Ribosomal 40S and 60S subunits associate in the nucleolus and are exported to the cytoplasm. The protein encoded by this gene is involved in the passage of the 60S subunit through the nuclear pore complex and into the cytoplasm. Several transcript variants exist for this gene, but the full-length natures of only two have been described to date. [provided by RefSeq, Feb 2016] See more...

Aliases for NMD3 Gene

Aliases for NMD3 Gene

  • NMD3 Ribosome Export Adaptor 2 3 5
  • 60S Ribosomal Export Protein NMD3 3 4
  • HNMD3 3 4
  • NMD3 Homolog (S. Cerevisiae) 2
  • NMD3 Homolog 3
  • CGI-07 3

External Ids for NMD3 Gene

Previous GeneCards Identifiers for NMD3 Gene

  • GC03P162422
  • GC03P160822
  • GC03P158337

Summaries for NMD3 Gene

Entrez Gene Summary for NMD3 Gene

  • Ribosomal 40S and 60S subunits associate in the nucleolus and are exported to the cytoplasm. The protein encoded by this gene is involved in the passage of the 60S subunit through the nuclear pore complex and into the cytoplasm. Several transcript variants exist for this gene, but the full-length natures of only two have been described to date. [provided by RefSeq, Feb 2016]

GeneCards Summary for NMD3 Gene

NMD3 (NMD3 Ribosome Export Adaptor) is a Protein Coding gene. Diseases associated with NMD3 include Shwachman-Diamond Syndrome 1 and Noonan Syndrome 1. Among its related pathways are Ribosome biogenesis in eukaryotes and RNA transport. Gene Ontology (GO) annotations related to this gene include ribosomal large subunit binding.

UniProtKB/Swiss-Prot Summary for NMD3 Gene

  • Acts as an adapter for the XPO1/CRM1-mediated export of the 60S ribosomal subunit.

Gene Wiki entry for NMD3 Gene

Additional gene information for NMD3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for NMD3 Gene

Genomics for NMD3 Gene

GeneHancer (GH) Regulatory Elements for NMD3 Gene

Promoters and enhancers for NMD3 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
GH03J161220 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 511.1 +117.6 117613 4.2 ZBTB40 ZNF217 EP300 TCF12 POLR2G SP1 PHF8 ZFX REST POLR2A NMD3 ENSG00000271052 lnc-B3GALNT1-2 SPTSSB B3GALNT1 PSMC1P7 IFT80 EEF1GP4 piR-56883-117
GH03J161104 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE CraniofacialAtlas 500.7 +0.3 305 2 ZNF217 MYC TEAD4 ZFX POLR2A CLOCK ZBTB26 HDAC2 CTBP1 SIN3A B3GALNT1 HSALNG0030253 NMD3 lnc-B3GALNT1-1 SPTSSB
GH03J161412 Enhancer 1.2 Ensembl ENCODE dbSUPER 10.2 +309.5 309544 5.5 ZNF217 TCF12 ZFX CTCF CLOCK RFX1 CUX1 CHD1 EP300 CTBP1 lnc-SPTSSB-8 SPTSSB LINC02067 B3GALNT1 NMD3 PSMC1P7 piR-50968-088
GH03J161067 Enhancer 1 Ensembl ENCODE 10.9 -35.0 -34995 7 ZNF217 JUND EP300 RFX1 RELA RCOR1 TRIM22 ATF2 EZH2 CTBP1 B3GALNT1 NMD3 PSMC1P7 lnc-NMD3-1 piR-34822-235 PPM1L
GH03J161041 Enhancer 0.9 Ensembl ENCODE 11 -62.5 -62520 1.2 EP300 ZSCAN9 FOXA2 NR2F2 ARNT JUND POU2F2 BCL6 RAD21 RXRA B3GALNT1 NMD3 SPTSSB PSMC1P7 RF00017-4156 piR-40476-051 PPM1L
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around NMD3 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for NMD3

Top Transcription factor binding sites by QIAGEN in the NMD3 gene promoter:
  • AML1a
  • HNF-1
  • HNF-1A
  • Ik-3
  • p53
  • POU2F1a
  • POU2F1b
  • POU2F1c

