WormMine: Gene WBGene00003026

• WormBase Gene ID: WBGene00003026
• Gene Name: lin-41
• Sequence Name: C12C8.3
• Brief Description: lin-41 encodes a novel RBCC (Ring finger-B box-Coiled coil) protein that is a member of the NHL (NCL-1, HT2A, and LIN-41) family of proteins; lin-41 is a heterochronic gene required for temporal control of specific postembryonic cell fates; lin-41 is also required for proper male tail morphogenesis; lin-41 translation is negatively regulated during L4 and adult stages by the let-7 microRNA that binds to two sites in the lin-41 3'UTR; LIN-41 is a widely expressed cytoplasmic protein and negatively regulates post-transcriptional expression of LIN-29, a transcription factor required for adult cell fates.
• Organism: Caenorhabditis elegans
• Automated Description: Enables mRNA binding activity and translation repressor activity. Involved in several processes, including negative regulation of gene expression; nematode male tail tip morphogenesis; and regulation of developmental process. Acts upstream of or within positive regulation of transcription by RNA polymerase II. Located in cytoplasm and ribonucleoprotein granule. Expressed in several structures, including germ cell; hypodermal cell; intestine; neurons; and ventral nerve cord. Human ortholog(s) of this gene implicated in hydrocephalus. Is an ortholog of human TRIM71 (tripartite motif containing 71).
• Biotype: SO:0001217
• Genetic Position: I :3.75248 ±0.000711
• Length (nt): 7697

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00003026

Genomics

4 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:C12C8.3a.2	C12C8.3a.2	4631	I: 9334800-9341919
Transcript:C12C8.3b.2	C12C8.3b.2	4613	I: 9334806-9341919
Transcript:C12C8.3b.1	C12C8.3b.1	4785	I: 9334807-9342496
Transcript:C12C8.3a.1	C12C8.3a.1	4796	I: 9334808-9342496

Other

2 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:C12C8.3a	C12C8.3a	3444	I: 9335965-9336126
CDS:C12C8.3b	C12C8.3b	3432	I: 9335965-9336126

64 RNAi Result

• WBRNAi00096310
• WBRNAi00095492
• WBRNAi00096308
• WBRNAi00094734
• WBRNAi00061039
• WBRNAi00061040
• WBRNAi00024540
• WBRNAi00077068
• WBRNAi00077069
• WBRNAi00099772
• WBRNAi00100352
• WBRNAi00085490
• WBRNAi00065398
• WBRNAi00024541
• WBRNAi00040374
• WBRNAi00002947
• WBRNAi00076115
• WBRNAi00061029
• WBRNAi00028817
• WBRNAi00100726
• WBRNAi00071039
• WBRNAi00099570
• WBRNAi00099166
• WBRNAi00099368
• WBRNAi00078060
• WBRNAi00063924
• WBRNAi00096256
• WBRNAi00095873
• WBRNAi00100913
• WBRNAi00096515

158 Allele

• gk962858
• gk962706
• gk963902
• gk963849
• gk964316
• WBVar02066339
• tn1486
• tn1487
• tn1488
• tn1489
• tn1490
• tn1491
• tn1492
• tn1493
• tn1494
• tn1495
• tn1496
• tn1497
• tn1498
• tn1499
• tn1500
• tn1501
• tn1502
• tn1503
• WBVar02011913
• tn1504
• tn1505
• tn1506
• tn1507
• tn1508

1 Chromosome

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

1 Chromosome Location

• Feature . Primary Identifier: WBGene00003026
• Start: 9334800
• End: 9342496
• 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_9333044..9334799
• Length (nt): 1756
• Chromosome Location: I: 9333044-9334799
• Organism: Caenorhabditis elegans

215 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
	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:AVE-neuron_L1-larva_expressed
Bacteria: E.faecalis strain OG1RF	Transcripts that showed significantly increased expression after infection by E. faecalis OG1RF.	Ballgown was used to calculate differential expression of genes using FPKM data and to generate tables with fold change and P values. Genes were shortlisted with a cutoff of 2-fold change and P values of less than 0.05.	WBPaper00059754:E.faecalis_OG1RF_upregulated
Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours.	Transcripts that showed significantly decreased expression in N2 after animals were exposed to E. faecalis OG1RF for 16 hours comparing to exposure to E. Coli OP50.	Cuffcompare and Cuffdiff	WBPaper00056090:E.faecalis_downregulated_N2
	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 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 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
Bacteria diet: Escherichia coli HB101. Fed for 30 generations.	Transcripts that showed significantly decreased expression after fed by bacteria E. coli HB101 for 30 generations comparing to animals fed by E. coli OP50.	DESeq2 fold change > 2, p-value < 0.01.	WBPaper00061007:HB101_downregulated
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 12h), according to RNAseq.	Cuffdiff, ajusted p-value < 0.01.	WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h
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
	Transcripts that showed significantly increased expression in hrde-1(tm1200) animals, comparing to in N2, after growing at 25C for five generations (late generation).	CuffDiff2	WBPaper00051265:F4_hrde-1(tm1200)_upregulated
Bacteria infection: Staphylococcus aureus MW2. 4 hours of exposure.	Transcripts that showed significantly increased expression after N2 animals had 4 hours of infection by Staphylococcus aureus (MW2).	DEseq 1.18.0, adjusted p-value < 0.05.	WBPaper00056471:S.aureus-4h_upregulated_N2
	Transcripts that showed significantly increased expression in alg-1(gk214), comparing to in N2.	DESeq2, Fold change > 1.5.	WBPaper00051404:alg-1(gk214)_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
Heat Shock: 35C 4 hours at L4 larva stage.	Transcripts that showed significantly decreased expression after L4 larva N2 animals were heat stressed at 35C for 4 hours	DESeq2	WBPaper00057154:HeatShock_downregulated_mRNA

13 Expression Patterns

• Primary Identifier: Expr4467
• Remark: No detailed description on expression pattern in other life stage.
• Pattern: Expressed in main body hypodermis at L2/L3, ventral nerve cord at L4, lateral hypodermal cells at L2/L3, anterior neurons (not individually identified in this study) at L2/L3, L4 and adult, pharynx at L2/L3, L4 and adult, cells adjacent to posterior of gut around rectum during L4 and adult stage.

