WormMine: Gene WBGene00001595

• WormBase Gene ID: WBGene00001595
• Gene Name: gld-1
• Sequence Name: T23G11.3
• Brief Description: gld-1 encodes a protein containing a K homology (KH) RNA binding domain; GLD-1 is required for regulation of the mitosis/meiosis decision during germline development (promotion of meiotic entry) in parallel with gld-2, gld-3, and nos-3 and also affects spermatogenesis; GLD-1 physically interacts with the 3'- and 5'UTR of its putative mRNA targets in vitro to negatively regulate their translation; GLD-1 also physically interacts with FOG-2, an F-box protein that promotes spermatogenesis; GLD-1 is expressed in the germ cell cytoplasm at high levels during meiotic prophase; GLD-1 phosphorylation and levels in the distal, mitotic germline are negatively regulated by CYE-1/cyclin E, CDK-2, and the RNA-binding protein FBF-1.
• Organism: Caenorhabditis elegans
• Automated Description: Enables mRNA 3'-UTR binding activity; mRNA 5'-UTR binding activity; and single-stranded RNA binding activity. Involved in several processes, including negative regulation of nitrogen compound metabolic process; oocyte fate determination; and positive regulation of reproductive process. Located in P granule and cytosol. Expressed in body wall musculature; germ line; neurons; ventral nerve cord; and in male. Is an ortholog of human QKI (QKI, KH domain containing RNA binding).
• Biotype: SO:0001217
• Genetic Position: I :2.25242 ±0.007012
• Length (nt): 2542

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00001595

Genomics

1 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:T23G11.3.1	T23G11.3.1	2219	I: 7695681-7698222

Other

1 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:T23G11.3	T23G11.3	1392	I: 7695696-7695884

81 RNAi Result

• WBRNAi00095741
• WBRNAi00107855
• WBRNAi00107850
• WBRNAi00107832
• WBRNAi00107833
• WBRNAi00107834
• WBRNAi00107835
• WBRNAi00107831
• WBRNAi00107836
• WBRNAi00063492
• WBRNAi00117275
• WBRNAi00066960
• WBRNAi00067417
• WBRNAi00067460
• WBRNAi00067470
• WBRNAi00067697
• WBRNAi00067829
• WBRNAi00067996
• WBRNAi00068067
• WBRNAi00085141
• WBRNAi00061003
• WBRNAi00061004
• WBRNAi00085356
• WBRNAi00065409
• WBRNAi00065412
• WBRNAi00007899
• WBRNAi00026383
• WBRNAi00053963
• WBRNAi00027808
• WBRNAi00078208

77 Allele

• gk962858
• gk962706
• gk963902
• gk963849
• q266
• q268
• q343
• q361
• q365
• q93
• q93oz45
• q93oz12
• q93oz50
• q93oz49
• q93oz53
• q93oz52
• q93oz56
• q93oz55
• q126
• q485
• q495
• q62
• WBVar01432146
• q1485
• WBVar01832211
• WBVar00154509
• WBVar00154510
• WBVar00154511
• h12328
• op236

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00001595
• Start: 7695681
• End: 7698222
• 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_7698223..7698300
• Length (nt): 78
• Chromosome Location: I: 7698223-7698300
• Organism: Caenorhabditis elegans

235 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 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
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
	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 expressed in seam cells, according to PAT-Seq analysis using Pgrd-10-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:seam_expressed
	Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-1-adult_vs_L4_upregulated_fem-3(q20)
	Transcripts that showed significantly increased expression in day 3 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals.	Fold change > 2, FDR < 0.05	WBPaper00064088:Day-3-adult_vs_L4_upregulated_fem-3(q20)
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
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_6h
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 6h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_6h
Bacteria infection: Bacillus thuringiensis	mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
	Transcripts that showed significantly decreased expression in hsp-6(mg585) comparing to in N2 at L4 larva stage.	EdgeR, fold change > 2, FDR < 0.001.	WBPaper00056290:hsp-6(mg585)_downregulated
Transgeneration hypoxia treatment.	Transcripts that are significantly upregulated in F1 animals after P0 parents were exposed to 0.1% oxygen for 16 hours at L4 larva stage.	For calling the significant differentially expressed genes (DEGs),the false discovery rate (FDR) after multiple testing correction was set as 0.05 and analyzed in edgeR.	WBPaper00064871:hypoxia_upregulated_F1
	Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage.	DESeq	WBPaper00053302:stavudine_24h_regulated
25C vs. 20C	Transcripts that showed significantly increased expression in 1-day post L4 adult hermaphrodite N2 grown at 25C, comparing to in N2 animals grown at 20C.	CuffDiff, fold change > 2.	WBPaper00065096:25C_vs_20C_upregulated
	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
Temprature shift to 28C for 24 hours.	Transcripts that showed significantly decreased expression after animals were exposed to 28C temperature for 24 hours.	Differentially expressed genes wereidentified using DESeq (v.1.18.0) by normalizing readsbased on the negative binomial distribution method andcomparing each HS timepoint to the 0-h control.	WBPaper00061341:28C_24h_downregulated
	Transcripts that showed significantly decreased expression in tetraploid N2 comparing to diploid N2 animals at L4 larva stage.	DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05.	WBPaper00066110:tetraploid_vs_diploid_downregulated
Temprature shift to 28C for 48 hours.	Transcripts that showed significantly decreased expression after animals were exposed to 28C temperature for 48 hours.	Differentially expressed genes wereidentified using DESeq (v.1.18.0) by normalizing readsbased on the negative binomial distribution method andcomparing each HS timepoint to the 0-h control.	WBPaper00061341:28C_48h_downregulated

16 Expression Patterns

• Primary Identifier: Expr4231
• Remark: No detailed description on expression pattern in other life stages..
• Pattern: Protein abundance was quantitated along the isolated gonad. Expression was highest between 6/15 - 13/15 of the gonad away from distal tip cells.

