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Aliases for LRRC39 Gene

Aliases for LRRC39 Gene

  • Leucine Rich Repeat Containing 39 2 3 5
  • Densin Hlg 4

External Ids for LRRC39 Gene

Previous GeneCards Identifiers for LRRC39 Gene

  • GC01M100327
  • GC01M100614
  • GC01M098737

Summaries for LRRC39 Gene

GeneCards Summary for LRRC39 Gene

LRRC39 (Leucine Rich Repeat Containing 39) is a Protein Coding gene. An important paralog of this gene is LRRC2.

Gene Wiki entry for LRRC39 Gene

Additional gene information for LRRC39 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LRRC39 Gene

Genomics for LRRC39 Gene

Regulatory Elements for LRRC39 Gene

Enhancers for LRRC39 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01H100046 1.4 FANTOM5 Ensembl ENCODE 16 +129.8 129824 4 HDAC1 PKNOX1 FOXA2 ZNF133 TCF12 POLR3A ATF7 RUNX3 IKZF2 ZNF202 SASS6 LRRC39 HNRNPA1P68 TRMT13 RTCA FRRS1 MFSD14A ENSG00000241073
GH01H100036 1.3 ENCODE dbSUPER 16.6 +139.5 139547 4 MLX ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 SP3 SP5 ZHX2 MFSD14A SASS6 LRRC39 TRMT13 SLC30A7 BRI3P1 RTCA AGL ENSG00000241073
GH01H099943 1.2 Ensembl ENCODE 14.1 +234.4 234384 1 HDAC1 PKNOX1 ATF1 ARNT CHAMP1 TCF12 GATA2 ZSCAN5C ATF7 NCOA1 LRRC39 SLC35A3 ENSG00000228084 FRRS1 GC01P099965 AGL
GH01H100028 0.9 FANTOM5 ENCODE 16.6 +149.4 149445 1 ZNF362 ATF1 ZBTB33 RUNX3 CREM LRRC39 RTCA FRRS1 CDC14A MFSD14A GC01P100031 RNU6-1318P
GH01H100077 0.7 ENCODE 17.2 +100.5 100451 0 HDGF SMARCA5 CHD1 JUNB RFX5 SP1 PRDM6 IKZF1 ETV6 RUNX3 LRRC39 SASS6 TRMT13 ENSG00000241073 MFSD14A
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around LRRC39 on UCSC Golden Path with GeneCards custom track

Genomic Location for LRRC39 Gene

Chromosome:
1
Start:
100,148,448 bp from pter
End:
100,178,273 bp from pter
Size:
29,826 bases
Orientation:
Minus strand

Genomic View for LRRC39 Gene

Genes around LRRC39 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRRC39 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRRC39 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LRRC39 Gene

Proteins for LRRC39 Gene

  • Protein details for LRRC39 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96DD0-LRC39_HUMAN
    Recommended name:
    Leucine-rich repeat-containing protein 39
    Protein Accession:
    Q96DD0
    Secondary Accessions:
    • B3KUD2
    • D3DT56
    • Q5VVK7

    Protein attributes for LRRC39 Gene

    Size:
    335 amino acids
    Molecular mass:
    38793 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for LRRC39 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LRRC39 Gene

Post-translational modifications for LRRC39 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LRRC39 Gene

No data available for DME Specific Peptides for LRRC39 Gene

Domains & Families for LRRC39 Gene

Gene Families for LRRC39 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for LRRC39 Gene

Suggested Antigen Peptide Sequences for LRRC39 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with LRRC39: view

No data available for UniProtKB/Swiss-Prot for LRRC39 Gene

Function for LRRC39 Gene

genes like me logo Genes that share phenotypes with LRRC39: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for LRRC39
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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 LRRC39 Gene

Localization for LRRC39 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 LRRC39 gene
Compartment Confidence
cytosol 4
nucleus 3
mitochondrion 1

Gene Ontology (GO) - Cellular Components for LRRC39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0031430 M band IEA --
genes like me logo Genes that share ontologies with LRRC39: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for LRRC39 Gene

Pathways & Interactions for LRRC39 Gene

SuperPathways for LRRC39 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LRRC39 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for LRRC39 Gene

