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SNX3 sorting nexin 3 [ Homo sapiens (human) ]

Gene ID: 8724, updated on 17-Jun-2019

Summary

Official Symbol
SNX3provided by HGNC
Official Full Name
sorting nexin 3provided by HGNC
Primary source
HGNC:HGNC:11174
See related
Ensembl:ENSG00000112335 MIM:605930
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SDP3; Grd19; MCOPS8
Summary
This gene encodes a member of the sorting nexin family. Members of this family contain a phox (PX) domain, which is a phosphoinositide binding domain, and are involved in intracellular trafficking. This protein does not contain a coiled coil region, like most family members. This protein interacts with phosphatidylinositol-3-phosphate, and is involved in protein trafficking. A pseudogene of this gene is present on the sex chromosomes. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2014]
Expression
Ubiquitous expression in fat (RPKM 95.7), adrenal (RPKM 90.6) and 25 other tissues See more
Orthologs

Genomic context

See SNX3 in Genome Data Viewer
Location:
6q21
Exon count:
4
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (108211222..108261040, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (108532712..108582478, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene OSTM1 antisense RNA 1 Neighboring gene nuclear receptor subfamily 2 group E member 1 Neighboring gene RNA, 5S ribosomal pseudogene 212 Neighboring gene RNA, U6 small nuclear 1144, pseudogene Neighboring gene AFG1 like ATPase Neighboring gene ribosomal protein L36a pseudogene 24

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Deubiquitination, organism-specific biosystem (from REACTOME)
    Deubiquitination, organism-specific biosystemUbiquitination, the modification of proteins by the covalent attachment of ubiquitin (Ub), is a key regulatory mechanism for many many cellular processes, including protein degradation by the 26S pro...
  • Endocytosis, organism-specific biosystem (from KEGG)
    Endocytosis, organism-specific biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
  • Endocytosis, conserved biosystem (from KEGG)
    Endocytosis, conserved biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by Wnt, organism-specific biosystem (from REACTOME)
    Signaling by Wnt, organism-specific biosystemWNT signaling pathways control a wide range of developmental and adult process in metozoans including cell proliferation, cell fate decisions, cell polarity and stem cell maintenance (reviewed in Sai...
  • Ub-specific processing proteases, organism-specific biosystem (from REACTOME)
    Ub-specific processing proteases, organism-specific biosystemUb-specific processing proteases (USPs) are the largest of the DUB families with more than 50 members in humans. The USP catalytic domain varies considerably in size and consists of six conserved mo...
  • WNT ligand biogenesis and trafficking, organism-specific biosystem (from REACTOME)
    WNT ligand biogenesis and trafficking, organism-specific biosystem19 WNT proteins have been identified in human cells. The WNTs are members of a conserved metazoan family of secreted morphogens that activate several signaling pathways in the responding cell: the c...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC17570

Gene Ontology Provided by GOA

Function Evidence Code Pubs
phosphatidylinositol-3,5-bisphosphate binding ISS
Inferred from Sequence or Structural Similarity
more info
 
phosphatidylinositol-3-phosphate binding IDA
Inferred from Direct Assay
more info
PubMed 
phosphatidylinositol-4-phosphate binding ISS
Inferred from Sequence or Structural Similarity
more info
 
phosphatidylinositol-5-phosphate binding ISS
Inferred from Sequence or Structural Similarity
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein phosphatase binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
Wnt signaling pathway TAS
Traceable Author Statement
more info
 
intralumenal vesicle formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
membrane invagination IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of early endosome to late endosome transport IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of phagocytosis IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of protein catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of protein transport IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of viral entry into host cell IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of neuron projection development ISS
Inferred from Sequence or Structural Similarity
more info
 
protein deubiquitination TAS
Traceable Author Statement
more info
 
protein to membrane docking IDA
Inferred from Direct Assay
more info
PubMed 
protein transport IEA
Inferred from Electronic Annotation
more info
 
regulation of Wnt signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to bacterium IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
clathrin-coated vesicle IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
early endosome IDA
Inferred from Direct Assay
more info
PubMed 
early endosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
early phagosome IDA
Inferred from Direct Assay
more info
PubMed 
endosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
endosome membrane TAS
Traceable Author Statement
more info
 
extracellular exosome HDA PubMed 
colocalizes_with retromer complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
sorting nexin-3
Names
sorting nexin 3A

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_023278.1 RefSeqGene

    Range
    5001..55044
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001300928.2NP_001287857.1  sorting nexin-3 isoform c

    See identical proteins and their annotated locations for NP_001287857.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an exon in the 3' coding region, compared to variant 1, which results in a frameshift and a protein (isoform c) with a shorter and distinct C-terminus, compared to isoform a.
    Source sequence(s)
    AI921483, BQ432490, CA442762, CN422502, HY156437
    Conserved Domains (1) summary
    cl02563
    Location:2886
    PX_domain; The Phox Homology domain, a phosphoinositide binding module
  2. NM_001300929.2NP_001287858.1  sorting nexin-3 isoform d

    See identical proteins and their annotated locations for NP_001287858.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an in-frame portion of the first coding exon, compared to variant 1. It encodes isoform d, which is shorter than isoform a.
    Source sequence(s)
    AI921483, BQ432490, CA442762, CN422502, HY023148
    Consensus CDS
    CCDS75501.1
    UniProtKB/Swiss-Prot
    O60493
    Related
    ENSP00000296991.7, ENST00000349379.5
    Conserved Domains (1) summary
    cl02563
    Location:12128
    PX_domain; The Phox Homology domain, a phosphoinositide binding module
  3. NM_003795.6NP_003786.1  sorting nexin-3 isoform a

    See identical proteins and their annotated locations for NP_003786.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AF034546, BQ432490, CA442762, HY023148
    Consensus CDS
    CCDS5064.1
    UniProtKB/Swiss-Prot
    O60493
    Related
    ENSP00000230085.8, ENST00000230085.13
    Conserved Domains (1) summary
    cd07293
    Location:28150
    PX_SNX3; The phosphoinositide binding Phox Homology domain of Sorting Nexin 3
  4. NM_152827.4NP_690040.1  sorting nexin-3 isoform b

    See identical proteins and their annotated locations for NP_690040.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame coding exon, compared to variant 1. It encodes isoform b, also known as SNX3A, which is shorter than isoform a.
    Source sequence(s)
    AB047360, BQ432490, CA442762, HY023148
    Consensus CDS
    CCDS5065.1
    UniProtKB/Swiss-Prot
    O60493
    Related
    ENSP00000401779.2, ENST00000426155.6
    Conserved Domains (1) summary
    cl02563
    Location:28118
    PX_domain; The Phox Homology domain, a phosphoinositide binding module

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    108211222..108261040 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_152828.2: Suppressed sequence

    Description
    NM_152828.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein, and because the transcript is a nonsense-mediated mRNA decay (NMD) candidate.
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