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    NIPSNAP3A nipsnap homolog 3A [ Homo sapiens (human) ]

    Gene ID: 25934, updated on 2-Nov-2024

    Summary

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    Official Symbol
    NIPSNAP3Aprovided by HGNC
    Official Full Name
    nipsnap homolog 3Aprovided by HGNC
    Primary source
    HGNC:HGNC:23619
    See related
    Ensembl:ENSG00000136783 MIM:608871; AllianceGenome:HGNC:23619
    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
    TASSC; HSPC299; NIPSNAP4
    Summary
    NIPSNAP3A belongs to a family of proteins with putative roles in vesicular transport (Buechler et al., 2004 [PubMed 15177564]).[supplied by OMIM, Mar 2008]
    Expression
    Ubiquitous expression in adrenal (RPKM 23.3), colon (RPKM 20.0) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    See NIPSNAP3A in Genome Data Viewer
    Location:
    9q31.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (104747683..104760120)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (116922473..116934903)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (107509964..107522401)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107987105 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:107486341-107487540 Neighboring gene olfactory receptor family 13 subfamily D member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28729 Neighboring gene olfactory receptor family 13 subfamily D member 3 pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr9:107526139-107526338 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20144 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28730 Neighboring gene nipsnap homolog 3B Neighboring gene Sharpr-MPRA regulatory region 1797 Neighboring gene ATP binding cassette subfamily A member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28731 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:107648026-107648752 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:107648753-107649478 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:107649479-107650205 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:107650206-107650931 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:107665454-107666366 Neighboring gene uncharacterized LOC124902239

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Identification of a NIPSNAP homologue as host cell target for Salmonella virulence protein SpiC. Lee AH, et al. Cell Microbiol, 2002 Nov. PMID 12427096
    2. Expression pattern and raft association of NIPSNAP3 and NIPSNAP4, highly homologous proteins encoded by genes in close proximity to the ATP-binding cassette transporter A1. Buechler C, et al. Genomics, 2004 Jun. PMID 15177564
    3. Discovery of genetic biomarkers contributing to variation in drug response of cytidine analogues using human lymphoblastoid cell lines. Li L, et al. BMC Genomics, 2014 Feb 1. PMID 24483146, Free PMC Article
    4. KCMF1 (potassium channel modulatory factor 1) Links RAD6 to UBR4 (ubiquitin N-recognin domain-containing E3 ligase 4) and lysosome-mediated degradation. Hong JH, et al. Mol Cell Proteomics, 2015 Mar. PMID 25582440, Free PMC Article
    5. Genomic study in Mexicans identifies a new locus for triglycerides and refines European lipid loci. Weissglas-Volkov D, et al. J Med Genet, 2013 May. PMID 23505323, Free PMC Article

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Discovery of genetic biomarkers contributing to variation in drug response of cytidine analogues using human lymphoblastoid cell lines.
    EBI GWAS Catalog
    Genomic study in Mexicans identifies a new locus for triglycerides and refines European lipid loci.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Clone Names

    • FLJ13953, MGC14553, DKFZp564D177

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in mitophagy IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus HDA PubMed 

    General protein information

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    Preferred Names
    protein NipSnap homolog 3A
    Names
    protein NipSnap homolog 4
    target for Salmonella secreted protein C

    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_001329570.2 → NP_001316499.1  protein NipSnap homolog 3A isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AK024015, AL359846, BP373678, HY046409
      UniProtKB/Swiss-Prot
      Q9UFN0

    2. NM_015469.3 → NP_056284.1  protein NipSnap homolog 3A isoform 1

      See identical proteins and their annotated locations for NP_056284.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      BC005935, HY046409
      Consensus CDS
      CCDS6760.1
      UniProtKB/Swiss-Prot
      A6NM55, Q5VX32, Q9BRV7, Q9H843, Q9P083, Q9UFN0
      UniProtKB/TrEMBL
      B4DW81
      Related
      ENSP00000363899.4, ENST00000374767.5
      Conserved Domains (1) summary
      pfam07978
      Location:37 → 136
      NIPSNAP; NIPSNAP

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      104747683..104760120
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      116922473..116934903
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UFN0.2 GenPept UniProtKB/Swiss-Prot:Q9UFN0

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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