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Aliases for NDC1 Gene

Aliases for NDC1 Gene

  • NDC1 Transmembrane Nucleoporin 2 3 5
  • Transmembrane Protein 48 2 3 4
  • TMEM48 3 4
  • Nuclear Division Cycle 1 Homolog (S. Cerevisiae) 2
  • Nuclear Division Cycle 1 Homolog 3
  • Nucleoporin NDC1 3
  • HNDC1 4
  • NET3 3

External Ids for NDC1 Gene

Previous HGNC Symbols for NDC1 Gene

  • TMEM48

Previous GeneCards Identifiers for NDC1 Gene

  • GC01M054232

Summaries for NDC1 Gene

GeneCards Summary for NDC1 Gene

NDC1 (NDC1 Transmembrane Nucleoporin) is a Protein Coding gene. Among its related pathways are Cell Cycle, Mitotic and Transport of the SLBP independent Mature mRNA. Gene Ontology (GO) annotations related to this gene include structural constituent of nuclear pore.

UniProtKB/Swiss-Prot for NDC1 Gene

  • Component of the nuclear pore complex (NPC), which plays a key role in de novo assembly and insertion of NPC in the nuclear envelope. Required for NPC and nuclear envelope assembly, possibly by forming a link between the nuclear envelope membrane and soluble nucleoporins, thereby anchoring the NPC in the membrane.

Gene Wiki entry for NDC1 Gene

Additional gene information for NDC1 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NDC1 Gene

Genomics for NDC1 Gene

GeneHancer (GH) Regulatory Elements for NDC1 Gene

Promoters and enhancers for NDC1 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
GH01J053835 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 663.1 +1.7 1728 4.1 MLX DMAP1 YBX1 IRF4 YY1 ZNF213 E2F8 ZNF143 SP3 MEF2D NDC1 MAGOH SSBP3-AS1 HSPB11 LRRC42 ECHDC2 ENSG00000256407 CYB5RL C1orf123 ENSG00000279049
GH01J054051 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 49.2 -214.3 -214294 3.7 DMAP1 YY1 SLC30A9 E2F8 ZNF416 ZNF143 ZNF548 SP3 NFYC SSRP1 TCEANC2 TMEM59 MIR4781 MAGOH NDC1 ENSG00000228838 HSPB11 SSBP3-AS1 LRRC42 PARS2
GH01J053942 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 31.8 -106.5 -106452 5.4 HDGF SMAD1 ARID4B SIN3A YBX1 FEZF1 ZNF2 YY1 POLR2B ZNF766 HSPB11 LRRC42 YIPF1 SSBP3-AS1 MAGOH ENSG00000228838 NDC1 ENSG00000226938 CYB5RL PARS2
GH01J053237 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 22.3 +600.3 600262 2 HDGF PKNOX1 FOXA2 SMAD1 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 MAGOH LOC100507564 C1orf123 NDC1 CYB5RL TUT4 ENSG00000230953 SSBP3-AS1 ENSG00000236723 LRP8
GH01J054763 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 23.5 -925.6 -925566 1.9 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A DMAP1 ZNF2 POLR2B E2F8 PARS2 NDC1 LRRC42 SSBP3-AS1 TTC4 PIR47125
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around NDC1 on UCSC Golden Path with GeneCards custom track

Genomic Locations for NDC1 Gene

Genomic Locations for NDC1 Gene
chr1:53,765,460-53,838,860
(GRCh38/hg38)
Size:
73,401 bases
Orientation:
Minus strand
chr1:54,231,133-54,304,533
(GRCh37/hg19)
Size:
73,401 bases
Orientation:
Minus strand

Genomic View for NDC1 Gene

Genes around NDC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NDC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NDC1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NDC1 Gene

Proteins for NDC1 Gene

  • Protein details for NDC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BTX1-NDC1_HUMAN
    Recommended name:
    Nucleoporin NDC1
    Protein Accession:
    Q9BTX1
    Secondary Accessions:
    • B4DHA3
    • B4DQQ5
    • G3XA81
    • Q8NB76
    • Q9H9T6
    • Q9NSG3
    • Q9NSG4
    • Q9NVZ7

