WormMine: Gene WBGene00004010

• WormBase Gene ID: WBGene00004010
• Gene Name: pha-1
• Sequence Name: Y48A6C.5
• Brief Description: pha-1 encodes a novel protein that contains a DUF1114 domain of unknown function found in a number of other nematode proteins; during embryonic development, pha-1 functions redundantly with class B SynMuv genes such as lin-35/Rb and efl-1 to effect pharyngeal morphogenesis; in regulating pharyngeal development, PHA-1 also appears to act with the UBC-18 ubiquitin conjugating enzyme; a PHA-1::GFP reporter is broadly expressed during embryonic development and localizes to the cytoplasm; expression is also observed in early- and late-larval-stage animals, as well as adults, although postembryonic expression is generally weaker than that seen in the embryo.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to enable alpha-(1->3)-fucosyltransferase activity. Involved in embryonic digestive tract morphogenesis and nematode larval development. Located in cytoplasm. Expressed in body wall muscle cell and pharynx.
• Biotype: SO:0001217
• Genetic Position: III :6.14398 ±0.074527
• Length (nt): 4914

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00004010

Genomics

2 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:Y48A6C.5b.1	Y48A6C.5b.1	2092	III: 11131775-11136688
Transcript:Y48A6C.5a.1	Y48A6C.5a.1	2171	III: 11131799-11136677

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:Y48A6C.5b	Y48A6C.5b	1362	III: 11131799-11131846
CDS:Y48A6C.5a	Y48A6C.5a	1476	III: 11131799-11131846

34 RNAi Result

• WBRNAi00114161
• WBRNAi00114239
• WBRNAi00114120
• WBRNAi00056741
• WBRNAi00056872
• WBRNAi00056873
• WBRNAi00072310
• WBRNAi00068515
• WBRNAi00068514
• WBRNAi00064535
• WBRNAi00073655
• WBRNAi00073657
• WBRNAi00073659
• WBRNAi00068953
• WBRNAi00068952
• WBRNAi00068955
• WBRNAi00068954
• WBRNAi00063013
• WBRNAi00020731
• WBRNAi00006231
• WBRNAi00063014
• WBRNAi00063019
• WBRNAi00063020
• WBRNAi00030252
• WBRNAi00063012
• WBRNAi00114003
• WBRNAi00114276
• WBRNAi00073656
• WBRNAi00073658
• WBRNAi00114082

70 Allele

• gk964518
• gk963887
• WBVar01269235
• WBVar01269234
• WBVar01269233
• gk944697
• gk944696
• WBVar01657166
• tm3671
• kry8
• gk185552
• gk185551
• gk185554
• gk185553
• gk185550
• gk185560
• gk185559
• gk185556
• gk185555
• gk185558
• gk185557
• WBVar01896389
• tm7034
• ee2123
• fd1
• e2275
• ttTi45454
• WBVar02072359
• gk424227
• tm3569

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00004010
• Start: 11131775
• End: 11136688
• 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

77 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons.	DESeq. False discovry rate (FDR) < 0.1.	WBPaper00048988:neuron_expressed
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 increased expression after animals were treated with 100uM Psora and 250uM Allantoin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Psora-Allantoin_upregulated
	Transcripts that showed significantly increased expression after animals were treated with 100uM Rapamycin and 50mM Metformin from day 1 to day 3 adult hermaphradite.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:Rapamycin-Metformin_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
	Transcripts that showed significantly decreased expression in atfs-1(cmh15) (null allele) animals comparing to in N2 animals at L4 larva stage.	edgeR, fold change > 2, FDR < 0.05	WBPaper00060909:atfs-1(cmh15)_downregulated
	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
	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
	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 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 (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:dopaminergic-neurons_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:excretory-cell_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:GABAergic-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: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 decreased expression in eat-2(ad1116) comparing to in N2 at 3-days post L4 adult hermaphrodite animals.	DESeq2(v1.14.1), fold change > 2, p-value < 0.05	WBPaper00055354:eat-2(ad1116)_downregulated
	Transcripts that showed significantly decreased expression in adbp-1(qj1) comparing to in N2 animals at L4 larva stage.	DESeq2, FDR < 0.05, fold change > 2.	WBPaper00067079:adbp-1(qj1)_downregulated_L4
	Transcripts that showed significantly increased expression in pry-1(mu38) animals comparing to in N2 at L1 larva stage.	DESeq, FDR < 0.05	WBPaper00055626:pry-1(mu38)_upregulated
	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
	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
Starvation 48 hours at L1 arrest	Transcripts that showed significantly increased expression in starved N2 animals (48 hours at L1 arrest)	Fold change > 2.	WBPaper00064005:starvation_upregulated_N2_mRNA
Bacteria infection: Serratia marcescens	Genes with increased expression after 24 hours of infection by S.marcescens 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:S.marcescens_24hr_upregulated_TilingArray
	Transcripts unqiuely expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:intestine_enriched
	Transcripts that showed significantly increased expression in jmjd-3.1p::jmjd-3.1 comparing to in N2.	DESeq2 Benjamini-Hochberg adjusted p-value < 0.05.	WBPaper00049545:jmjd-3.1(+)_upregulated
	Transcripts that showed significantly increased expression in rgef-1p::jmjd-1.2 comparing to in N2.	DESeq2 Benjamini-Hochberg adjusted p-value < 0.05.	WBPaper00049545:rgef-1p-jmjd-1.2(+)_upregulated
	Transcripts that showed significantly increased expression in sur-5p::jmjd-1.2 comparing to in N2.	DESeq2 Benjamini-Hochberg adjusted p-value < 0.05.	WBPaper00049545:sur-5p-jmjd-1.2(+)_upregulated

