WormMine

WSWS298

An integrated data resource for C. elegans and related nematodes

Gene :

WormBase Gene ID  ? WBGene00003071 Gene Name  lrp-1
Sequence Name  ? F29D11.1 Brief Description  lrp-1 encodes a low-density lipoprotein (LDL) receptor-like protein most closely related to the vertebrate gp330/megalin/LRP-2 proteins; during development, lrp-1 activity is required in the hyp7 syncytium for completion of molting and for growth beyond the third larval stage; LRP-1 is expressed on the apical surface of the hyp6 and hyp7 syncytia in hermaphrodites and males from hatching through adulthood; as sterol starvation mimics the lrp-1 mutant phenotype, LRP-1 is likely to function as a receptor for sterols normally endocytosed by the hyp7 syncytium.
Organism  Caenorhabditis elegans Automated Description  Enables lipoprotein particle receptor activity. Involved in several processes, including ecdysis, collagen and cuticulin-based cuticle; nematode larval development; and regulation of locomotion. Located in apical plasma membrane and endocytic vesicle. Expressed in head; hyp6; hyp7 syncytium; and hypodermal cell. Human ortholog(s) of this gene implicated in Donnai-Barrow syndrome and autoimmune thyroiditis. Is an ortholog of human LRP2 (LDL receptor related protein 2).
Biotype  SO:0001217 Genetic Position  I :2.21043 ±0.000575
Length (nt)  ? 19968
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Lists
This Gene is in one list:
metrics_list_union (10192)

1 Organism

Name Taxon Id
Caenorhabditis elegans 6239

1 Synonyms

Value
WBGene00003071

Genomics

1 Transcripts

WormMine ID Sequence Name Length (nt) Chromosome Location
Transcript:F29D11.1.1 F29D11.1.1 14711   I: 7614176-7634143
 

Other

1 CDSs

WormMine ID Sequence Name Length (nt) Chromosome Location
CDS:F29D11.1 F29D11.1 14262   I: 7614271-7614361

24 RNAi Result

WormBase ID
WBRNAi00063260
WBRNAi00025311
WBRNAi00025312
WBRNAi00061220
WBRNAi00067051
WBRNAi00067532
WBRNAi00067851
WBRNAi00067920
WBRNAi00067951
WBRNAi00067958
WBRNAi00068123
WBRNAi00007430
WBRNAi00003528
WBRNAi00066787
WBRNAi00063259
WBRNAi00102158
WBRNAi00109587
WBRNAi00109198
WBRNAi00109393
WBRNAi00109296
WBRNAi00109490
WBRNAi00045927
WBRNAi00102157
WBRNAi00063261

210 Allele

Public Name
gk962858
gk962706
gk963902
gk963849
gk963871
gk963872
WBVar01694822
WBVar01712963
WBVar01826412
gk317492
gk939988
gk519322
gk939989
gk632460
gk529575
gk815233
gk422064
gk372047
gk384985
gk544978
gk533947
gk648436
gk871279
gk562816
gk495783
gk559906
gk609453
gk802886
ttTi40060
gk664521

1 Chromosome

WormBase ID Organism Length (nt)
I Caenorhabditis elegans 15072434  

1 Chromosome Location


Feature . Primary Identifier 		Start End Strand
WBGene00003071 7614176 7634143 1

4 Data Sets

Name URL
WormBaseAcedbConverter  
GO Annotation data set  
C. elegans genomic annotations (GFF3 Gene)  
Panther orthologue and paralogue predictions  

1 Downstream Intergenic Region

WormBase ID Name Sequence Name Length (nt) Chromosome Location Organism
intergenic_region_chrI_7634144..7634491   348 I: 7634144-7634491 Caenorhabditis elegans

