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NDC1 NDC1 transmembrane nucleoporin [ Homo sapiens (human) ]

Gene ID: 55706, updated on 4-Jan-2025

Summary

Official Symbol
NDC1provided by HGNC
Official Full Name
NDC1 transmembrane nucleoporinprovided by HGNC
Primary source
HGNC:HGNC:25525
See related
Ensembl:ENSG00000058804 MIM:610115; AllianceGenome:HGNC:25525
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NET3; TMEM48
Summary
A structural constituent of nuclear pore. Involved in nuclear pore complex assembly and nuclear pore localization. Located in actin cytoskeleton; nuclear membrane; and plasma membrane. Part of nuclear pore. [provided by Alliance of Genome Resources, Jan 2025]
Expression
Ubiquitous expression in lymph node (RPKM 8.4), colon (RPKM 6.8) and 25 other tissues See more
Orthologs
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Genomic context

See NDC1 in Genome Data Viewer
Location:
1p32.3
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (53765478..53838296, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (53648324..53721147, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (54231151..54303969, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene GLIS family zinc finger 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54159647-54160273 Neighboring gene RNA, U7 small nuclear 95 pseudogene Neighboring gene MPRA-validated peak235 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54181253-54181752 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54204253-54204971 Neighboring gene uncharacterized LOC124904179 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54236211-54236773 Neighboring gene small nucleolar RNA SNORA58 Neighboring gene uncharacterized LOC124904725 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:54277212-54277746 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 912 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1050 Neighboring gene ribosomal protein L37 pseudogene 7 Neighboring gene Sharpr-MPRA regulatory region 6831 Neighboring gene Sharpr-MPRA regulatory region 3939 Neighboring gene Yip1 domain family member 1

Genomic regions, transcripts, and products

Expression

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

General gene information

Clone Names

  • FLJ10407, FLJ12556, FLJ34120

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in homologous chromosome pairing at meiosis  
involved_in mRNA transport  
involved_in nuclear pore complex assembly PubMed 
involved_in nuclear pore localization PubMed 
involved_in nuclear pore organization  
involved_in nucleocytoplasmic transport PubMed 
involved_in protein transport PubMed 
involved_in spermatogenesis  
Component Evidence Code Pubs
located_in actin cytoskeleton  
located_in cytoplasm  
located_in membrane PubMed 
located_in nuclear envelope PubMed 
located_in nuclear envelope  
located_in nuclear membrane  
part_of nuclear pore PubMed 
part_of nuclear pore PubMed 
part_of nuclear pore transmembrane ring  
located_in plasma membrane  

General protein information

Preferred Names
nucleoporin NDC1
Names
nuclear division cycle 1 homolog
transmembrane protein 48

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001168551.2NP_001162023.1  nucleoporin NDC1 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AK295000, AL354612, BC003082
    UniProtKB/Swiss-Prot
    Q9BTX1
    Conserved Domains (1) summary
    pfam09531
    Location:20626
    Ndc1_Nup; Nucleoporin protein Ndc1-Nup
  2. NM_018087.5NP_060557.3  nucleoporin NDC1 isoform 1

    See identical proteins and their annotated locations for NP_060557.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
    Source sequence(s)
    AL049745, AL354612, BC003082
    Consensus CDS
    CCDS583.1
    UniProtKB/Swiss-Prot
    B4DHA3, B4DQQ5, G3XA81, Q8NB76, Q9BTX1, Q9H9T6, Q9NSG3, Q9NSG4, Q9NVZ7
    Related
    ENSP00000360483.3, ENST00000371429.4
    Conserved Domains (1) summary
    pfam09531
    Location:20666
    Ndc1_Nup; Nucleoporin protein Ndc1-Nup

RNA

  1. NR_033142.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK298909, AL354612, BC003082

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    53765478..53838296 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011541766.3XP_011540068.1  nucleoporin NDC1 isoform X1

    Conserved Domains (1) summary
    pfam09531
    Location:18665
    Ndc1_Nup; Nucleoporin protein Ndc1-Nup

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    53648324..53721147 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054337564.1XP_054193539.1  nucleoporin NDC1 isoform X1

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