The protein encoded by this gene is part of the SMC5-6 chromatin reorganizing complex and is a member of the MAGE superfamily. This is an intronless gene. [provided by RefSeq, May 2011] See more...

Aliases for NSMCE3 Gene

Aliases for NSMCE3 Gene

  • NSE3 Homolog, SMC5-SMC6 Complex Component 2 3 5
  • MAGEG1 2 3 4
  • HCA4 2 3 4
  • Non-Structural Maintenance Of Chromosomes Element 3 Homolog 3 4
  • Hepatocellular Carcinoma-Associated Protein 4 3 4
  • Necdin-Like 2, SMC5-SMC6 Complex Component 2 3
  • Melanoma-Associated Antigen G1 3 4
  • Non-SMC Element 3 Homolog 3 4
  • Necdin-Like Protein 2 3 4
  • MAGE-G1 Antigen 3 4
  • MAGEL3 2 3
  • NDNL2 3 4
  • NSE3 2 3
  • Hepatocellular Carcinoma-Associated Protein HCA4 3
  • Melanoma Antigen, Family G, 1 3
  • Necdin-Like Gene 2 3
  • Necdin-Like 2 2
  • NSMCE3 5
  • LICS 3

External Ids for NSMCE3 Gene

Previous HGNC Symbols for NSMCE3 Gene

  • NDNL2

Summaries for NSMCE3 Gene

Entrez Gene Summary for NSMCE3 Gene

  • The protein encoded by this gene is part of the SMC5-6 chromatin reorganizing complex and is a member of the MAGE superfamily. This is an intronless gene. [provided by RefSeq, May 2011]

GeneCards Summary for NSMCE3 Gene

NSMCE3 (NSE3 Homolog, SMC5-SMC6 Complex Component) is a Protein Coding gene. Diseases associated with NSMCE3 include Lung Disease, Immunodeficiency, And Chromosome Breakage Syndrome and Lung Disease. Among its related pathways are SUMOylation and p75(NTR)-mediated signaling. An important paralog of this gene is MAGEF1.

UniProtKB/Swiss-Prot Summary for NSMCE3 Gene

  • Component of the SMC5-SMC6 complex, a complex involved in repair of DNA double-strand breaks by homologous recombination (PubMed:20864041, PubMed:27427983). The complex may promote sister chromatid homologous recombination by recruiting the SMC1-SMC3 cohesin complex to double-strand breaks. The complex is required for telomere maintenance via recombination in ALT (alternative lengthening of telomeres) cell lines and mediates sumoylation of shelterin complex (telosome) components which is proposed to lead to shelterin complex disassembly in ALT-associated PML bodies (APBs). In vitro enhances ubiquitin ligase activity of NSMCE1. Proposed to act through recruitment and/or stabilization of the Ubl-conjugating enzyme (E2) at the E3:substrate complex (PubMed:20864041). May be a growth suppressor that facilitates the entry of the cell into cell cycle arrest (By similarity).

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NSMCE3 Gene

Genomics for NSMCE3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for NSMCE3 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
GH15J029268 Promoter/Enhancer 1.6 Ensembl ENCODE CraniofacialAtlas 256.1 +0.5 470 4.7 BCLAF1 SP1 ZNF207 MYC POLR2A CEBPA BRCA1 MXD4 BCL11A CEBPB NSMCE3 piR-45035-064 APBA2 FAM189A1
GH15J029819 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 5.6 -551.9 -551878 5 MYC ZNF600 ATF2 ZSCAN16 NFIC POLR2A ZIC2 ZBTB10 YY1 MXD4 ENSG00000259523 TJP1 NSMCE3 HSALNG0104735 piR-61945-152 lnc-FAM189A1-8 FAM189A1
GH15J029139 Enhancer 0.9 ENCODE CraniofacialAtlas 11.1 +129.8 129824 0.8 ZNF654 REST CTCF HCFC1 SMC3 YY1 GABPB1 SAFB RAD21 ZNF189 NSMCE3 HERC2P9 GOLGA8M piR-58725 piR-33422-147 APBA2 FAM189A1
GH15J028984 Enhancer 1.3 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 6.3 +284.5 284501 2.2 ATF2 ZIC2 SP2 SPI1 BHLHE40 ZNF398 ZNF629 CREB1 RAD21 POLR2A APBA2 NSMCE3 HERC2P9 ENSG00000259277 piR-60357
GH15J029309 Enhancer 0.7 ENCODE 11.4 -39.5 -39490 0.2 BCL11A IRF4 BHLHE40 RFX5 BATF NFATC1 NR2F1 ATF2 JUNB BACH1 NSMCE3 RF00994-352 FAM189A1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NSMCE3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NSMCE3