259 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 expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons. DESeq. False discovry rate (FDR) < 0.1. WBPaper00048988:neuron_expressed
  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 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 that showed significantly increased expression in ogt-1(ok1474) neuronal cells isolated by FACs comparing to in FACs isolated neuronal cells from wild type. DESeq2, fold change > 2, FDR < 0.05. WBPaper00066485:ogt-1(ok1474)_upregulated_neuron
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
  Transcripts that showed significantly decreased expression in eat-2(ad465) comparing to in N2. DESeq2 1.30.1, fold change > 2, FDR < 0.05. WBPaper00066890:eat-2(ad465)_downregulated
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
  Transcripts that showed significantly increased expression in eif-2alpha(RNAi) animals at N2 background. DESeq2, fold change > 2 and p-value < 0.01. WBPaper00067953:eif-2alpha(RNAi)_upregulated_N2
  Transcripts that showed significantly increased expression in eif-2alpha(RNAi) animals at zip-2(tm4248) background. DESeq2, fold change > 2 and p-value < 0.01. WBPaper00067953:eif-2alpha(RNAi)_upregulated_zip-2(tm4248)
  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
  Proteins interacting with NHR-49-GFP according to co-IP and LC-MS. N.A. WBPaper00064071:NHR-49_interacting
  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
Bacteria: Pseudomonas donghuensis HYS Transcripts that showed significantly increased expression after 24 hours of infection by Pseudomonas donghuensis HYS with deletion of ferric uptake regulator (FUR), comparing to control animals exposed to OP50. DESeq2, fold change > 2, FDR < 0.05. WBPaper00068216:FUR_vs_OP50_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 detected in germline isolated from day-1 adult hermaphrodite animals. All three experiments have CPM >= 1. WBPaper00067147:germline_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 hrde-1(tm1200) animals, comparing to in N2, after growing at 25C for five generations (late generation). CuffDiff2 WBPaper00051265:F4_hrde-1(tm1200)_upregulated
  Transcripts that showed significantly increased expression in exos-8(RNAi) animals. fold change > 2, FDR < 0.05 WBPaper00068292:exos-8(RNAi)_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
starvation 12 hours Transcripts that showed significantly increased expression in dissected intestines of N2 L1 larva that were starved for 12 hours, comparing to fed animals. EdgeR, FDR < 0.05, fold change >= 2. WBPaper00067259:starvation_upregulated_intestine
  Genes that showed significantly increased expression in daf-2(e1370);hel-1(gk148684) comparing to in hel-1(gk148684) To identify DEGs, Students t test and the log2 median ratio test were performed to compute t values and median ratios for all the annotated genes. The adjusted P values from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjusted P values from the individual tests were combined to compute the overall P values using Stouffers method , and genes with overall P < 0.05 and fold change > 1.5 were selected as DEGs. WBPaper00047131:daf-2(e1370)_upregulated_hel-1(gk148684)-background
  Genes that showed significantly increased expression in daf-2(e1370) comparing to in N2. To identify DEGs, Students t test and the log2 median ratio test were performed to compute t values and median ratios for all the annotated genes. The adjusted P values from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjusted P values from the individual tests were combined to compute the overall P values using Stouffers method , and genes with overall P < 0.05 and fold change > 1.5 were selected as DEGs. WBPaper00047131:daf-2(e1370)_upregulated_N2-background
  Transcripts that showed significantly decreased expression in N2 animals exposed to 0.1mM Paraquat from hatching to reaching adult stage. DESeq2 version 1.22.2, p < 0.05 WBPaper00064716:paraquat_downregulated
  Transcripts that showed signifcantly increased expression in ubr-5(miy31) injected with empty vector comparing to in N2 animals injected with empty vector at L1 larva stage and collected at L4 larva stage. FDR < 0.05, fold change > 2 WBPaper00067368:ubr-5(miy31)_upregulated_N2
  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 increased expression after 24-hour exposure to 10uM benzyl butyl phthalate (BBP) in col-121(nx3) animals. DESeq2v1.38.3, FDR < 0.05 WBPaper00067417:benzyl-butyl-phthalate_regulated
  Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage. DESeq WBPaper00053302:stavudine_24h_regulated

12 Expression Patterns

Remark Reporter Gene Primary Identifier Pattern Subcellular Localization
    Expr1031446 Tiling arrays expression graphs  
Strain: BC13051 [lrp-1::gfp] transcriptional fusion. PCR products were amplified using primer A: 5' [TTCGTTTTGAAATGAGTCATCTGT] 3' and primer B 5' [TAATTATTCTCGAAGCATTTGATG] 3'. Expr5915 Adult Expression: hypodermis; unidentified cells in head; Larval Expression: hypodermis;  
No GO_term assigned.   Expr1296 Stained hyp6 and hyp7. Staining is confined to the dorsal and ventral ridges and to wider sections that are adjacent to the lateral seam cells, which themselves fail to stain. Therefore, the regions of staining correspond to the thick regions of this epidermis (with respect to a cross-sectional view of worms); staining is absent from longitudinal bands that correspond to the thin regions of hyp7 to which body muscles attach. The staining is evident in both sexes at hatching, in each of the four larval stages, and in adults. The staining is often brighter in hyp6 in L1 larvae and in the posterior part of hyp7 in adult males. Most of the staining is punctate, has an appearance consistent with circular or spheroidal aggregates of the protein, and is evident only in hyp6 and hyp7.
    Expr10654 LRP-1::GFP is enriched in hyp7. LRP-1::GFP localizes to the apical region of the cell, similar to endogenous LRP-1 (Yochem et al., 1999).
    Expr14967 Consistent with previous reports, LRP-1::GFP was expressed in wild-type in a punctate pattern in the apical epidermis of larvae and adults.  
    Expr2013283 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).  
    Expr1018593 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012  
Original chronogram file: chronogram.2431.xml [F29D11.1:gfp] transcriptional fusion. Chronogram1310    
    Expr2031514 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).  
    Expr1149827 Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015  
Original chronogram file: chronogram.2128.xml [F29D11.1:gfp] transcriptional fusion. Chronogram1062    
Original chronogram file: chronogram.387.xml [F29D11.1:gfp] transcriptional fusion. Chronogram1513    

17 GO Annotation

Annotation Extension Qualifier
  involved_in
  enables
  enables
  enables
  located_in
  involved_in
  involved_in
  involved_in
  involved_in
  involved_in
  involved_in
  involved_in
  located_in
  located_in
  located_in
  located_in
  located_in

12 Homologues

Type
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue
orthologue

1 Locations


Feature . Primary Identifier 		Start End Strand
WBGene00003071 7614176 7634143 1

17 Ontology Annotations

Annotation Extension Qualifier
  involved_in
  enables
  enables
  enables
  located_in
  involved_in
  involved_in
  involved_in
  involved_in
  involved_in
  involved_in
  involved_in
  located_in
  located_in
  located_in
  located_in
  located_in

0 Regulates Expr Cluster

1 Sequence

Length
19968

1 Sequence Ontology Term

Identifier Name Description
gene  

5 Strains

WormBase ID
WBStrain00024195
WBStrain00026497
WBStrain00062660
WBStrain00002462
WBStrain00003528

1 Upstream Intergenic Region

WormBase ID Name Sequence Name Length (nt) Chromosome Location Organism
intergenic_region_chrI_7611316..7614175   2860 I: 7611316-7614175 Caenorhabditis elegans