WormMine: Gene WBGene00002054

• WormBase Gene ID: WBGene00002054
• Gene Name: ifb-2
• Sequence Name: F10C1.7
• Brief Description: ifb-2 encodes an intermediate filament protein; IFB-2 is expressed exclusively in the intestine and functions as a structural component of the intestinal terminal web; within the terminal web, IFB-2 localizes to a discrete substructure known as the endotube.
• Organism: Caenorhabditis elegans
• Automated Description: Predicted to be a structural constituent of cytoskeleton. Predicted to be involved in several processes, including heterochromatin formation; nucleus organization; and protein localization to nuclear envelope. Located in apical cortex; cell junction; and terminal web. Expressed in intestine. Human ortholog(s) of this gene implicated in partial lipodystrophy; primary autosomal recessive microcephaly; and progressive myoclonus epilepsy 9. Is an ortholog of human LMNB2 (lamin B2).
• Biotype: SO:0001217
• Genetic Position: II :-0.954772 ±0.000663
• Length (nt): 3953

1 Organism

• Name: Caenorhabditis elegans
• Taxon Id: 6239

1 Synonyms

• Value: WBGene00002054

Genomics

3 Transcripts

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
Transcript:F10C1.7c.1	F10C1.7c.1	1755	II: 5750188-5754140
Transcript:F10C1.7a.1	F10C1.7a.1	1804	II: 5750190-5754140
Transcript:F10C1.7e.1	F10C1.7e.1	1734	II: 5750200-5753978

Other

3 CDSs

WormMine ID	Sequence Name	Length (nt)	Chromosome Location
CDS:F10C1.7a	F10C1.7a	1632	II: 5750200-5750263
CDS:F10C1.7c	F10C1.7c	1581	II: 5750200-5750263
CDS:F10C1.7e	F10C1.7e	1734	II: 5750200-5750263

10 RNAi Result

• WBRNAi00044220
• WBRNAi00007219
• WBRNAi00030750
• WBRNAi00062647
• WBRNAi00062648
• WBRNAi00113732
• WBRNAi00062659
• WBRNAi00062660
• WBRNAi00113728
• WBRNAi00065111

88 Allele

• gk963801
• gk963053
• gk964349
• WBVar01826582
• gk143560
• gk143559
• gk143562
• WBVar01413459
• gk143561
• WBVar02002719
• gk143556
• ok2420
• gk143558
• gk143557
• WBVar00103943
• WBVar00103942
• gk143564
• WBVar02120625
• gk143563
• WBVar01934744
• WBVar01306304
• WBVar01306303
• WBVar01306302
• WBVar01306301
• WBVar01306308
• WBVar01306307
• WBVar01306305
• WBVar02097676
• WBVar01306312
• WBVar01306311

1 Chromosome

• WormBase ID: II
• Organism: Caenorhabditis elegans
• Length (nt): 15279421

1 Chromosome Location

• Feature . Primary Identifier: WBGene00002054
• Start: 5750188
• End: 5754140
• 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_chrII_5754141..5754467
• Length (nt): 327
• Chromosome Location: II: 5754141-5754467
• Organism: Caenorhabditis elegans

279 Expression Clusters

Regulated By Treatment	Description	Algorithm	Primary Identifier
	oocyte proteins identified by two or more unique peptides during proteomics study.	In the pooled data set, 1453 C. elegans proteins were identified with a probability >= 0.9 according to ProteinProphet, of which 1165 proteins were identified by more than one unique peptide.	WBPaper00038289:oocyte_protein
	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 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 no food was present	DESeq(version 1.10.1), FDR < 0.05.	WBPaper00050726:OsmoticStress_regulated_NoFood
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
	Genes that showed significantly increased expression in wrn-1(gk99) comparing to in N2, according to RNAseq.	DESeq was used to calculate the fold changes, log fold changes, and significance of the changes for each comparison.	WBPaper00045934:wrn-1(gk99)_upregulated
	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 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 expressed in NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging.	Cufflinks FPKM value >=1.	WBPaper00050990:NMDA-neuron_expressed
	Genes up regulated in alg-1(gk214) comparing to in N2.	Differential expression was assessed using an empirical Bayes statistics using the eBayes function.	WBPaper00040823:alg-1(gk214)_upregulated
	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 old adults stage (214 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_aging
	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 that showed significantly increased expression in rrf-3(pk1426) comparing to in N2 at embryo stage.	DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01.	WBPaper00056169:rrf-3(pk1426)_upregulated_embryo
	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

