This gene encodes a protein containing NCL-1, HT2A and Lin-41 (NHL) family repeats. Mammalian NHL-repeat containing proteins may be involved in a variety of enzymatic processes, including protein modification through ubiquitination. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Aug 2012] See more...

Aliases for NHLRC3 Gene

Aliases for NHLRC3 Gene

  • NHL Repeat Containing 3 2 3 5
  • NHL Repeat-Containing Protein 3 3 4
  • NHLRC3 5

External Ids for NHLRC3 Gene

Previous GeneCards Identifiers for NHLRC3 Gene

  • GC13P038512
  • GC13P039612
  • GC13P020412

Summaries for NHLRC3 Gene

Entrez Gene Summary for NHLRC3 Gene

  • This gene encodes a protein containing NCL-1, HT2A and Lin-41 (NHL) family repeats. Mammalian NHL-repeat containing proteins may be involved in a variety of enzymatic processes, including protein modification through ubiquitination. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Aug 2012]

GeneCards Summary for NHLRC3 Gene

NHLRC3 (NHL Repeat Containing 3) is a Protein Coding gene. Among its related pathways are Innate Immune System.

Additional gene information for NHLRC3 Gene

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NHLRC3 Gene

Genomics for NHLRC3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for NHLRC3 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
GH13J039034 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 622 -0.6 -573 7.1 SP1 CREB1 GATAD2A PRDM10 ZNF629 REST TFE3 ZNF692 POLR2A ZNF7 PROSER1 NHLRC3 NONHSAG013280.2 lnc-STOML3-7 LHFPL6 STOML3
GH13J039042 Promoter 0.3 EPDnew 600.7 +4.4 4354 0.1 NHLRC3 NONHSAG013280.2 ENSG00000273507 LOC112268119
GH13J039483 Enhancer 0.9 FANTOM5 Ensembl ENCODE 19.4 +447.1 447095 4.4 CEBPB ZNF26 JUND TBX21 SMARCA4 BHLHE40 NHLRC3 LHFPL6 piR-57133-134 piR-31534-153 LOC112268119
GH13J039385 Enhancer 1 Ensembl ENCODE 15 +347.6 347595 2.2 PRDM10 ZNF629 PRDM1 ZIC2 POLR2A ZNF561 SCRT2 ZBTB44 ZNF140 TCF7L2 NHLRC3 COG6 piR-48325-028 L13714-102 LHFPL6 LOC112268119
GH13J039493 Enhancer 1 Ensembl ENCODE CraniofacialAtlas 10.9 +461.5 461495 12.8 CEBPG TEAD4 ZIC2 POLR2A SCRT2 CEBPB EZH2 USF1 YY1 MYC NHLRC3 LOC105370170 piR-57133-134 LHFPL6 LOC112268119
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NHLRC3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NHLRC3

Top Transcription factor binding sites by QIAGEN in the NHLRC3 gene promoter:
  • AREB6
  • E47
  • FOXO3
  • FOXO3a
  • FOXO3b
  • Hand1
  • HSF2
  • NF-kappaB1
  • Nkx2-2
  • SRY

Genomic Locations for NHLRC3 Gene

Genomic Locations for NHLRC3 Gene
chr13:39,038,306-39,050,109
(GRCh38/hg38)
Size:
11,804 bases
Orientation:
Plus strand
chr13:39,612,443-39,624,246
(GRCh37/hg19)
Size:
11,804 bases
Orientation:
Plus strand

Genomic View for NHLRC3 Gene

Genes around NHLRC3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NHLRC3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NHLRC3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NHLRC3 Gene

Proteins for NHLRC3 Gene

  • Protein details for NHLRC3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5JS37-NHLC3_HUMAN
    Recommended name:
    NHL repeat-containing protein 3
    Protein Accession:
    Q5JS37
    Secondary Accessions:
    • B2RTZ2
    • B4DTL0
    • Q69YI9

    Protein attributes for NHLRC3 Gene

    Size:
    347 amino acids
    Molecular mass:
    38283 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for NHLRC3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NHLRC3 Gene

Post-translational modifications for NHLRC3 Gene

  • Glycosylation at Asn32, Asn101, Asn206, and Asn278
  • Ubiquitination at Lys86
  • Modification sites at PhosphoSitePlus

Other Protein References for NHLRC3 Gene

No data available for DME Specific Peptides for NHLRC3 Gene

Domains & Families for NHLRC3 Gene

Gene Families for NHLRC3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for NHLRC3 Gene

Suggested Antigen Peptide Sequences for NHLRC3 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ52655 (B4DTL0_HUMAN)
  • NHL repeat-containing protein 3 (NHLC3_HUMAN)
genes like me logo Genes that share domains with NHLRC3: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for NHLRC3 Gene

Function for NHLRC3 Gene

Phenotypes From GWAS Catalog for NHLRC3 Gene

Gene Ontology (GO) - Molecular Function for NHLRC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA --
GO:0061630 ubiquitin protein ligase activity IBA 21873635
genes like me logo Genes that share ontologies with NHLRC3: view
genes like me logo Genes that share phenotypes with NHLRC3: view

Animal Model Products

CRISPR Products

miRNA for NHLRC3 Gene

miRTarBase miRNAs that target NHLRC3

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NHLRC3

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NHLRC3 Gene

Localization for NHLRC3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NHLRC3 Gene

Secreted.

