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

Gene ID: 55335, updated on 10-Dec-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: 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

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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)

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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