    Protein attributes for NDC1 Gene

    Size:
    674 amino acids
    Molecular mass:
    76305 Da
    Quaternary structure:
    • Interacts with the NUP35/NUP53 (By similarity). Interacts with AAAS, anchoring it to the nuclear envelope.
    Miscellaneous:
    • Depletion of NDC1 from HeLa cells interferes with the assembly of phenylalanine-glycine (FG) repeat Nups into nuclear pore complexes.
    SequenceCaution:
    • Sequence=BAB14135.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAC03665.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for NDC1 Gene

neXtProt entry for NDC1 Gene

Post-translational modifications for NDC1 Gene

  • Ubiquitination at Lys628, Lys430, and Lys379
  • Modification sites at PhosphoSitePlus

Other Protein References for NDC1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for NDC1 Gene

Domains & Families for NDC1 Gene

Gene Families for NDC1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted membrane proteins
  • Transporters

Protein Domains for NDC1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for NDC1 Gene

Graphical View of Domain Structure for InterPro Entry

Q9BTX1

UniProtKB/Swiss-Prot:

NDC1_HUMAN :
  • Belongs to the NDC1 family.
Family:
  • Belongs to the NDC1 family.
genes like me logo Genes that share domains with NDC1: view

Function for NDC1 Gene

Molecular function for NDC1 Gene

UniProtKB/Swiss-Prot Function:
Component of the nuclear pore complex (NPC), which plays a key role in de novo assembly and insertion of NPC in the nuclear envelope. Required for NPC and nuclear envelope assembly, possibly by forming a link between the nuclear envelope membrane and soluble nucleoporins, thereby anchoring the NPC in the membrane.

Phenotypes From GWAS Catalog for NDC1 Gene

Gene Ontology (GO) - Molecular Function for NDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0017056 structural constituent of nuclear pore IMP 16600873
genes like me logo Genes that share ontologies with NDC1: view
genes like me logo Genes that share phenotypes with NDC1: view

Animal Model Products

  • Taconic Biosciences Mouse Models for NDC1

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NDC1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NDC1 Gene

Localization for NDC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NDC1 Gene

Nucleus, nuclear pore complex. Nucleus membrane; Multi-pass membrane protein. Note=Central core structure of the nuclear pore complex.

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 NDC1 gene
Compartment Confidence
plasma membrane 5
nucleus 5
cytoskeleton 4
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear membrane (3)
  • Plasma membrane (2)
  • Actin filaments (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005635 nuclear envelope TAS --
GO:0005643 nuclear pore IEA,IDA 16600873
GO:0005737 cytoplasm IEA --
GO:0005816 NOT spindle pole body IBA --
GO:0005886 plasma membrane IDA --
genes like me logo Genes that share ontologies with NDC1: view

Pathways & Interactions for NDC1 Gene

SuperPathway Contained pathways
1 Transport of the SLBP independent Mature mRNA
2 HIV Life Cycle
.45
3 Cell Cycle, Mitotic
.60
4 Mitotic Prophase
5 Influenza Viral RNA Transcription and Replication
genes like me logo Genes that share pathways with NDC1: view

Pathways by source for NDC1 Gene

Gene Ontology (GO) - Biological Process for NDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006110 regulation of glycolytic process TAS --
GO:0006406 mRNA export from nucleus TAS --
GO:0006409 tRNA export from nucleus TAS --
GO:0006999 nuclear pore organization IBA --
GO:0007077 mitotic nuclear envelope disassembly TAS --
genes like me logo Genes that share ontologies with NDC1: view

No data available for SIGNOR curated interactions for NDC1 Gene

Drugs & Compounds for NDC1 Gene

No Compound Related Data Available

Transcripts for NDC1 Gene

mRNA/cDNA for NDC1 Gene

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for NDC1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NDC1 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11a · 11b ^ 12 ^ 13a · 13b · 13c ^ 14 ^ 15 ^ 16 ^ 17 ^ 18a · 18b ^
SP1: -
SP2: - - -
SP3: - -
SP4: - - - -
SP5:
SP6: - - - - - - - -

ExUns: 19a · 19b · 19c
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:

Relevant External Links for NDC1 Gene

GeneLoc Exon Structure for
NDC1
ECgene alternative splicing isoforms for
NDC1

Expression for NDC1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NDC1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for NDC1 Gene

This gene is overexpressed in Breast (26.6) and Placenta (10.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for NDC1 Gene



Protein tissue co-expression partners for NDC1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of NDC1 Gene:

NDC1

Evidence on tissue expression from TISSUES for NDC1 Gene

  • Nervous system(4.6)
genes like me logo Genes that share expression patterns with NDC1: 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 NDC1 Gene

Orthologs for NDC1 Gene

This gene was present in the common ancestor of animals.