7 Expression Patterns

• Primary Identifier: Expr1031918
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr1579
• Remark: The expression of pha-1::lacZ with additional 2kb of 5'UTR showed identical expression pattern.
• Pattern: The first expression of the pha-1:lacZ hybrid gene is detectable at the 100 cell stage of embryogenesis (130 minutes of embryonic development; all developmental times refer to time after the first cleavage at 20 degree) in cells that have positions in the embryo corresponding to the pharyngeal and body wall muscle precursors. Expression of the pha-1:lacZ hybrid gene at around 200 minutes of development is detected in about 25 cells that form a cylinder in the anterior part of the embryo. These pha-1:lacZ expressing cells are the pharyngeal precursors. The lineage of most of these cells (26 of 27) is restricted to pharyngeal fate and only the MSaaaaa cell produces pharyngeal cells and non-pharyngeal cells (two neurons of the ring ganglion). As soon as these 27 pharynx precursor cells divide (230-250 minutes), expression of the pha-1:lacZ gene in the pharyngeal precursors ceases and only a few cells in the presumptive pharynx region express the hybrid protein. At 420 minutes of development (2 fold stage) no pha-1:lacZ gene expression in the pharyngeal precursor cells is detectable. pha-1:lacZ expression was also observed in body wall muscle cell precursors. Expression of the pha-1 hybrid protein starts early in all body wall muscle cell precursors and is detectable throughout embryonic development in these cells.

• Primary Identifier: Expr1025653
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2014879
• 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: Expr1160324
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr2985
• Remark: Similar expression patterns were also observed using reporter constructs containing approximately 2.9 kb of upstream regulatory sequences together with genomic sequences encoding the first 137 aa of PHA-1 fused to a GFP containing a nuclear localization signal.
• Pattern: Expression of the pha-1 reporter was first detected at the approximately 100-cell stage in all somatic cells of the embryo. This pattern of widespread expression continued through later stages of embryonic development, diminishing somewhat in intensity by the time of hatching. Expression was also observed in early-larval-stage animals and was present but reduced in late-stage larvae and adults.
• Subcellular Localization: Most if not all PHA-1::GFP fusion protein localized to the cytoplasm. This was particularly apparent in larvae, where the contribution of nonspecific GFP fluorescence coming from layers outside of the central focal plane was minimized. No evidence was observed for any dynamic regulation of PHA-1 with respect to its subcellular localization. Although these findings do not rule out the possibility that some PHA-1 protein may normally be present in nuclei, they strongly suggest that PHA-1 resides primarily, if not exclusively, in the cytoplasmic compartment. Moreover, although it was possible that the tagged fusion protein may have been mislocalized, either due to the presence of the C-terminal GFP extension, or simply through overexpression, the ability of the fusion protein to substitute functionally for wild-type PHA-1 suggests that it is localizing to the correct cellular compartment.

• Primary Identifier: Expr2033114
• 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

21 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00004010
• Start: 11131775
• End: 11136688
• Strand: 1

19 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 4914

1 Sequence Ontology Term

• Name: gene

593 Strains

• WBStrain00023998
• WBStrain00023999
• WBStrain00023995
• WBStrain00023996
• WBStrain00023997
• WBStrain00024002
• WBStrain00024001
• WBStrain00024004
• WBStrain00024003
• WBStrain00024000
• WBStrain00024009
• WBStrain00024006
• WBStrain00024005
• WBStrain00024008
• WBStrain00024007
• WBStrain00024013
• WBStrain00024012
• WBStrain00024015
• WBStrain00024014
• WBStrain00024011
• WBStrain00024010
• WBStrain00024017
• WBStrain00024016
• WBStrain00024019
• WBStrain00024018
• WBStrain00024026
• WBStrain00024025
• WBStrain00024073
• WBStrain00024072
• WBStrain00024075

0 Upstream Intergenic Region