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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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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

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