• Primary Identifier: Expr4468
• Remark: No detailed description on expression pattern in other life stage.
• Pattern: Expressed in main body hypodermis at L2/L3, ventral nerve cord at L4, anterior neurons (not individually identified in this study) at L2/L3, L4 and adult, intestine at L2/L3, L4 and adult, pharynx at L2/L3, L4 and adult.

• Primary Identifier: Expr1031416
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr15558

• Primary Identifier: Expr10882
• Pattern: The let-7 promoter drives GFP expression in AVM and ALM touch neurons in L2-stage and YA animals. Expression of the mature let-7 micro-RNA is almost undetectable from embryonic to L2 stages and becomes apparent at L3. lin-41 is broadly expressed in the nervous system at the L2 stage. GFP expression is seen in the head ganglion, tail neurons, SDQR, AVM, ALM, and ventral cord motor neurons.

• Primary Identifier: Expr14649
• Pattern: The lin-41 reporter allele showed broad expression in the nervous system from the L1 until the L4 stage in both sexes, when it becomes downregulated

• Primary Identifier: Expr12001
• Subcellular Localization: LIN-41 is strongly expressed in adult hermaphrodite germ cells beginning in mid-pachytene. LIN-41 protein levels rise dramatically at this time, increasing several-fold over a distance corresponding to just a few cell diameters. The timing of this rise consistently occurs just before the peak of MPK-1 mitogen-activated protein kinase (MAPK) activation in mid-pachytene, which may promote the progression of oogenic germ cells from early to late pachytene (Lee et al. 2007). LIN-41 is also abundantly expressed in diplotene and diakinesis-stage oocytes, but is generally reduced in abundance in the -1 oocyte as it undergoes meiotic maturation (14/17 oocytes identified), suggesting that LIN-41 may be eliminated at this time. Consistent with this interpretation, an N-terminal GFP::LIN-41 fusion protein, generated by CRISPR-Cas9 genome editing of the endogenous locus, is expressed in oocytes, disappears during meiotic maturation, and is absent from early embryos. Most LIN-41 is diffusely cytoplasmic, with a small amount of punctate LIN-41 that is most evident during pachytene. LIN-41 was also not detected in the germ lines of males or mid-L4 stage larvae, both of which have late pachytene-stage germ cells undergoing spermatogenesis, suggesting that pachytene-stage LIN-41 expression is restricted to germ cells committed to oogenesis. The primary, and possibly exclusive, site of LIN-41 expression in adults appears to be the oogenic germ line. LIN-41 expression in the C. elegans germ line is strongly associated, both developmentally and spatially, with the oogenic fate.

• Primary Identifier: Expr2013184
• 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: Expr15559
• Subcellular Localization: Perinuclear expression of LIN-41 proteins in a pair of AWC olfactory neurons (AWCleft and AWCright ), and FLP and PVD nociceptive neurons.

• Primary Identifier: Expr3680
• Pattern: A significant decline in lin-41 mRNA levels was observed during the later larval stages of development. The decrease in lin-41 mRNA correlates with the appearance of mature let-7 miRNA, which begins in the third larval stage.

• Primary Identifier: Expr1144436
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

• Primary Identifier: Expr1028758
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2031416
• 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).

26 GO Annotation

16 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00003026
• Start: 9334800
• End: 9342496
• Strand: -1

26 Ontology Annotations

3 Regulates Expr Cluster

Regulated By Treatment	Description	Algorithm	Primary Identifier
	Proteins that physically interacted with LIN-41-GFP, according to immunoprecipitation.	N.A.	WBPaper00051310:LIN-41_interacting
	Transcripts upregulated consistently in let-7(n2853), lin-41(xe11) and lin-41(xe11); let-7(n2853) mutant worms, compared to wild-type worms (on RPF, ribosome-protected fragments, level)	N.A.	WBPaper00050717:let-7(n2853)_lin-41(xe11)_upregulated
	Transcripts downregulated consistently in let-7(n2853), lin-41(xe11) and lin-41(xe11); let-7(n2853) mutant worms, compared to wild-type worms (on RPF, ribosome-protected fragments, level)	N.A.	WBPaper00050717:let-7(n2853)_lin-41(xe11)_downregulated

1 Sequence

• Length: 7697

1 Sequence Ontology Term

• Name: gene

11 Strains

• WBStrain00027307
• WBStrain00029079
• WBStrain00040229
• WBStrain00007159
• WBStrain00007161
• WBStrain00005706
• WBStrain00005714
• WBStrain00005178
• WBStrain00008564
• WBStrain00008559
• WBStrain00008560

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrI_9342497..9344723
• Length (nt): 2227
• Chromosome Location: I: 9342497-9344723
• Organism: Caenorhabditis elegans