• Primary Identifier: Expr1030956
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr583
• Remark: The antibodies recognized both isoforms of GLD-1. early embryo(author) = blastula embryo(curator).
• Pattern: GLD-1 is first detected in EMS and P2 at the 4-cell stage. It remains in the germ line throughout embryogenesis, but is lost from MS, E, C and D when these somatic cells divide.

• Primary Identifier: Expr584
• Remark: early embryo(author) = blastula embryo(curator).
• Pattern: gld-1 mRNA is contained in all blastmeres of embryos with 8 or fewer cells. Subsequently, gld-1 mRNA disappears rapidly from somatic blastmeres and is only detected in the germ lineage. By the 16 cell stage, gld-1 mRNA is only detected in P3.

• Primary Identifier: Expr8533
• Remark: Picture: Figure 4D, Figure 5B.
• Pattern: In wild-type germlines, GLD-1 was difficult to detect in the distal mitotic region, became easily detectable in the proximal mitotic region and increased dramatically in the transition zone. In wild-type male germlines, GLD-1 was low in the distal-most mitotic region, but increased visibly in the proximal mitotic region and transition zone.

• Primary Identifier: Expr582
• Remark: The antibodies recognized both isoforms of GLD-1.
• Pattern: Both GLD-1 protein and gld-1 mRNA are present at lower levels in adult males compared to hermaphrodites. The weak signals are present in the distal mitotic and transition zones, and disappear from the pachytene region.

• Primary Identifier: Expr16474
• Pattern: gld-1::mScarlet is expressed in the pachytene region of germline. unc-54::mEos3.2 expressed in body wall muscle.

• Primary Identifier: Expr11385
• Pattern: Somatic expression of an mCherry::H2B transcriptional reporter (the histone fusion used to focus diffuse, low level cytoplasmic GFP expression to the nucleus) under the control of the gld-1 promoter and the gld-1 3'UTR was mainly localized to the head, tail and ventral side of the animals. DIC microscopy analysis indicates that most of the positive cells are neuronal cells in the head and tail ganglia and the ventral nerve cord.

• Primary Identifier: Expr580
• Remark: The antibodies recognized both isoforms of GLD-1.
• Pattern: Weak GLD-1 staining is present at L1 and L2 in the germ line. At L3, GLD-1 becomes stronger in the presumptive male germ cells of the hermaphrodite. At L4, pachtene male germ cells no longer stain for GLP-1. In the adult hermaphrodite, GLD-1 is nonuniformly distributed along the distal-proximal germ line axis. Staining is weak in the mitotic region. Staining is stronger in the transition to the meiotic region and in the pachytene region, drops off in the diplotene region, and disappears as oocytes are formed. Compare mRNA pattern in Expression pattern 581 and Expression pattern 582 for GLD-1 in males.
• Subcellular Localization: GLD-1 is a cytoplasmic protein.

• Primary Identifier: Expr581
• Pattern: In adult hermaphrodites, the level of gld-1 mRNA increses steadily in the distal mitotic region, and remains high during oocyte formation. In contrast, GLD-1 protein declines once oocytes are formed.

• Primary Identifier: Expr10645
• Pattern: GLD-1 is expressed in a graded pattern with lower expression at the distal tip and higher expression at the mitotic zone/transition zone boundary.

• Primary Identifier: Expr1011240
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2030322
• 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: Expr2012086
• 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: Expr2792
• Pattern: gld-1 was highly expressed at the adult stage and at a decreased level in eggs.

• Primary Identifier: Expr1157510
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

26 GO Annotation

6 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00001595
• Start: 7695681
• End: 7698222
• Strand: 1

26 Ontology Annotations

2 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Proteins that showed differential expression in (B) let-7(mg279);[let-7 sponge] when comparing to (A) [let-7 sponge], and in (C) gld-1(op236); let-7(mg279);[let-7 sponge] when comparing to (A) [let-7 sponge]	N.A.	WBPaper00044501:gld-1_let-7_regulated
	948 reproductively enriched mRNAs that co-immunoprecipitate with GLD-1. To identify GLD-1 mRNA targets, authors performed immunoprecipitation (IP) of GLD-1, followed by microarray analysis of the co-IPed mRNAs (RIP-chip). Extracts from young adult transgenic worms expressing a rescuing FLAG and GFP-tagged GLD-1, hereafter referred to as tagged GLD-1, were subjected to IP in triplicate with anti-FLAG (aFLAG IP) or anti-MYC (aMYC IP) antibodies as controls. Comparison of aFLAG IP versus aMYC IP to input revealed a large population of GLD-1-associated transcripts. Authors additionally performed complementary aFLAG IPs upon worms expressing either tagged GLD-1(GGF IP) or non-tagged GLD-1(N2 IP). Comparing transcript 'IP-enrichment values' from both approaches revealed a correlation of 0.96, which indicated high reproducibility of GLD-1 association with specific mRNAs even on a quantitative level.	Authors calculated the mean IP enrichment from the two analyses and given a cutoff of three-fold, they identified 948 reproducibly enriched mRNAs (14.2%) from of a total of 6635 detected by the array.	WBPaper00037901:GLD-1_mRNA_targets

1 Sequence

• Length: 2542

1 Sequence Ontology Term