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    SNX5 sorting nexin 5 [ Homo sapiens (human) ]

    Gene ID: 27131, updated on 7-Jul-2024

    Summary

    Official Symbol
    SNX5provided by HGNC
    Official Full Name
    sorting nexin 5provided by HGNC
    Primary source
    HGNC:HGNC:14969
    See related
    Ensembl:ENSG00000089006 MIM:605937; AllianceGenome:HGNC:14969
    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
    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 functions in endosomal sorting, the phosphoinositide-signaling pathway, and macropinocytosis. This gene may play a role in the tumorigenesis of papillary thyroid carcinoma. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Sep 2013]
    Expression
    Ubiquitous expression in thyroid (RPKM 76.1), kidney (RPKM 52.7) and 24 other tissues See more
    Orthologs
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    Genomic context

    See SNX5 in Genome Data Viewer
    Location:
    20p11.23
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (17941600..17968794, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (17992739..18019917, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (17922244..17949437, complement)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:17856497-17857399 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:17862693-17863606 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr20:17868266-17869465 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:17876154-17876830 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17568 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:17887704-17887865 Neighboring gene RNA, U6 small nuclear 192, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:17909901-17910427 Neighboring gene MPRA-validated peak4160 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:17919356-17919949 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17570 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:17921137-17921728 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17572 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17573 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:17948150-17948904 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:17948905-17949659 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:17950167-17951366 Neighboring gene small nucleolar RNA, C/D box 17 Neighboring gene NANOG hESC enhancer GRCh37_chr20:17964055-17965008 Neighboring gene mitochondrial genome maintenance exonuclease 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17579 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:17980569-17981070 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:17985803-17986364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17580 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:17988051-17988612 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:17988613-17989173 Neighboring gene prothymosin alpha pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:18017759-18018259 Neighboring gene ovo like zinc finger 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:18034137-18034637 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:18036965-18037752

    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?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ10931

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables D1 dopamine receptor binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables cadherin binding HDA PubMed 
    enables dynactin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables dynactin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables phosphatidylinositol binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables phosphatidylinositol binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables phosphatidylinositol binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables phosphatidylinositol-3,5-bisphosphate binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables phosphatidylinositol-4-phosphate binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables phosphatidylinositol-5-phosphate binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in brush border IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoplasmic side of early endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasmic side of plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    is_active_in endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    located_in macropinocytic cup IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in phagocytic cup IEA
    Inferred from Electronic Annotation
    more info
     
    part_of retromer complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of retromer, tubulation complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in ruffle IEA
    Inferred from Electronic Annotation
    more info
     
    located_in tubular endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 

    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_001282454.2NP_001269383.1  sorting nexin-5 isoform b

      See identical proteins and their annotated locations for NP_001269383.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' structure, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (b) has a shorter N-terminus, compared to isoform a.
      Source sequence(s)
      BC000100, BC062638, DA567854
      UniProtKB/TrEMBL
      Q6P5V6
      Related
      ENST00000490175.5
      Conserved Domains (2) summary
      cd07663
      Location:80297
      BAR_SNX5; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 5
      cl02563
      Location:164
      PX_domain; The Phox Homology domain, a phosphoinositide binding module
    2. NM_014426.4NP_055241.1  sorting nexin-5 isoform a

      See identical proteins and their annotated locations for NP_055241.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) represents the longest transcript. Variants 1 and 2 encode the same protein (isoform a).
      Source sequence(s)
      BC000100, BC093623, DB118420
      Consensus CDS
      CCDS13130.1
      UniProtKB/Swiss-Prot
      B7ZKN3, D3DW26, Q52LC4, Q7KZN0, Q9BWP0, Q9Y5X3
      UniProtKB/TrEMBL
      Q53FH8
      Related
      ENSP00000366988.3, ENST00000377759.9
      Conserved Domains (2) summary
      cd07291
      Location:29169
      PX_SNX5; The phosphoinositide binding Phox Homology domain of Sorting Nexin 5
      cd07663
      Location:185402
      BAR_SNX5; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 5
    3. NM_152227.3NP_689413.1  sorting nexin-5 isoform a

      See identical proteins and their annotated locations for NP_689413.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) differs in the 5' UTR, compared to variant 2. Variants 1 and 2 encode the same protein (isoform a).
      Source sequence(s)
      AF121855, BC000100
      Consensus CDS
      CCDS13130.1
      UniProtKB/Swiss-Prot
      B7ZKN3, D3DW26, Q52LC4, Q7KZN0, Q9BWP0, Q9Y5X3
      UniProtKB/TrEMBL
      Q53FH8
      Related
      ENSP00000366998.3, ENST00000377768.7
      Conserved Domains (2) summary
      cd07291
      Location:29169
      PX_SNX5; The phosphoinositide binding Phox Homology domain of Sorting Nexin 5
      cd07663
      Location:185402
      BAR_SNX5; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 5

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      17941600..17968794 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      17992739..18019917 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)