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SNX5 sorting nexin 5 [ Homo sapiens (human) ]

Gene ID: 27131, updated on 17-Jun-2019

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
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

Genomic context

See SNX5 in Genome Data Viewer
Location:
20p11.23
Exon count:
14
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 20 NC_000020.11 (17941600..17968794, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (17922244..17949490, complement)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 192, pseudogene Neighboring gene uncharacterized LOC105372549 Neighboring gene small nucleolar RNA, C/D box 17 Neighboring gene mitochondrial genome maintenance exonuclease 1 Neighboring gene prothymosin alpha pseudogene 3 Neighboring gene ovo like zinc finger 2

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?

Pathways from BioSystems

  • Clathrin derived vesicle budding, organism-specific biosystem (from REACTOME)
    Clathrin derived vesicle budding, organism-specific biosystemThere at least two classes of clathrin coated vesicles in cells, one predominantly Golgi-associated, involved in budding from the trans-Golgi network and the other at the plasma membrane. Here the cl...
  • Endocytosis, organism-specific biosystem (from KEGG)
    Endocytosis, organism-specific biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
  • Endocytosis, conserved biosystem (from KEGG)
    Endocytosis, conserved biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
  • Golgi Associated Vesicle Biogenesis, organism-specific biosystem (from REACTOME)
    Golgi Associated Vesicle Biogenesis, organism-specific biosystemProteins that have been synthesized, processed and sorted eventually reach the final steps of the secretory pathway. This pathway is responsible not only for proteins that are secreted from the cell ...
  • Membrane Trafficking, organism-specific biosystem (from REACTOME)
    Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
  • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
    Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...
  • trans-Golgi Network Vesicle Budding, organism-specific biosystem (from REACTOME)
    trans-Golgi Network Vesicle Budding, organism-specific biosystemAfter passing through the Golgi complex, secretory cargo is packaged into post-Golgi transport intermediates (post-Golgi), which translocate plus-end directed along microtubules to the plasma membran...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ10931

Gene Ontology Provided by GOA

Function Evidence Code Pubs
D1 dopamine receptor binding IEA
Inferred from Electronic Annotation
more info
 
cadherin binding HDA PubMed 
dynactin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
dynactin binding IDA
Inferred from Direct Assay
more info
PubMed 
phosphatidylinositol binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
phosphatidylinositol binding IDA
Inferred from Direct Assay
more info
PubMed 
phosphatidylinositol binding ISS
Inferred from Sequence or Structural Similarity
more info
 
phosphatidylinositol-3,5-bisphosphate binding IEA
Inferred from Electronic Annotation
more info
 
phosphatidylinositol-4-phosphate binding IEA
Inferred from Electronic Annotation
more info
 
phosphatidylinositol-5-phosphate binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein heterodimerization activity NAS
Non-traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
epidermal growth factor catabolic process IEA
Inferred from Electronic Annotation
more info
 
intracellular protein transport IEA
Inferred from Electronic Annotation
more info
 
negative regulation of blood pressure IEA
Inferred from Electronic Annotation
more info
 
pinocytosis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
pinocytosis IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of renal sodium excretion IEA
Inferred from Electronic Annotation
more info
 
regulation of macroautophagy NAS
Non-traceable Author Statement
more info
PubMed 
retrograde transport, endosome to Golgi IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
retrograde transport, endosome to Golgi IMP
Inferred from Mutant Phenotype
more info
PubMed 
retrograde transport, endosome to Golgi NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
brush border IEA
Inferred from Electronic Annotation
more info
 
cytoplasmic vesicle membrane IEA
Inferred from Electronic Annotation
more info
 
cytosol IEA
Inferred from Electronic Annotation
more info
 
colocalizes_with early endosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
endosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extrinsic component of cytoplasmic side of plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
extrinsic component of endosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
macropinocytic cup IDA
Inferred from Direct Assay
more info
PubMed 
phagocytic cup IEA
Inferred from Electronic Annotation
more info
 
retromer complex IDA
Inferred from Direct Assay
more info
PubMed 
retromer, tubulation complex NAS
Non-traceable Author Statement
more info
PubMed 
ruffle IEA
Inferred from Electronic Annotation
more info
 
tubular endosome IDA
Inferred from Direct Assay
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_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
    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
    Q9Y5X3
    Related
    ENSP00000366988.3, ENST00000377759.8
    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
    Q9Y5X3
    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: 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_000020.11 Reference GRCh38.p13 Primary Assembly

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