11 Expression Patterns

• Primary Identifier: Expr1031207
• Pattern: Tiling arrays expression graphs

• Primary Identifier: Expr8185
• Remark: Picture: Fig. 1.
• Subcellular Localization: Anti-IFB-2 fluorescence was detectable diffusely in the cytoplasm of intestinal cells accumulating over time in the sub-apical domain next to the newly forming lumen (e.g., plum stage). Anti-IFC-2 antibodies reacted only very weakly with the intestinal cells at plum stage although co-distribution with anti-IFB-2 was detectable in some sub-apical areas. The major IFC-2 immunofluorescence, however, was seen in hypodermal cells presenting a multipunctate staining of cell borders indicating a junctional localization. In subsequent stages, anti-IFB-2 reactivity further concentrated in the periluminal compartment, i.e., in the electron-dense endotube ultrastructure. Strongest immunofluorescence was noted in junctional regions due to the localization of IFB-2 along the entire junctional complex. In addition, multiple cytoplasmic puncta were seen that had not been described previously. These fluorescent structures began to accumulate in L3-larvae and were most abundant in old adults with a predilection for the posterior intestine. The anti-IFC-2-staining gradually increased in the intestine becoming quite prominent in L3-larvae in which it presented a very similar distribution to anti-IFB-2 fluorescence although diffuse cytoplasmic and junctional staining were more pronounced. In adult intestines anti-IFC-2 fluorescence was essentially identical to that of anti-IFB-2.

• Primary Identifier: Expr8186
• Remark: Overall, IFB-2::CFP fluorescence matched almost completely that of anti-IFC-2 (see Expr8185). Picture: Figure 2, Figure 3, Movies 1, 2
• Pattern: The fluorescence of the fusion polypeptides was restricted to intestinal cells presenting a characteristic endotube-like sub-apical distribution.
• Subcellular Localization: In adult worms, most of the fluorescence was concentrated in the sub-apical cytoplasm forming a dense fibrous meshwork with regularly spaced fenestrations. Substantial enrichment was noted in junctional areas, where it decorated the entire junctional complex as seen in the close-up of the adjoining lateral membranes. Furthermore, multiple fluorescent cytoplasmic granules were noted.

• Primary Identifier: Expr15262
• Pattern: The expression of IFB-2, IFC-1, IFD-1, IFD-2 and IFP-1 is mostly, if not completely restricted to the intestine.

• Primary Identifier: Expr2913
• Remark: MH33 antigen = ifb-2
• Pattern: MH33 reactivity in the adult worm is completely restricted to the central region of the intestine, apparently surrounding the intestinal lumen. This is seen more clearly with the isolated adult intestine: MH33 reacts with a tubular structure that can often be seen protruding from the cut end of a dissected intestine where the gut cell cytoplasm has apparently dissociated. This structure presumably corresponds to the ``endotube'' described in the intestines of many larger nematodes. Immunoelectron microscopy shows that MH33 reacts exclusively with a discrete circumferential layer within the terminal web, closely underlying the intestinal microvillar brush border. The MH33 reactive layer continues directly into the electron dense regions that define the CeAJ and that join adjacent gut cells.

• Primary Identifier: Expr3396
• Remark: The transformation experiments with the B2-promoter gfp reporters as well as with the B2-promoter/cDNA/gfp reporters fully confirmed these results.
• Pattern: Expression is exclusively seen in the terminal web of the intestinal cells of the embryo starting in the bean developmental stage. The same expression pattern was also detected in all larval developmental stages and in adults.

• Primary Identifier: Expr14279
• Pattern: Animals grown on control bacteria (OP50, control JM103) reach adulthood and display smooth periluminal localization of IFC-2a::YFP in the intestine indistinguishable from IFB-2a::CFP.

• Primary Identifier: Expr1024793
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012

• Primary Identifier: Expr2012680
• 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: Expr2030916
• 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: Expr1148179
• Pattern: Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015

18 GO Annotation

13 Homologues

1 Locations

• Feature . Primary Identifier: WBGene00002054
• Start: 5750188
• End: 5754140
• Strand: 1

18 Ontology Annotations

0 Regulates Expr Cluster

1 Sequence

• Length: 3953

1 Sequence Ontology Term

• Name: gene

1 Strains

• WBStrain00036909

1 Upstream Intergenic Region

• WormBase ID: intergenic_region_chrII_5750030..5750187
• Length (nt): 158
• Chromosome Location: II: 5750030-5750187
• Organism: Caenorhabditis elegans