Genomic Locations for NSMCE3 Gene

Latest Assembly
chr15:29,264,989-29,269,822
(GRCh38/hg38)
Size:
4,834 bases
Orientation:
Minus strand

Previous Assembly
chr15:29,557,193-29,562,026
(GRCh37/hg19 by Entrez Gene)
Size:
4,834 bases
Orientation:
Minus strand

chr15:29,560,353-29,562,033
(GRCh37/hg19 by Ensembl)
Size:
1,681 bases
Orientation:
Minus strand

Alternative Locations (GRCh38/hg38)

  • chr15(ALT_REF_LOCI_2):1,540,540-1,545,373 (-)
  • chr15(PATCHES):1,428,056-1,432,889 (-)

Genomic View for NSMCE3 Gene

Genes around NSMCE3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NSMCE3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NSMCE3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NSMCE3 Gene

Proteins for NSMCE3 Gene

  • Protein details for NSMCE3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96MG7-NSE3_HUMAN
    Recommended name:
    Non-structural maintenance of chromosomes element 3 homolog
    Protein Accession:
    Q96MG7
    Secondary Accessions:
    • Q8IW16
    • Q8TEI6
    • Q9H214

    Protein attributes for NSMCE3 Gene

    Size:
    304 amino acids
    Molecular mass:
    34308 Da
    Quaternary structure:
    • Component of the SMC5-SMC6 complex which consists at least of SMC5, SMC6, NSMCE2, NSMCE1, NSMCE4A or EID3 and NSMCE3. NSMCE1, NSMCE4A or EID3 and NSMCE3 probably form a subcomplex that bridges the head domains of the SMC5:SMC6 heterodimer (PubMed:18086888). Interacts with PJA1 (PubMed:20864041). Interacts with E2F1 (via C-terminus) (By similarity). Interacts with NGFR (via C-terminus) (By similarity). Interacts with NSMCE1 (PubMed:18086888, PubMed:21364888, PubMed:20864041, PubMed:27427983). Interacts with NSMCE4 (PubMed:20864041, PubMed:27427983). Interacts with SMC6 (PubMed:18086888). Interacts with EID3 (PubMed:21364888).
    SequenceCaution:
    • Sequence=BAB84964.1; Type=Frameshift; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for NSMCE3 Gene

neXtProt entry for NSMCE3 Gene

Post-translational modifications for NSMCE3 Gene

  • Ubiquitination at Lys113, Lys128, and Lys141
  • Modification sites at PhosphoSitePlus

Other Protein References for NSMCE3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for NSMCE3 Gene

Domains & Families for NSMCE3 Gene

Gene Families for NSMCE3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for NSMCE3 Gene

InterPro:
Blocks:
  • MAGE protein

Suggested Antigen Peptide Sequences for NSMCE3 Gene

GenScript: Design optimal peptide antigens:
  • Necdin-like protein 2 (MAGG1_HUMAN)
genes like me logo Genes that share domains with NSMCE3: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for NSMCE3 Gene

Function for NSMCE3 Gene

Molecular function for NSMCE3 Gene

UniProtKB/Swiss-Prot Function:
Component of the SMC5-SMC6 complex, a complex involved in repair of DNA double-strand breaks by homologous recombination (PubMed:20864041, PubMed:27427983). The complex may promote sister chromatid homologous recombination by recruiting the SMC1-SMC3 cohesin complex to double-strand breaks. The complex is required for telomere maintenance via recombination in ALT (alternative lengthening of telomeres) cell lines and mediates sumoylation of shelterin complex (telosome) components which is proposed to lead to shelterin complex disassembly in ALT-associated PML bodies (APBs). In vitro enhances ubiquitin ligase activity of NSMCE1. Proposed to act through recruitment and/or stabilization of the Ubl-conjugating enzyme (E2) at the E3:substrate complex (PubMed:20864041). May be a growth suppressor that facilitates the entry of the cell into cell cycle arrest (By similarity).

