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SNX3 sorting nexin 3 [ Homo sapiens (human) ]

Gene ID: 8724, updated on 8-Aug-2021

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
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Genomic context

See SNX3 in Genome Data Viewer
Location:
6q21
Exon count:
4
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (108211222..108261040, complement)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (108532426..108582244, 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 Functions

What's a GeneRIF?

Pathways from PubChem

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
enables phosphatidylinositol-3,5-bisphosphate binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enables phosphatidylinositol-3-phosphate binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables phosphatidylinositol-3-phosphate binding IDA
Inferred from Direct Assay
more info
PubMed 
enables phosphatidylinositol-4-phosphate binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enables phosphatidylinositol-5-phosphate binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein phosphatase binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables retromer complex binding IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
located_in clathrin-coated vesicle IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
 
located_in early endosome IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in early endosome membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in early endosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in early phagosome IDA
Inferred from Direct Assay
more info
PubMed 
located_in endosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in endosome membrane TAS
Traceable Author Statement
more info
 
located_in extracellular exosome HDA PubMed 
part_of retromer complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
sorting nexin-3
Names
sorting nexin 3A

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.

Genomic

  1. NG_023278.1 RefSeqGene

    Range
    5221..55039
    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 Updated Annotation Release 109.20210514

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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