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SNX16 sorting nexin 16 [ Homo sapiens (human) ]

Gene ID: 64089, updated on 17-Jun-2019

Summary

Official Symbol
SNX16provided by HGNC
Official Full Name
sorting nexin 16provided by HGNC
Primary source
HGNC:HGNC:14980
See related
Ensembl:ENSG00000104497 MIM:614903
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. The protein encoded by this gene associates with late endosome membranes as is involved in tubule formation, cholesterol transport, and transport of tetraspanin CD81. The encoded protein also inhibits cell migration and tumorigenesis. [provided by RefSeq, Jan 2017]
Expression
Ubiquitous expression in testis (RPKM 6.1), esophagus (RPKM 5.5) and 24 other tissues See more
Orthologs

Genomic context

See SNX16 in Genome Data Viewer
Location:
8q21.13
Exon count:
10
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 8 NC_000008.11 (81799583..81842326, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (82711816..82754539, complement)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene zinc finger AN1-type containing 1 Neighboring gene charged multivesicular body protein 4C Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 36 Neighboring gene uncharacterized LOC105375928 Neighboring gene long intergenic non-protein coding RNA 2839 Neighboring gene uncharacterized LOC105375930

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 FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants.
NHGRI GWA Catalog
Association of genome-wide variation with the risk of incident heart failure in adults of European and African ancestry: a prospective meta-analysis from the cohorts for heart and aging research in genomic epidemiology (CHARGE) consortium.
NHGRI GWA Catalog
Genome-wide data reveal novel genes for methotrexate response in a large cohort of juvenile idiopathic arthritis cases.
NHGRI GWA Catalog
GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Homology

Clone Names

  • DKFZp666H147

Gene Ontology Provided by GOA

Function Evidence Code Pubs
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
phosphatidylinositol binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
early endosome to late endosome transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
endosome to lysosome transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of ATPase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of ion transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein targeting to lysosome IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of membrane potential IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol IEA
Inferred from Electronic Annotation
more info
 
early endosome IDA
Inferred from Direct Assay
more info
PubMed 
early endosome membrane IEA
Inferred from Electronic Annotation
more info
 
extrinsic component of endosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
late endosome IDA
Inferred from Direct Assay
more info
PubMed 
late endosome membrane IEA
Inferred from Electronic Annotation
more info
 
lysosome IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

NCBI Reference Sequences (RefSeq)

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_001348189.2NP_001335118.1  sorting nexin-16 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (c) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AC087349, AC132219
    Conserved Domains (2) summary
    cd07276
    Location:76185
    PX_SNX16; The phosphoinositide binding Phox Homology domain of Sorting Nexin 16
    cl25732
    Location:202307
    SMC_N; RecF/RecN/SMC N terminal domain
  2. NM_022133.3NP_071416.2  sorting nexin-16 isoform a

    See identical proteins and their annotated locations for NP_071416.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1 and 2 both encode the same isoform (a).
    Source sequence(s)
    AL833763, BC033630, BG700892, CB962009, DA307370
    Consensus CDS
    CCDS6234.1
    UniProtKB/Swiss-Prot
    P57768
    Related
    ENSP00000379621.2, ENST00000396330.6
    Conserved Domains (2) summary
    cd07276
    Location:105214
    PX_SNX16; The phosphoinositide binding Phox Homology domain of Sorting Nexin 16
    cl25732
    Location:231336
    SMC_N; RecF/RecN/SMC N terminal domain
  3. NM_152836.3NP_690049.1  sorting nexin-16 isoform a

    See identical proteins and their annotated locations for NP_690049.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (a).
    Source sequence(s)
    AL833763, BC033630, CB962009
    Consensus CDS
    CCDS6234.1
    UniProtKB/Swiss-Prot
    P57768
    Related
    ENSP00000322652.4, ENST00000345957.9
    Conserved Domains (2) summary
    cd07276
    Location:105214
    PX_SNX16; The phosphoinositide binding Phox Homology domain of Sorting Nexin 16
    cl25732
    Location:231336
    SMC_N; RecF/RecN/SMC N terminal domain
  4. NM_152837.3NP_690050.1  sorting nexin-16 isoform b

    See identical proteins and their annotated locations for NP_690050.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
    Source sequence(s)
    AL833763, BC033630, CB962009
    Consensus CDS
    CCDS6235.1
    UniProtKB/Swiss-Prot
    P57768
    Related
    ENSP00000322631.4, ENST00000353788.8
    Conserved Domains (2) summary
    cl02563
    Location:105185
    PX_domain; The Phox Homology domain, a phosphoinositide binding module
    cl23720
    Location:193246
    RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

RNA

  1. NR_145472.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087349, AC132219
  2. NR_145473.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087349, AC132219
  3. NR_145474.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087349, AC132219
  4. NR_145475.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC087349, AC132219

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p13 Primary Assembly

    Range
    81799583..81842326 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005251282.4XP_005251339.1  sorting nexin-16 isoform X1

    See identical proteins and their annotated locations for XP_005251339.1

    Conserved Domains (2) summary
    cd07276
    Location:76185
    PX_SNX16; The phosphoinositide binding Phox Homology domain of Sorting Nexin 16
    cl25732
    Location:202307
    SMC_N; RecF/RecN/SMC N terminal domain
  2. XM_011517574.2XP_011515876.1  sorting nexin-16 isoform X2

    Conserved Domains (2) summary
    pfam12269
    Location:75130
    zf-CpG_bind_C; CpG binding protein zinc finger C terminal domain
    cl02563
    Location:157
    PX_domain; The Phox Homology domain, a phosphoinositide binding module

RNA

  1. XR_002956641.1 RNA Sequence

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