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    SNX17 sorting nexin 17 [ Homo sapiens (human) ]

    Gene ID: 9784, updated on 10-Feb-2018
    Official Symbol
    SNX17provided by HGNC
    Official Full Name
    sorting nexin 17provided by HGNC
    Primary source
    HGNC:HGNC:14979
    See related
    Ensembl:ENSG00000115234 MIM:605963; Vega:OTTHUMG00000097781
    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 does not contain a coiled coil region, like some family members, but contains a B41 domain. This protein interacts with the cytoplasmic domain of P-selectin, and may function in the intracellular trafficking of P-selectin. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2012]
    Expression
    Ubiquitous expression in spleen (RPKM 29.0), lymph node (RPKM 26.3) and 25 other tissues See more
    Orthologs
    Location:
    2p23.3
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 2 NC_000002.12 (27370496..27377533)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (27593363..27600400)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene general transcription factor IIIC subunit 2 Neighboring gene uncharacterized LOC105374363 Neighboring gene eukaryotic translation initiation factor 2B subunit delta Neighboring gene zinc finger protein 513 Neighboring gene protein phosphatase, Mg2+/Mn2+ dependent 1G Neighboring gene ferritin heavy chain 1 pseudogene 3 Neighboring gene nuclear receptor binding protein 1

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    NHGRI GWAS Catalog

    Description
    Genetic variants associated with breast size also influence breast cancer risk.
    NHGRI GWA Catalog
    Genome-wide characterization of shared and distinct genetic components that influence blood lipid levels in ethnically diverse human populations.
    NHGRI GWA Catalog
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • KIAA0064

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    low-density lipoprotein particle receptor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    phosphatidylinositol binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein C-terminus binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    receptor binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    aorta development IEA
    Inferred from Electronic Annotation
    more info
     
    cardiac septum development IEA
    Inferred from Electronic Annotation
    more info
     
    cholesterol catabolic process IC
    Inferred by Curator
    more info
    PubMed 
    coronary vasculature development IEA
    Inferred from Electronic Annotation
    more info
     
    endosomal transport NAS
    Non-traceable Author Statement
    more info
    PubMed 
    intracellular protein transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    intracellular protein transport NAS
    Non-traceable Author Statement
    more info
    PubMed 
    receptor-mediated endocytosis IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of endocytosis NAS
    Non-traceable Author Statement
    more info
    PubMed 
    retrograde transport, endosome to plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    signal transduction IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasmic vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytoplasmic vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
     
    cytosol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    early endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    protein complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    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_001267059.1NP_001253988.1  sorting nexin-17 isoform 2

      See identical proteins and their annotated locations for NP_001253988.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region compared to variant 1. The resulting protein (isoform 2) is shorter compared to isoform 1.
      Source sequence(s)
      AC074117, AK300144
      UniProtKB/TrEMBL
      B4DTB8
      Conserved Domains (3) summary
      cd06885
      Location:294
      PX_SNX17_31; The phosphoinositide binding Phox Homology domain of Sorting Nexins 17 and 31
      cd13337
      Location:257376
      FERM-like_C_SNX17; Atypical FERM-like domain C-lobe of Sorting nexin 17
      cl00155
      Location:104174
      UBQ; Ubiquitin-like proteins
    2. NM_001267060.1NP_001253989.1  sorting nexin-17 isoform 3

      See identical proteins and their annotated locations for NP_001253989.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The resulting protein (isoform 3) is shorter compared to isoform 1.
      Source sequence(s)
      AC074117, AK298869
      Consensus CDS
      CCDS58704.1
      UniProtKB/Swiss-Prot
      Q15036
      Related
      ENSP00000439208.1, ENST00000537606.5
      Conserved Domains (3) summary
      cd13337
      Location:244363
      FERM-like_C_SNX17; Atypical FERM-like domain C-lobe of Sorting nexin 17
      cl02563
      Location:281
      PX_domain; The Phox Homology domain, a phosphoinositide binding module
      cl09511
      Location:94226
      FERM_B-lobe; FERM domain B-lobe
    3. NM_001267061.1NP_001253990.1  sorting nexin-17 isoform 4

      See identical proteins and their annotated locations for NP_001253990.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) contains an alternate 5' exon contains an alternate exon, lacks a portion of the 5' coding region, and initiates translation at an alternate upstream start codon, compared to variant 1. The encoded protein (isoform 4) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC074117, AK298620
      UniProtKB/TrEMBL
      B4DQ37
      Conserved Domains (3) summary
      cd06885
      Location:286
      PX_SNX17_31; The phosphoinositide binding Phox Homology domain of Sorting Nexins 17 and 31
      cd13337
      Location:249368
      FERM-like_C_SNX17; Atypical FERM-like domain C-lobe of Sorting nexin 17
      cl00155
      Location:96166
      UBQ; Ubiquitin-like proteins
    4. NM_014748.3NP_055563.1  sorting nexin-17 isoform 1

      See identical proteins and their annotated locations for NP_055563.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest protein (isoform 1).
      Source sequence(s)
      AC074117, D31764, DB177194
      Consensus CDS
      CCDS1750.1
      UniProtKB/Swiss-Prot
      Q15036
      Related
      ENSP00000233575.2, OTTHUMP00000123418, ENST00000233575.6, OTTHUMT00000215024
      Conserved Domains (3) summary
      cd06885
      Location:2106
      PX_SNX17_31; The phosphoinositide binding Phox Homology domain of Sorting Nexins 17 and 31
      cd13337
      Location:269388
      FERM-like_C_SNX17; Atypical FERM-like domain C-lobe of Sorting nexin 17
      cl09511
      Location:119251
      FERM_B-lobe; FERM domain B-lobe

    RNA

    1. NR_049782.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate splice site in an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC074117, AK297054
    2. NR_049783.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) uses an alternate splice site in an internal exon and lacks an alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC074117, AK293252
    3. NR_049784.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) lacks an alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC074117, BC021108
    4. NR_049785.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) uses an alternate splice site in an internal exon and lacks an alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC074117, AK308487
    5. NR_049786.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9) lacks an alternate exon and contains an alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC074117, AK298856
    6. NR_049787.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (10) lacks two alternate 5' exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC074117, AK295278
    7. NR_049788.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (11) lacks three exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC074117, BC032320

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p7 Primary Assembly

      Range
      27370496..27377533
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017005405.1XP_016860894.1  sorting nexin-17 isoform X1

      UniProtKB/TrEMBL
      B4DDM3
      Conserved Domains (2) summary
      cd13337
      Location:55174
      FERM-like_C_SNX17; Atypical FERM-like domain C-lobe of Sorting nexin 17
      cl09511
      Location:2760
      FERM_B-lobe; FERM domain B-lobe
    2. XM_011533203.1XP_011531505.1  sorting nexin-17 isoform X1

      See identical proteins and their annotated locations for XP_011531505.1

      UniProtKB/TrEMBL
      B4DDM3
      Conserved Domains (2) summary
      cd13337
      Location:55174
      FERM-like_C_SNX17; Atypical FERM-like domain C-lobe of Sorting nexin 17
      cl09511
      Location:2760
      FERM_B-lobe; FERM domain B-lobe

    Alternate CHM1_1.1

    Genomic

    1. NC_018913.2 Alternate CHM1_1.1

      Range
      27523311..27530348
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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