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 NHLRC3 gene
Compartment Confidence
extracellular 4
lysosome 4
plasma membrane 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 0
cytosol 0
golgi apparatus 0

Gene Ontology (GO) - Cellular Components for NHLRC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0035578 azurophil granule lumen TAS --
genes like me logo Genes that share ontologies with NHLRC3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for NHLRC3 Gene

Pathways & Interactions for NHLRC3 Gene

PathCards logo

SuperPathways for NHLRC3 Gene

genes like me logo Genes that share pathways with NHLRC3: view

Pathways by source for NHLRC3 Gene

3 Reactome pathways for NHLRC3 Gene

Gene Ontology (GO) - Biological Process for NHLRC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000209 protein polyubiquitination IBA 21873635
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process IBA 21873635
GO:0043312 neutrophil degranulation TAS --
genes like me logo Genes that share ontologies with NHLRC3: view

No data available for SIGNOR curated interactions for NHLRC3 Gene

Drugs & Compounds for NHLRC3 Gene

No Compound Related Data Available

Transcripts for NHLRC3 Gene

mRNA/cDNA for NHLRC3 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NHLRC3

Alternative Splicing Database (ASD) splice patterns (SP) for NHLRC3 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b · 3c ^ 4a · 4b ^ 5a · 5b · 5c ^ 6 ^ 7
SP1: - - - -
SP2: - - - - -
SP3: - - - - -
SP4:
SP5: - -
SP6:

Relevant External Links for NHLRC3 Gene

GeneLoc Exon Structure for
NHLRC3

Expression for NHLRC3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for NHLRC3 Gene

Protein differential expression in normal tissues from HIPED for NHLRC3 Gene

This gene is overexpressed in Urine (14.3), Testis (7.3), and Oral epithelium (6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for NHLRC3 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NHLRC3

SOURCE GeneReport for Unigene cluster for NHLRC3 Gene:

Hs.507783
genes like me logo Genes that share expression patterns with NHLRC3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for NHLRC3 Gene

Orthologs for NHLRC3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for NHLRC3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia NHLRC3 30 31
  • 99.9 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia NHLRC3 30 31
  • 89.82 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia NHLRC3 30 31
  • 86.76 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Nhlrc3 30 17 31
  • 83.19 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Nhlrc3 30
  • 82.9 (n)
Oppossum
(Monodelphis domestica)
Mammalia NHLRC3 31
  • 78 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia NHLRC3 31
  • 70 (a)
OneToOne
Chicken
(Gallus gallus)
Aves NHLRC3 30 31
  • 68.62 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia NHLRC3 31
  • 61 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia nhlrc3 30
  • 63.85 (n)
Zebrafish
(Danio rerio)
Actinopterygii NHLRC3 31
  • 53 (a)
OneToOne
Species where no ortholog for NHLRC3 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)
  • 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 NHLRC3 Gene

ENSEMBL:
Gene Tree for NHLRC3 (if available)
TreeFam:
Gene Tree for NHLRC3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NHLRC3: view image

Paralogs for NHLRC3 Gene

(1) SIMAP similar genes for NHLRC3 Gene using alignment to 2 proteins:

  • NHLC3_HUMAN
  • C9J973_HUMAN
genes like me logo Genes that share paralogs with NHLRC3: view

No data available for Paralogs for NHLRC3 Gene

Variants for NHLRC3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NHLRC3 Gene

SNP ID Clinical significance and condition Chr 13 pos Variation AA Info Type
rs9603498 - p.Leu221Arg

Additional dbSNP identifiers (rs#s) for NHLRC3 Gene

Structural Variations from Database of Genomic Variants (DGV) for NHLRC3 Gene

Variant ID Type Subtype PubMed ID
nsv1035255 CNV gain 25217958

Variation tolerance for NHLRC3 Gene

Residual Variation Intolerance Score: 87.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.20; 52.18% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NHLRC3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NHLRC3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NHLRC3 Gene

Disorders for NHLRC3 Gene

Additional Disease Information for NHLRC3

No disorders were found for NHLRC3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for NHLRC3 Gene

Publications for NHLRC3 Gene

  1. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3
  2. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin EL … Gygi SP (Cell 2015) 3
  3. Proteomic analysis of podocyte exosome-enriched fraction from normal human urine. (PMID: 23376485) Prunotto M … Moll S (Journal of proteomics 2013) 3
  4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. (PMID: 21873635) Gaudet P … Thomas PD (Briefings in bioinformatics 2011) 3
  5. The full-ORF clone resource of the German cDNA Consortium. (PMID: 17974005) Bechtel S … Schupp I (BMC genomics 2007) 4

Products for NHLRC3 Gene

Sources for NHLRC3 Gene