPaper00037682:sma-2_sma-4_upregulated
	Transcripts that showed significantly decreased expression in npr-8(ok1439) animals comparing to N2 animals.	DESeq2, fold change > 1.5, FDR < 0.05.	WBPaper00058948:npr-8(ok1439)_downregulated_OP50
Bacteria infection: Pseudomonas aeruginosa PA14. 24 hours of exposure at 25C.	Transcripts that showed significantly decreased expression in N2 animals with 24 hours of exposure to P. aeruginosa PA14 for 24 hrs at 25C, comparing to N2 animals without exposure to PA14.	DESeq2, fold change > 2, FDR < 0.05.	WBPaper00058948:PA14_downregulated

14 Expression Patterns

• Primary Identifier: Expr4696
• Pattern: Expressed in head muscle only.

• Primary Identifier: Marker51
• Remark: Picture: N.A. Reporter gene fusion type not specified.
• Pattern: Expressed in AIY neurons

• Primary Identifier: Marker93
• Remark: Picture: N.A.
• Pattern: Marker for ALN, SDQ neurons.

• Primary Identifier: Expr2707
• Reporter Gene: [ser-2::gfp] transcriptional fusion constructs. Ser-2 reporter constructs were generated by using a PCR fusion protocol, using pPD95.75 as a template for green fluorescent protein (gfp). For all gfp fusion primers listed, gfp vector sequence is indicated in lowercase, and gene-specific sequence is indicated in uppercase. [ser-2::gfp] translational fusion. A translational fusion of the whole ser-2 locus to gfp was created by using an in vivo recombination technique. Specifically, two overlapping PCR fragments, one containing the 5' part of a locus, the other containing the remainder of the locus PCR-fused to gfp, were coinjected into the worm. Recombination of these two fragments via the homologous region leads to the expression of a full-length ser-2::gfp fusion.
• Pattern: Expression using the upstream regulatory regions of exon 1bc (ser-2prom2::gfp) is mostly restricted to the AIYL/R, AIZL/R, RID, DVA, BDUL/R, SIADL/R, and SIAVL/R interneurons. Less consistent expression is observed in PVT. In addition, expression is observed in the RMEL/R motor neurons. Outside the nervous system, expression can be observed in the excretory gland cells. No more transcriptional regulatory information is contained within intronic regions by generating a fusion of gfp to the full coding genomic ser-2 locus using an in vivo recombination technique([ser-2::gfp] translational fusion. Transgenic animals expressing such a construct show an expression pattern similar to the one observed with the ser-2prom1::gfp construct. The upstream regulatory region of the third splice form, containing exon 1d(ser-2prom3::gfp), drives expression exclusively in two sensory neuron classes, OLL(L/R) and PVD(L/R). ser-2prom1::gfp is expressed in the AIY interneuron class and a set of unidentified neurons. These neurons were identified as head and tail interneuron classes, namely AVHL/R, AUAL/R, AIYL/R, RICL/R, SABVL/R, RID, RIAL/R, SABD, SDQ, CANL/R, DA9, LUAL/R, ALNL/R, and PVCL/R. In addition to its expression in neurons, ser-2prom1::gfp is also expressed in pharyngeal cells (NSM neurons and pm1/6 muscles) and in head muscles. In males, expression can be observed in posterior dorsal and ventral body wall muscles, the male-specific diagonal muscles, and several posterior neurons likely to be CP neurons.

• Primary Identifier: Expr3206
• Pattern: In addition to expression in a number of neurons (RMEL/R, RID, BDUL/R, AIYL/R, AVHL/R, AIZL/R, ALNL/R, RICL/R, RIAL/R and PDA) as has been reported previously, intense fluorescence was also observed in uterine toroid cells (ut1 and ut2).

• Primary Identifier: Expr15409
• Pattern: ser-2(promCE)

• Primary Identifier: Expr15407
• Pattern: ser-2(prom1B)

• Primary Identifier: Expr10758
• Pattern: Pser-2::mCherry reporter was expressed in head muscles, as well as several neurons in the head and ventral cord. The ser-2 reporter was expressed in the first and second row of muscle cells, which are distinct from neck muscles (third and fourth row of muscle cells). The ser-2 reporter was not expressed in interneurons that control locomotion, as expression did not overlap with Pglr-1::GFP and Plgc-55::GFP reporters that are expressed in the locomotion command neurons (unpublished data). ser-2 reporter expression was also observed in 13 cells in the ventral cord that send commissures to the dorsal cord. Coexpression analysis with GFP reporters that specifically label cholinergic or GABAergic neurons showed that Pser-2::mCherry was highly expressed in a subset of GABAergic motor neurons, specifically the VD motor neurons.

• Primary Identifier: Expr1021348
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr15408
• Pattern: ser-2(prom3)

• Primary Identifier: Expr13473
• Pattern: Onset of expression: DA8: L1 or earlier.

• Primary Identifier: Expr1143527
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2015747
• 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: Expr2033980
• 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).

19 GO Annotation

16 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004777
• Start: 15286533
• End: 15302963
• Strand: -1

19 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 16431

1 Sequence Ontology Term