Genomic Locations for NMD3 Gene

Genomic Locations for NMD3 Gene
chr3:161,104,696-161,253,532
(GRCh38/hg38)
Size:
148,837 bases
Orientation:
Plus strand
chr3:160,822,484-160,971,320
(GRCh37/hg19)
Size:
148,837 bases
Orientation:
Plus strand

Genomic View for NMD3 Gene

Genes around NMD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NMD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NMD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NMD3 Gene

Proteins for NMD3 Gene

  • Protein details for NMD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96D46-NMD3_HUMAN
    Recommended name:
    60S ribosomal export protein NMD3
    Protein Accession:
    Q96D46
    Secondary Accessions:
    • D3DNM7
    • Q9Y2Z6

    Protein attributes for NMD3 Gene

    Size:
    503 amino acids
    Molecular mass:
    57603 Da
    Quaternary structure:
    • Found in a 60S ribosomal subunit export complex with RAN and XPO1. Interacts with XPO1. Associates with the 60S ribosomal subunit.

neXtProt entry for NMD3 Gene

Post-translational modifications for NMD3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for NMD3 Gene

Domains & Families for NMD3 Gene

Gene Families for NMD3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for NMD3 Gene

Blocks:
  • NMD3 family
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for NMD3 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ57520, highly similar to Homo sapiens NMD3 homolog (NMD3), mRNA (B4DKU1_HUMAN)
  • 60S ribosomal export protein NMD3 (NMD3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96D46

UniProtKB/Swiss-Prot:

NMD3_HUMAN :
  • Belongs to the NMD3 family.
Family:
  • Belongs to the NMD3 family.
genes like me logo Genes that share domains with NMD3: view

Function for NMD3 Gene

Molecular function for NMD3 Gene

UniProtKB/Swiss-Prot Function:
Acts as an adapter for the XPO1/CRM1-mediated export of the 60S ribosomal subunit.

Phenotypes From GWAS Catalog for NMD3 Gene

Gene Ontology (GO) - Molecular Function for NMD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA 22658674
GO:0030674 protein binding, bridging IDA 12773398
GO:0043023 ribosomal large subunit binding IPI 12724356
genes like me logo Genes that share ontologies with NMD3: view
genes like me logo Genes that share phenotypes with NMD3: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NMD3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NMD3 Gene

Localization for NMD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NMD3 Gene

Cytoplasm. Nucleus. Note=Shuttles between the nucleus/nucleolus and the cytoplasm in a XPO1/CRM1-dependent manner. {ECO:0000269 PubMed:12724356, ECO:0000269 PubMed:12773398}.

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 NMD3 gene
Compartment Confidence
nucleus 5
cytosol 3
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NMD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
GO:0005654 nucleoplasm IDA 12773398
GO:0005730 nucleolus IDA 12773398
GO:0005737 cytoplasm IDA 12724356
GO:0016020 membrane HDA 19946888
genes like me logo Genes that share ontologies with NMD3: view

Pathways & Interactions for NMD3 Gene

PathCards logo

SuperPathways for NMD3 Gene

genes like me logo Genes that share pathways with NMD3: view

Pathways by source for NMD3 Gene

2 KEGG pathways for NMD3 Gene

Gene Ontology (GO) - Biological Process for NMD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000055 ribosomal large subunit export from nucleus IMP 12773398
GO:0015031 protein transport IEA --
GO:0032092 positive regulation of protein binding IMP 12724356
GO:1902680 positive regulation of RNA biosynthetic process IMP 23782956
GO:1904751 positive regulation of protein localization to nucleolus IMP 23782956
genes like me logo Genes that share ontologies with NMD3: view

No data available for SIGNOR curated interactions for NMD3 Gene

Drugs & Compounds for NMD3 Gene

No Compound Related Data Available

Transcripts for NMD3 Gene

mRNA/cDNA for NMD3 Gene

2 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
10 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 NMD3

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NMD3 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17
SP1: - - -
SP2: - - - -
SP3: - -
SP4: - - -
SP5:

Relevant External Links for NMD3 Gene

GeneLoc Exon Structure for
NMD3

Expression for NMD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for NMD3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for NMD3 Gene

This gene is overexpressed in Lung (52.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for NMD3 Gene



Protein tissue co-expression partners for NMD3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for NMD3