Phenotypes From GWAS Catalog for NSMCE3 Gene

Gene Ontology (GO) - Molecular Function for NSMCE3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 18086888
GO:0046983 protein dimerization activity IDA 27427983
genes like me logo Genes that share ontologies with NSMCE3: view
genes like me logo Genes that share phenotypes with NSMCE3: view

Human Phenotype Ontology for NSMCE3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

miRNA for NSMCE3 Gene

miRTarBase miRNAs that target NSMCE3

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NSMCE3

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for NSMCE3 Gene

Localization for NSMCE3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NSMCE3 Gene

Cytoplasm. Nucleus. Chromosome, telomere.

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 NSMCE3 gene
Compartment Confidence
nucleus 4
cytoskeleton 1
cytosol 1
plasma membrane 0
mitochondrion 0
peroxisome 0

Gene Ontology (GO) - Cellular Components for NSMCE3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000781 chromosome, telomeric region IEA --
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome IEA --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with NSMCE3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for NSMCE3 Gene

Pathways & Interactions for NSMCE3 Gene

genes like me logo Genes that share pathways with NSMCE3: view

Gene Ontology (GO) - Biological Process for NSMCE3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006281 DNA repair IMP 27427983
GO:0006310 DNA recombination IEA --
GO:0006974 cellular response to DNA damage stimulus IEA --
GO:0031398 positive regulation of protein ubiquitination IDA 20864041
GO:0034644 cellular response to UV IMP 27427983
genes like me logo Genes that share ontologies with NSMCE3: view

No data available for SIGNOR curated interactions for NSMCE3 Gene

Drugs & Compounds for NSMCE3 Gene

No Compound Related Data Available

Transcripts for NSMCE3 Gene

mRNA/cDNA for NSMCE3 Gene

1 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
1 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 NSMCE3

Alternative Splicing Database (ASD) splice patterns (SP) for NSMCE3 Gene

No ASD Table

Relevant External Links for NSMCE3 Gene

GeneLoc Exon Structure for
NSMCE3

Expression for NSMCE3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NSMCE3

mRNA Expression by UniProt/SwissProt for NSMCE3 Gene:

Q96MG7-NSE3_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for NSMCE3 Gene

  • Nervous system(4.5)
  • Muscle(4.3)
  • Spleen(4.2)
  • Lung(4.2)
  • Liver(4.1)

Primer products for research

No data available for mRNA expression in normal human tissues , mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for NSMCE3 Gene

Orthologs for NSMCE3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for NSMCE3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia NDNL2 29
  • 99.45 (n)
Dog
(Canis familiaris)
Mammalia NDNL2 29
  • 87.06 (n)
Rat
(Rattus norvegicus)
Mammalia Ndnl2 29
  • 81.06 (n)
Mouse
(Mus musculus)
Mammalia Ndnl2 29 30
  • 80.34 (n)
OneToOne
Nsmce3 16
Cow
(Bos Taurus)
Mammalia NDNL2 29 30
  • 80 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia -- 30
  • 46 (a)
ManyToMany
-- 30
  • 35 (a)
ManyToMany
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 30
  • 44 (a)
OneToMany
Chicken
(Gallus gallus)
Aves NDNL2 29
  • 62.52 (n)
MAGE 30
  • 47 (a)
OneToMany
Lizard
(Anolis carolinensis)
Reptilia -- 30
  • 50 (a)
OneToMany
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia ndnl2 29
  • 60.09 (n)
Zebrafish
(Danio rerio)
Actinopterygii ndnl2 30
  • 45 (a)
OneToMany
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4035 29
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 39 (a)
OneToMany
Species where no ortholog for NSMCE3 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)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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 NSMCE3 Gene

