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Aliases for LRRC42 Gene

Aliases for LRRC42 Gene

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

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.

Additional gene information for LRRC42 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LRRC42 Gene

Genomics for LRRC42 Gene

GeneHancer (GH) Regulatory Elements for LRRC42 Gene

Promoters and enhancers for LRRC42 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I053942 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 570.1 -0.8 -765 5.4 HDGF SMAD1 ARID4B SIN3A YBX1 FEZF1 ZNF2 YY1 POLR2B ZNF766 HSPB11 LRRC42 MAGOH SSBP3-AS1 NDC1 CYB5RL PARS2 TTC4 TCEANC2 GC01P053939
GH01I054051 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 29.8 +107.1 107077 3.7 DMAP1 YY1 SLC30A9 E2F8 ZNF416 ZNF143 ZNF548 SP3 NFYC SSRP1 TCEANC2 MIR4781 TMEM59 MAGOH NDC1 SSBP3-AS1 HSPB11 LRRC42 PARS2 CYB5RL
GH01I053835 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 21.5 -108.9 -108945 4.1 MLX DMAP1 YBX1 IRF4 YY1 ZNF213 E2F8 ZNF143 SP3 MEF2D NDC1 MAGOH SSBP3-AS1 HSPB11 LRRC42 ECHDC2 ENSG00000256407 CYB5RL C1orf123 ENSG00000279049
GH01I054474 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 19.9 +530.1 530130 3.8 HDAC1 YBX3 HDGF ZNF473 ZSCAN4 NFXL1 ARID2 SMARCA5 MCM3 PHF21A NDC1 LRRC42 SSBP3-AS1 SSBP3 TCEANC2 LOC105378735 ENSG00000232245
GH01I054882 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 10.5 +940.1 940117 7.8 FOXA2 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ENSG00000233203 DHCR24 ENSG00000242396 SSBP3-AS1 HSPB11 ENSG00000279049 TMEM61 TTC22 PARS2 LRRC42
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around LRRC42 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LRRC42 gene promoter:

Genomic Locations for LRRC42 Gene

Genomic Locations for LRRC42 Gene
chr1:53,946,077-53,968,168
(GRCh38/hg38)
Size:
22,092 bases
Orientation:
Plus strand
chr1:54,411,750-54,433,841
(GRCh37/hg19)

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

Suggested Antigen Peptide Sequences for LRRC42 Gene

GenScript: Design optimal peptide antigens:

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

genes like me logo Genes that share phenotypes with LRRC42: view

Animal Model Products

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Gene Ontology (GO) - Molecular Function , 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

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

Unigene Clusters for LRRC42 Gene

Leucine rich repeat containing 42:
Representative Sequences:

Clone Products

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
ECgene alternative splicing isoforms for
LRRC42

Expression for LRRC42 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for LRRC42 Gene



Protein tissue co-expression partners for LRRC42 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LRRC42 Gene:

LRRC42

SOURCE GeneReport for Unigene cluster for LRRC42 Gene:

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

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 33 34
  • 99.14 (n)
dog
(Canis familiaris)
Mammalia LRRC42 33 34
  • 92.13 (n)
cow
(Bos Taurus)
Mammalia LRRC42 33 34
  • 91.74 (n)
rat
(Rattus norvegicus)
Mammalia Lrrc42 33
  • 86.62 (n)
mouse
(Mus musculus)
Mammalia Lrrc42 33 16 34
  • 84.96 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 72 (a)
OneToMany
-- 34
  • 58 (a)
OneToMany
chicken
(Gallus gallus)
Aves LRRC42 33 34
  • 71.97 (n)
lizard
(Anolis carolinensis)
Reptilia LRRC42 34
  • 62 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lrrc42 33
  • 57.46 (n)
Str.11262 33
zebrafish
(Danio rerio)
Actinopterygii lrrc42 33 34
  • 54.81 (n)
wufe17g08 33
Species where no ortholog for LRRC42 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 squirt (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)

Paralogs for LRRC42 Gene

No data available for Paralogs for LRRC42 Gene

Variants for LRRC42 Gene

Sequence variations from dbSNP and Humsavar for LRRC42 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000200831 -- 53,949,909(+) C/G intron_variant
rs1000234590 -- 53,965,946(+) T/C intron_variant
rs1000264949 -- 53,948,375(+) T/G intron_variant
rs1000493632 -- 53,964,923(+) G/A intron_variant
rs1000499240 -- 53,956,673(+) A/G intron_variant

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot 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. 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 58
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  3. 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 58
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 2 3 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for LRRC42 Gene

Sources for LRRC42 Gene

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