Aliases for LRRC42 Gene

Aliases for LRRC42 Gene

  • Leucine Rich Repeat Containing 42 2 3 5
  • Leucine-Rich Repeat-Containing Protein 42 3 4
  • DJ167A19.4 3
  • MGC8974 2
  • LRRC42 5

External Ids for LRRC42 Gene

Previous GeneCards Identifiers for LRRC42 Gene

  • GC01P054124
  • GC01P054184
  • GC01P054411
  • GC01P052527

Summaries for LRRC42 Gene

GeneCards Summary for LRRC42 Gene

LRRC42 (Leucine Rich Repeat Containing 42) is a Protein Coding gene.

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LRRC42 Gene

Genomics for LRRC42 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LRRC42 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LRRC42 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LRRC42

Top Transcription factor binding sites by QIAGEN in the LRRC42 gene promoter:
  • FOXO3
  • FOXO3a
  • FOXO3b
  • HNF-1
  • HNF-1A
  • MIF-1
  • Sox5
  • TBP
  • TFIID
  • ZID

Genomic Locations for LRRC42 Gene

Latest Assembly
chr1:53,946,085-53,968,168
(GRCh38/hg38)
Size:
22,084 bases
Orientation:
Plus strand

Previous Assembly
chr1:54,412,023-54,433,841
(GRCh37/hg19 by Entrez Gene)
Size:
21,819 bases
Orientation:
Plus strand

chr1:54,411,750-54,433,841
(GRCh37/hg19 by Ensembl)
Size:
22,092 bases
Orientation:
Plus strand

Genomic View for LRRC42 Gene

Genes around LRRC42 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRRC42 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRRC42 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LRRC42 Gene

Proteins for LRRC42 Gene

  • Protein details for LRRC42 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y546-LRC42_HUMAN
    Recommended name:
    Leucine-rich repeat-containing protein 42
    Protein Accession:
    Q9Y546
    Secondary Accessions:
    • D3DQ46
    • Q8N2Q8

    Protein attributes for LRRC42 Gene

    Size:
    428 amino acids
    Molecular mass:
    48571 Da
    Quaternary structure:
    No Data Available

neXtProt entry for LRRC42 Gene

Post-translational modifications for LRRC42 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LRRC42 Gene

No data available for DME Specific Peptides for LRRC42 Gene

Domains & Families for LRRC42 Gene

Gene Families for LRRC42 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for LRRC42 Gene

InterPro:
Blocks:
  • Leucine-rich repeat signature

Suggested Antigen Peptide Sequences for LRRC42 Gene

GenScript: Design optimal peptide antigens:
  • Leucine-rich repeat-containing protein 42 (LRC42_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9Y546

UniProtKB/Swiss-Prot:

LRC42_HUMAN :
  • Belongs to the LRRC42 family.
Family:
  • Belongs to the LRRC42 family.
genes like me logo Genes that share domains with LRRC42: view

Function for LRRC42 Gene

Phenotypes From GWAS Catalog for LRRC42 Gene

Gene Ontology (GO) - Molecular Function for LRRC42 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with LRRC42: view
genes like me logo Genes that share phenotypes with LRRC42: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRRC42

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LRRC42 Gene

Localization for LRRC42 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LRRC42 gene
Compartment Confidence
nucleus 3
cytosol 3

Subcellular locations from the

Human Protein Atlas (HPA)

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for LRRC42 Gene

Pathways & Interactions for LRRC42 Gene

PathCards logo

SuperPathways for LRRC42 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LRRC42 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for LRRC42 Gene

Drugs & Compounds for LRRC42 Gene

No Compound Related Data Available

Transcripts for LRRC42 Gene

mRNA/cDNA for LRRC42 Gene

2 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRRC42

Alternative Splicing Database (ASD) splice patterns (SP) for LRRC42 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10a · 10b · 10c
SP1: - - -
SP2: - -
SP3: -
SP4: - -
SP5:

Relevant External Links for LRRC42 Gene

GeneLoc Exon Structure for
LRRC42

Expression for LRRC42 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LRRC42 Gene

Protein differential expression in normal tissues from HIPED for LRRC42 Gene

This gene is overexpressed in Testis (31.0), Fetal testis (19.8), and Fetal ovary (18.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LRRC42 Gene



Protein tissue co-expression partners for LRRC42 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LRRC42

SOURCE GeneReport for Unigene cluster for LRRC42 Gene:

Hs.40094
genes like me logo Genes that share expression patterns with LRRC42: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for LRRC42 Gene

Orthologs for LRRC42 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LRRC42 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LRRC42 29 30
  • 99.14 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LRRC42 29 30
  • 92.13 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LRRC42 29 30
  • 91.74 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Lrrc42 29
  • 86.62 (n)
Mouse
(Mus musculus)
Mammalia Lrrc42 29 16 30
  • 84.96 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 30
  • 72 (a)
OneToMany
-- 30
  • 58 (a)
OneToMany
Chicken
(Gallus gallus)
Aves LRRC42 29 30
  • 71.97 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia LRRC42 30
  • 62 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia lrrc42 29
  • 57.46 (n)
Str.11262 29
Zebrafish
(Danio rerio)
Actinopterygii lrrc42 29 30
  • 54.81 (n)
OneToOne
wufe17g08 29
Species where no ortholog for LRRC42 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for LRRC42 Gene

ENSEMBL:
Gene Tree for LRRC42 (if available)
TreeFam:
Gene Tree for LRRC42 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LRRC42: view image
Alliance of Genome Resources:
Additional Orthologs for LRRC42

Paralogs for LRRC42 Gene

No data available for Paralogs for LRRC42 Gene

Variants for LRRC42 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for LRRC42 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for LRRC42 Gene

Variant ID Type Subtype PubMed ID
esv27044 CNV loss 19812545
nsv1011262 CNV gain 25217958
nsv1075933 CNV deletion 25765185
nsv1130903 CNV deletion 24896259
nsv546260 CNV gain+loss 21841781
nsv546261 CNV gain 21841781
nsv546262 CNV loss 21841781
nsv546263 CNV loss 21841781

Variation tolerance for LRRC42 Gene

Residual Variation Intolerance Score: 37.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.88; 35.14% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LRRC42 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LRRC42
Leiden Open Variation Database (LOVD)
LRRC42

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LRRC42 Gene

Disorders for LRRC42 Gene

Additional Disease Information for LRRC42

No disorders were found for LRRC42 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LRRC42 Gene

Publications for LRRC42 Gene

  1. Identification of a nuclear protein, LRRC42, involved in lung carcinogenesis. (PMID: 24806090) Fujitomo T … Nakamura Y (International journal of oncology 2014) 2 3
  2. Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries. (PMID: 16303743) Otsuki T … Isogai T (DNA research : an international journal for rapid publication of reports on genes and genomes 2005) 3 4
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  5. Systematic identification of cancer cell vulnerabilities to natural killer cell-mediated immune surveillance. (PMID: 31452512) Pech MF … Settleman J (eLife 2019) 3

Products for LRRC42 Gene

Sources for LRRC42 Gene