Orthologs for NDC1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TMEM48 34 33
  • 99.41 (n)
OneToOne
dog
(Canis familiaris)
Mammalia NDC1 34 33
  • 91.54 (n)
OneToOne
cow
(Bos Taurus)
Mammalia NDC1 34 33
  • 90.65 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ndc1 33
  • 86.66 (n)
mouse
(Mus musculus)
Mammalia Ndc1 16 34 33
  • 86.16 (n)
oppossum
(Monodelphis domestica)
Mammalia NDC1 34
  • 69 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia NDC1 34
  • 49 (a)
OneToOne
chicken
(Gallus gallus)
Aves TMEM48 33
  • 69.94 (n)
NDC1 34
  • 59 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NDC1 34
  • 65 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ndc1 33
  • 63 (n)
Str.20452 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.14211 33
zebrafish
(Danio rerio)
Actinopterygii ndc1 34 33
  • 60.02 (n)
OneToOne
wufk93f04 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004558 33
  • 43.43 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG5857 34 33
  • 39.6 (n)
OneToMany
CG32246 34
  • 17 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea npp-22 34
  • 23 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4001 34
  • 35 (a)
OneToMany
-- 34
  • 30 (a)
OneToMany
Species where no ortholog for NDC1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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 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)

Evolution for NDC1 Gene

ENSEMBL:
Gene Tree for NDC1 (if available)
TreeFam:
Gene Tree for NDC1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for NDC1: view image

Paralogs for NDC1 Gene

No data available for Paralogs for NDC1 Gene

Variants for NDC1 Gene

Sequence variations from dbSNP and Humsavar for NDC1 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000155418 -- 53,787,367(-) GG/G intron_variant
rs1000196524 -- 53,833,080(-) A/C intron_variant
rs1000222528 -- 53,785,357(-) G/T intron_variant
rs1000296310 -- 53,785,710(-) C/T intron_variant
rs1000301827 -- 53,827,324(-) A/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for NDC1 Gene

Variant ID Type Subtype PubMed ID
nsv1011262 CNV gain 25217958
esv3586075 CNV loss 21293372
esv2678912 CNV deletion 23128226

Variation tolerance for NDC1 Gene

Residual Variation Intolerance Score: 16.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.93; 49.07% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for NDC1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NDC1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NDC1 Gene

Disorders for NDC1 Gene

Additional Disease Information for NDC1

No disorders were found for NDC1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for NDC1 Gene

Publications for NDC1 Gene

  1. Nuclear membrane proteins with potential disease links found by subtractive proteomics. (PMID: 12958361) Schirmer EC … Gerace L (Science (New York, N.Y.) 2003) 2 3 4 58
  2. The nuclear pore complex protein ALADIN is anchored via NDC1 but not via POM121 and GP210 in the nuclear envelope. (PMID: 19782045) Kind B … Huebner A (Biochemical and biophysical research communications 2009) 3 4 58
  3. Topology of yeast Ndc1p: predictions for the human NDC1/NET3 homologue. (PMID: 16779818) Lau CK … Forbes DJ (The anatomical record. Part A, Discoveries in molecular, cellular, and evolutionary biology 2006) 2 3 58
  4. The conserved transmembrane nucleoporin NDC1 is required for nuclear pore complex assembly in vertebrate cells. (PMID: 16600873) Mansfeld J … Antonin W (Molecular cell 2006) 3 4 58
  5. NDC1: a crucial membrane-integral nucleoporin of metazoan nuclear pore complexes. (PMID: 16702233) Stavru F … Görlich D (The Journal of cell biology 2006) 3 4 58

Products for NDC1 Gene

Sources for NDC1 Gene

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