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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 HIV Life Cycle and Transport of the SLBP independent Mature mRNA. 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

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

Regulatory Elements for NDC1 Gene

Enhancers for NDC1 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
GH01G054051 1.2 ENCODE 9.7 -214.3 -214295 3.7 CREB3L1 DMAP1 YY1 SLC30A9 ZNF416 ZNF143 ZNF548 ZNF263 SP3 NFYC MAGOH TCEANC2 SSBP3-AS1 HSPB11 PARS2 CYB5RL C1orf123 LDLRAD1 NDC1 RPL37P7
GH01G053765 1.1 Ensembl ENCODE 9.9 +72.4 72430 2.3 ATF1 FOXA2 PKNOX1 ZBTB40 EGR1 GATA2 FOS CREM ZBTB11 TBX21 GLIS1 NDC1 RPL37P7 HSPB11 LRRC42 YIPF1 ENSG00000201003 GC01M053772
GH01G053910 0.9 ENCODE 10.9 -71.3 -71263 0.2 HDGF HDAC1 FOXA2 CREB3L1 RAD21 RARA TCF12 GLIS2 ZNF766 GATA2 YIPF1 HSPB11 LRRC42 RPL37P7 NDC1 LDLRAD1 TCEANC2 TMEM59 RNU7-95P GC01P053910
GH01G053918 0.8 ENCODE 10.7 -80.2 -80159 1.1 ELF3 CTCF SOX13 FOXA2 SAP130 CEBPG ZNF644 YY1 TEAD3 ZNF121 HSPB11 LRRC42 DIO1 YIPF1 RPL37P7 NDC1 LDLRAD1 RNU7-95P GC01P053910 GC01P053939
GH01G053046 1.2 Ensembl ENCODE 5.2 +791.1 791092 2.0 HDGF PKNOX1 ATF1 CREB3L1 FEZF1 YY1 ZNF121 GATA2 KLF7 FOS HSPB11 SLC1A7 ECHDC2 NDC1 SCP2 GC01P053051 GC01P053008
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around NDC1 on UCSC Golden Path with GeneCards custom track

Promoters for NDC1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000006569 660 2000 MLX CREB3L1 AGO1 FEZF1 DMAP1 YBX1 YY1 ZNF143 ZNF263 SP3

Genomic Location for NDC1 Gene

Chromosome:
1
Start:
53,765,460 bp from pter
End:
53,838,860 bp from pter
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 posLast=379379, posLast=430430, and Lys628
  • 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

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.

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

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

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 IDA,IEA 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:0006406 mRNA export from nucleus TAS --
GO:0006409 tRNA export from nucleus TAS --
GO:0006810 transport IEA --
GO:0007077 mitotic nuclear envelope disassembly TAS --
GO:0007129 synapsis IEA --
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

CRISPR Products

Inhibitory RNA Products

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, PaxDb, 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

Primer Products

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 35
  • 99.41 (n)
dog
(Canis familiaris)
Mammalia NDC1 34 35
  • 91.54 (n)
cow
(Bos Taurus)
Mammalia NDC1 34 35
  • 90.65 (n)
rat
(Rattus norvegicus)
Mammalia Ndc1 34
  • 86.66 (n)
mouse
(Mus musculus)
Mammalia Ndc1 16 35 34
  • 86.16 (n)
oppossum
(Monodelphis domestica)
Mammalia NDC1 35
  • 69 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia NDC1 35
  • 49 (a)
OneToOne
chicken
(Gallus gallus)
Aves TMEM48 34
  • 69.94 (n)
NDC1 35
  • 59 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NDC1 35
  • 65 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ndc1 34
  • 63 (n)
Str.20452 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.14211 34
zebrafish
(Danio rerio)
Actinopterygii ndc1 34 35
  • 60.02 (n)
wufk93f04 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004558 34
  • 43.43 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG5857 34 35
  • 39.6 (n)
CG32246 35
  • 17 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea npp-22 35
  • 23 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4001 35
  • 35 (a)
OneToMany
-- 35
  • 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)

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 Sequence Context AA Info Type
rs1000155418 -- 53,787,367(+) ATAAA(-/G)GCTGG intron-variant
rs1000196524 -- 53,833,080(+) CTTTA(A/C)AATTA intron-variant
rs1000222528 -- 53,785,357(+) GAATT(G/T)CTAGG intron-variant
rs1000296310 -- 53,785,710(+) TGGGA(C/T)TATAG intron-variant
rs1000301827 -- 53,827,324(+) GCAGG(A/G)GCTAT intron-variant

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

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

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)

Relevant External Links for NDC1 Gene

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

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

Disorders for NDC1 Gene

Relevant External Links for NDC1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 E.C. … Gerace L. (Science 2003) 2 3 4 64
  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. (Biochem. Biophys. Res. Commun. 2009) 3 4 64
  3. Topology of yeast Ndc1p: predictions for the human NDC1/NET3 homologue. (PMID: 16779818) Lau C.K. … Forbes D.J. (Anat Rec A Discov Mol Cell Evol Biol 2006) 2 3 64
  4. The conserved transmembrane nucleoporin NDC1 is required for nuclear pore complex assembly in vertebrate cells. (PMID: 16600873) Mansfeld J. … Antonin W. (Mol. Cell 2006) 3 4 64
  5. NDC1: a crucial membrane-integral nucleoporin of metazoan nuclear pore complexes. (PMID: 16702233) Stavru F. … GAPrlich D. (J. Cell Biol. 2006) 3 4 64

Products for NDC1 Gene

Sources for NDC1 Gene

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