ENSEMBL:
Gene Tree for NSMCE3 (if available)
TreeFam:
Gene Tree for NSMCE3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NSMCE3: view image
Alliance of Genome Resources:
Additional Orthologs for NSMCE3

Paralogs for NSMCE3 Gene

Variants for NSMCE3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NSMCE3 Gene

SNP ID Clinical significance and condition Chr 15 pos Variation AA Info Type
1002164 Uncertain Significance: not provided 29,269,647(-) T/C
NM_138704.4(NSMCE3):c.59A>G (p.Asp20Gly)
MISSENSE_VARIANT,INTRON
1004005 Uncertain Significance: not provided 29,268,829(-) C/T
NM_138704.4(NSMCE3):c.877G>A (p.Ala293Thr)
MISSENSE_VARIANT,INTRON
1019113 Uncertain Significance: not provided 29,268,835(-) TCTC/T
NM_138704.4(NSMCE3):c.865GAG[1] (p.Glu290del)
INFRAME_DELETION,INTRON
1022302 Uncertain Significance: not provided 29,269,402(-) T/C
NM_138704.4(NSMCE3):c.304A>G (p.Lys102Glu)
MISSENSE_VARIANT,INTRON
1034263 Uncertain Significance: Lung disease, immunodeficiency, and chromosome breakage syndrome 29,269,120(-) T/C
NM_138704.4(NSMCE3):c.586A>G (p.Thr196Ala)
MISSENSE_VARIANT,INTRON

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for NSMCE3 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 NSMCE3 Gene

Variant ID Type Subtype PubMed ID
esv2751526 CNV loss 17911159
esv2761859 CNV loss 21179565
nsv1039798 CNV gain 25217958
nsv1040778 CNV loss 25217958
nsv1148560 OTHER inversion 26484159
nsv515660 CNV gain 19592680
nsv522597 CNV loss 19592680
nsv527255 CNV gain 19592680
nsv568675 CNV gain 21841781

Variation tolerance for NSMCE3 Gene

Residual Variation Intolerance Score: 65.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.87; 74.11% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NSMCE3 Gene

Human Gene Mutation Database (HGMD)
NSMCE3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NSMCE3
Leiden Open Variation Database (LOVD)
NSMCE3

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NSMCE3 Gene

Disorders for NSMCE3 Gene

MalaCards: The human disease database

(8) MalaCards diseases for NSMCE3 Gene - From: OMI, CVR, GTR, SWI, COP, and GCD

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

NSE3_HUMAN
  • Lung disease, immunodeficiency, and chromosome breakage syndrome (LICS) [MIM:617241]: An autosomal recessive chromosome breakage syndrome associated with severe, fatal lung disease in early childhood, following viral pneumonia. LICS is characterized by combined T and B-cell immunodeficiency. Some patients may have mild dysmorphic features. {ECO:0000269 PubMed:27427983}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for NSMCE3

genes like me logo Genes that share disorders with NSMCE3: view

No data available for Genatlas for NSMCE3 Gene

Publications for NSMCE3 Gene

  1. Destabilized SMC5/6 complex leads to chromosome breakage syndrome with severe lung disease. (PMID: 27427983) van der Crabben SN … van Haaften G (The Journal of clinical investigation 2016) 3 4 72
  2. Identification of the proteins, including MAGEG1, that make up the human SMC5-6 protein complex. (PMID: 18086888) Taylor EM … Lehmann AR (Molecular and cellular biology 2008) 2 3 4
  3. Interactions between the Nse3 and Nse4 components of the SMC5-6 complex identify evolutionarily conserved interactions between MAGE and EID Families. (PMID: 21364888) Hudson JJ … Palecek J (PloS one 2011) 3 4
  4. MAGE-RING protein complexes comprise a family of E3 ubiquitin ligases. (PMID: 20864041) Doyle JM … Potts PR (Molecular cell 2010) 3 4
  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

Products for NSMCE3 Gene

Sources for NSMCE3 Gene