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    SNX3 sorting nexin 3 [ Homo sapiens (human) ]

    Gene ID: 8724, updated on 9-Dec-2024

    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; AllianceGenome:HGNC:11174
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SNX3 in Genome Data Viewer
    Location:
    6q21
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (108211222..108261040, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (109388338..109438159, complement)
    RS_2024_09 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 NANOG-H3K4me1 hESC enhancer GRCh37_chr6:108488071-108488972 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:108489873-108490774 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:108490775-108491674 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:108497591-108498326 Neighboring gene Sharpr-MPRA regulatory region 5034 Neighboring gene uncharacterized LOC124901369 Neighboring gene nuclear receptor subfamily 2 group E member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24910 Neighboring gene MPRA-validated peak6010 silencer Neighboring gene MPRA-validated peak6011 silencer Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17448 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17449 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:108582429-108583264 Neighboring gene RNA, 5S ribosomal pseudogene 212 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:108603498-108603672 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17450 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24911 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24912 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

    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
     
    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
     
    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
     
    part_of 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)

    NEW Try the new Transcript table

    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
      A8K0B1, E1P5E4, E1P5E5, O60493, O60718, Q4TT29, Q4TT31, Q5JXJ7, Q5JXJ8, Q96AP9, Q9C0J5, Q9NU45
      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: 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_000006.12 Reference GRCh38.p14 Primary Assembly

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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      109388338..109438159 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.