Drugs & Compounds for LRRC39 Gene

No Compound Related Data Available

Transcripts for LRRC39 Gene

Unigene Clusters for LRRC39 Gene

Leucine rich repeat containing 39:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for LRRC39
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for LRRC39 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7
SP1: - -
SP2: -
SP3:

Relevant External Links for LRRC39 Gene

GeneLoc Exon Structure for
LRRC39
ECgene alternative splicing isoforms for
LRRC39

Expression for LRRC39 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LRRC39 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LRRC39 Gene

This gene is overexpressed in Muscle - Skeletal (x17.4), Heart - Left Ventricle (x13.4), and Heart - Atrial Appendage (x7.2).

Protein differential expression in normal tissues from HIPED for LRRC39 Gene

This gene is overexpressed in Gallbladder (15.6), Plasma (14.7), Rectum (10.9), and Prostate (10.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for LRRC39 Gene



Protein tissue co-expression partners for LRRC39 Gene

NURSA nuclear receptor signaling pathways regulating expression of LRRC39 Gene:

LRRC39

SOURCE GeneReport for Unigene cluster for LRRC39 Gene:

Hs.44277

Evidence on tissue expression from TISSUES for LRRC39 Gene

  • Muscle(2.2)
  • Heart(2.1)
genes like me logo Genes that share expression patterns with LRRC39: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LRRC39 Gene

Orthologs for LRRC39 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LRRC39 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LRRC39 33 34
  • 99.6 (n)
dog
(Canis familiaris)
Mammalia LRRC39 33 34
  • 91.94 (n)
cow
(Bos Taurus)
Mammalia LRRC39 33 34
  • 91.52 (n)
mouse
(Mus musculus)
Mammalia Lrrc39 33 16 34
  • 86.03 (n)
rat
(Rattus norvegicus)
Mammalia Lrrc39 33
  • 84.93 (n)
oppossum
(Monodelphis domestica)
Mammalia LRRC39 34
  • 82 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LRRC39 34
  • 80 (a)
OneToOne
chicken
(Gallus gallus)
Aves LRRC39 33 34
  • 69.85 (n)
lizard
(Anolis carolinensis)
Reptilia LRRC39 34
  • 68 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lrrc39 33
  • 61.17 (n)
zebrafish
(Danio rerio)
Actinopterygii lrrc39 33 34
  • 63.43 (n)
Species where no ortholog for LRRC39 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)
  • 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 LRRC39 Gene

ENSEMBL:
Gene Tree for LRRC39 (if available)
TreeFam:
Gene Tree for LRRC39 (if available)

Paralogs for LRRC39 Gene

Paralogs for LRRC39 Gene

(2) SIMAP similar genes for LRRC39 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with LRRC39: view

Variants for LRRC39 Gene

Sequence variations from dbSNP and Humsavar for LRRC39 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs1000010624 -- 100,156,749(+) ATTTG(A/G)TAGTT intron-variant
rs1000020668 -- 100,161,281(+) TTGGT(A/G)ATCAC intron-variant
rs1000091392 -- 100,150,171(+) AGAAC(A/G)GTTCC intron-variant, nc-transcript-variant, downstream-variant-500B, utr-variant-3-prime
rs1000112530 -- 100,168,244(+) AGACA(A/C)ATTTA intron-variant
rs1000248172 -- 100,164,866(+) CACCA(C/T)GCCCA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for LRRC39 Gene

Variant ID Type Subtype PubMed ID
nsv2121 CNV insertion 18451855
nsv830804 CNV gain 17160897

Variation tolerance for LRRC39 Gene

Residual Variation Intolerance Score: 72.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.28; 62.68% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LRRC39 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LRRC39

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LRRC39 Gene

Disorders for LRRC39 Gene

Relevant External Links for LRRC39

Genetic Association Database (GAD)
LRRC39
Human Genome Epidemiology (HuGE) Navigator
LRRC39
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LRRC39

No disorders were found for LRRC39 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LRRC39 Gene

Publications for LRRC39 Gene

  1. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 2 3 4 60
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 45 60
  3. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 60
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60
  5. 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 60

Products for LRRC39 Gene

Sources for LRRC39 Gene

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