SOURCE GeneReport for Unigene cluster for NMD3 Gene:

Hs.598836

Evidence on tissue expression from TISSUES for NMD3 Gene

  • Liver(4.3)
  • Muscle(4.3)
  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with NMD3: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for NMD3 Gene

Orthologs for NMD3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for NMD3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NMD3 31 30
  • 99.73 (n)
OneToOne
cow
(Bos Taurus)
Mammalia NMD3 31 30
  • 92.64 (n)
OneToOne
dog
(Canis familiaris)
Mammalia NMD3 31 30
  • 92.51 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Nmd3 17 31 30
  • 91.39 (n)
rat
(Rattus norvegicus)
Mammalia Nmd3 30
  • 91.39 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia NMD3 31
  • 87 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia NMD3 31
  • 66 (a)
OneToOne
chicken
(Gallus gallus)
Aves NMD3 31 30
  • 77 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NMD3 31
  • 83 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nmd3 30
  • 75.48 (n)
zebrafish
(Danio rerio)
Actinopterygii nmd3 31 30
  • 69.65 (n)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8390 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005375 30
  • 56.18 (n)
fruit fly
(Drosophila melanogaster)
Insecta Nmd3 31 30
  • 56.04 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea T25G3.3 31 30
  • 56.03 (n)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NMD3 33 31 30
  • 54.75 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0A05159g 30
  • 54.62 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AER299C 30
  • 54.57 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G03820 30
  • 54.09 (n)
rice
(Oryza sativa)
Liliopsida Os10g0573900 30
  • 46.76 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes nmd3 30
  • 54.68 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.6714 31
  • 54 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU08663 30
  • 49.75 (n)
Species where no ortholog for NMD3 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for NMD3 Gene

ENSEMBL:
Gene Tree for NMD3 (if available)
TreeFam:
Gene Tree for NMD3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NMD3: view image

Paralogs for NMD3 Gene

Pseudogenes.org Pseudogenes for NMD3 Gene

genes like me logo Genes that share paralogs with NMD3: view

No data available for Paralogs for NMD3 Gene

Variants for NMD3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for NMD3 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
rs193920996 Uncertain Significance: Malignant tumor of prostate 161,235,138(+) C/T MISSENSE_VARIANT
rs12490341 - p.Glu6Lys

Additional dbSNP identifiers (rs#s) for NMD3 Gene

Structural Variations from Database of Genomic Variants (DGV) for NMD3 Gene

Variant ID Type Subtype PubMed ID
esv3598402 CNV loss 21293372
nsv1015063 CNV gain 25217958
nsv592128 CNV loss 21841781
nsv965228 CNV duplication 23825009

Variation tolerance for NMD3 Gene

Residual Variation Intolerance Score: 7.07% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.92; 35.71% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NMD3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NMD3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NMD3 Gene

Disorders for NMD3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for NMD3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
shwachman-diamond syndrome 1
  • sds1
noonan syndrome 1
  • ns1
diamond-blackfan anemia
  • diamond-blackfan anemia 1
- elite association - COSMIC cancer census association via MalaCards
Search NMD3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for NMD3

genes like me logo Genes that share disorders with NMD3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for NMD3 Gene

Publications for NMD3 Gene

  1. Coordinated nuclear export of 60S ribosomal subunits and NMD3 in vertebrates. (PMID: 12773398) Trotta CR … Dahlberg JE (The EMBO journal 2003) 2 3 4 23 54
  2. Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics. (PMID: 10810093) Lai CH … Lin W (Genome research 2000) 2 3 4 54
  3. CRM1 and its ribosome export adaptor NMD3 localize to the nucleolus and affect rRNA synthesis. (PMID: 23782956) Bai B … Laiho M (Nucleus (Austin, Tex.) 2013) 2 3 54
  4. Biogenesis and nuclear export of ribosomal subunits in higher eukaryotes depend on the CRM1 export pathway. (PMID: 12724356) Thomas F … Kutay U (Journal of cell science 2003) 3 4 54
  5. Proteomic profiling of VCP substrates links VCP to K6-linked ubiquitylation and c-Myc function. (PMID: 29467282) Heidelberger JB … Beli P (EMBO reports 2018) 3 54

Products for NMD3 Gene

Sources for NMD3 Gene