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    SNX9 sorting nexin 9 [ Homo sapiens (human) ]

    Gene ID: 51429, updated on 17-Jun-2024

    Summary

    Official Symbol
    SNX9provided by HGNC
    Official Full Name
    sorting nexin 9provided by HGNC
    Primary source
    HGNC:HGNC:14973
    See related
    Ensembl:ENSG00000130340 MIM:605952; AllianceGenome:HGNC:14973
    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
    SDP1; WISP; SH3PX1; SH3PXD3A
    Summary
    This gene encodes a member of the sorting nexin family. Members of this family contain a phosphoinositide binding domain, and are involved in intracellular trafficking. The encoded protein does not contain a coiled coil region, like some family members, but does contain a SRC homology domain near its N-terminus. The encoded protein is reported to have a variety of interaction partners, including of adaptor protein 2 , dynamin, tyrosine kinase non-receptor 2, Wiskott-Aldrich syndrome-like, and ARP3 actin-related protein 3. The encoded protein is implicated in several stages of intracellular trafficking, including endocytosis, macropinocytosis, and F-actin nucleation. [provided by RefSeq, Jul 2013]
    Expression
    Ubiquitous expression in gall bladder (RPKM 27.0), esophagus (RPKM 26.7) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SNX9 in Genome Data Viewer
    Location:
    6q25.3
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (157823246..157945077)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (159069178..159191298)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (158244278..158366109)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene zinc finger DHHC-type palmitoyltransferase 14 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157951781-157952686 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157952687-157953591 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:157954158-157954658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:157954659-157955159 Neighboring gene MPRA-validated peak6260 silencer Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157973253-157974075 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157977751-157978536 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25334 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157982847-157983820 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157993864-157994596 Neighboring gene microRNA 3692 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158014729-158015228 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158014227-158014728 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158037061-158037562 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158037563-158038062 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158066653-158067153 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:158069048-158070247 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158090399-158091006 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158091007-158091612 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158109923-158110424 Neighboring gene uncharacterized LOC107986663 Neighboring gene NANOG hESC enhancer GRCh37_chr6:158127150-158127715 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:158131630-158132829 Neighboring gene uncharacterized LOC124901555 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158134197-158134698 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158134699-158135198 Neighboring gene NANOG hESC enhancer GRCh37_chr6:158152966-158153487 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158153745-158154270 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158162257-158162797 Neighboring gene Sharpr-MPRA regulatory region 4686 Neighboring gene Sharpr-MPRA regulatory region 7014 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:158183852-158185051 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25338 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25339 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17727 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:158251124-158251862 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25340 Neighboring gene Sharpr-MPRA regulatory region 12251 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25341 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17728 Neighboring gene Sharpr-MPRA regulatory region 15079 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17729 Neighboring gene SNX9 antisense RNA 1 Neighboring gene NANOG hESC enhancer GRCh37_chr6:158351503-158352004 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17730 Neighboring gene CRISPRi-validated cis-regulatory element chr6.5510 Neighboring gene RNA, U6 small nuclear 786, pseudogene Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 26 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158394739-158395292 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158402661-158403176 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158402145-158402660 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158420467-158420966 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25345 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158447101-158447788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158447789-158448476 Neighboring gene Sharpr-MPRA regulatory region 12557 Neighboring gene SYNJ2 intronic transcript 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158458586-158459280 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158461967-158462502 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:158470498-158471112 Neighboring gene synaptojanin 2 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:158490014-158491213 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158492197-158492760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158492761-158493322 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:158516915-158517415 Neighboring gene MPRA-validated peak6269 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17733 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17734 Neighboring gene serine active site containing 1

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 1-phosphatidylinositol binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables Arp2/3 complex binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables cadherin binding HDA PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein homodimerization activity IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables ubiquitin protein ligase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in cleavage furrow formation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cleavage furrow formation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in endocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in endocytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in endosomal transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in endosomal transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in intracellular protein transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in lipid tube assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in mitotic cytokinesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in plasma membrane tubulation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in plasma membrane tubulation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of GTPase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of actin filament polymerization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of membrane protein ectodomain proteolysis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of protein kinase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein-containing complex assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in receptor-mediated endocytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of synaptic vesicle endocytosis IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in clathrin-coated pit IDA
    Inferred from Direct Assay
    more info
    PubMed 
    colocalizes_with clathrin-coated vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    colocalizes_with cuticular plate ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in cytoplasmic vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytoplasmic vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasmic vesicle membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in extracellular exosome HDA PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in presynapse IEA
    Inferred from Electronic Annotation
    more info
     
    located_in ruffle IEA
    Inferred from Electronic Annotation
    more info
     
    located_in trans-Golgi network IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    sorting nexin-9
    Names
    SH3 and PX domain-containing protein 1
    SH3 and PX domain-containing protein 3A
    Wiskott-Aldrich syndrome protein (WASP) interactor protein

    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.

    mRNA and Protein(s)

    1. NM_016224.5NP_057308.1  sorting nexin-9

      See identical proteins and their annotated locations for NP_057308.1

      Status: REVIEWED

      Source sequence(s)
      AF121859, AL139330, DA336311
      Consensus CDS
      CCDS5253.1
      UniProtKB/Swiss-Prot
      Q9BSI7, Q9BVM1, Q9UJH6, Q9UP20, Q9Y5X1
      UniProtKB/TrEMBL
      B2RAU5
      Related
      ENSP00000376024.3, ENST00000392185.8
      Conserved Domains (3) summary
      cd07285
      Location:250375
      PX_SNX9; The phosphoinositide binding Phox Homology domain of Sorting Nexin 9
      cd07668
      Location:386595
      BAR_SNX9; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 9
      cd11898
      Location:460
      SH3_SNX9; Src Homology 3 domain of Sorting nexin 9

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      157823246..157945077
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011535886.4XP_011534188.1  sorting nexin-9 isoform X1

      UniProtKB/TrEMBL
      A0A7P0T8Z7
      Conserved Domains (2) summary
      cd07285
      Location:156281
      PX_SNX9; The phosphoinositide binding Phox Homology domain of Sorting Nexin 9
      cd07668
      Location:292501
      BAR_SNX9; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 9

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      159069178..159191298
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054355583.1XP_054211558.1  sorting nexin-9 isoform X1

      UniProtKB/TrEMBL
      A0A7P0T8Z7