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    NIPSNAP3B nipsnap homolog 3B [ Homo sapiens (human) ]

    Gene ID: 55335, updated on 2-Nov-2024

    Summary

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    Official Symbol
    NIPSNAP3Bprovided by HGNC
    Official Full Name
    nipsnap homolog 3Bprovided by HGNC
    Primary source
    HGNC:HGNC:23641
    See related
    Ensembl:ENSG00000165028 MIM:608872; AllianceGenome:HGNC:23641
    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
    FP944; SNAP1; NIPSNAP3
    Summary
    NIPSNAP3B belongs to a family of proteins with putative roles in vesicular trafficking (Buechler et al., 2004 [PubMed 15177564]).[supplied by OMIM, Mar 2008]
    Expression
    Broad expression in fat (RPKM 5.8), heart (RPKM 4.2) and 23 other tissues See more
    Orthologs
    all
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    Genomic context

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    See NIPSNAP3B in Genome Data Viewer
    Location:
    9q31.1
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (104764129..104790899)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (116938912..116966026)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (107526410..107540045)

    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 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 nipsnap homolog 3A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28730 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 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20145 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20146 Neighboring gene uncharacterized LOC105376196 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28732 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28733 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20147

    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. 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
    2. Human and mouse ABCA1 comparative sequencing and transgenesis studies revealing novel regulatory sequences. Qiu Y, et al. Genomics, 2001 Apr 1. PMID 11352567
    3. 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
    4. Identification of host proteins required for HIV infection through a functional genomic screen. Brass AL, et al. Science, 2008 Feb 15. PMID 18187620
    5. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. Comuzzie AG, et al. PLoS One, 2012. PMID 23251661, Free PMC Article

    See all (15) 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
    Genomic study in Mexicans identifies a new locus for triglycerides and refines European lipid loci.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of nipsnap homolog 3B (NIPSNAP3B) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ11275, FLJ33186, FLJ34348

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in mitophagy IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    protein NipSnap homolog 3B

    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_018376.4 → NP_060846.2  protein NipSnap homolog 3B

      See identical proteins and their annotated locations for NP_060846.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the protein.
      Source sequence(s)
      AF370389, AL359846, BC017914, DA346124
      Consensus CDS
      CCDS6761.1
      UniProtKB/Swiss-Prot
      Q5VX30, Q9BS92, Q9NUM2
      Related
      ENSP00000363894.3, ENST00000374762.4
      Conserved Domains (1) summary
      pfam07978
      Location:146 → 245
      NIPSNAP; NIPSNAP

    RNA

    1. NR_130759.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon in the 5' region compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
      Source sequence(s)
      AF370389, AK310397, AL359846, BC017914, DA346124

    2. NR_130760.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an internal exon and a large segment in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC017914, BX107655, DA346124

    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
      104764129..104790899
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011518839.2 → XP_011517141.1  protein NipSnap homolog 3B isoform X2

      UniProtKB/TrEMBL
      F2Z3L7
      Related
      ENSP00000435209.1, ENST00000460936.5
      Conserved Domains (1) summary
      pfam07978
      Location:37 → 136
      NIPSNAP; NIPSNAP

    2. XM_047423561.1 → XP_047279517.1  protein NipSnap homolog 3B isoform X1

    RNA

    1. XR_007061325.1 RNA Sequence

    2. XR_001746344.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      116938912..116966026
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054363224.1 → XP_054219199.1  protein NipSnap homolog 3B isoform X2

      UniProtKB/TrEMBL
      F2Z3L7

    2. XM_054363223.1 → XP_054219198.1  protein NipSnap homolog 3B isoform X1

    RNA

    1. XR_008488039.1 RNA Sequence

    2. XR_008488038.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BS92.1 GenPept UniProtKB/Swiss-Prot:Q9BS92

    Gene LinkOut

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

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