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SNX1 sorting nexin 1 [ Homo sapiens (human) ]

Gene ID: 6642, updated on 17-Jun-2019

Summary

Official Symbol
SNX1provided by HGNC
Official Full Name
sorting nexin 1provided by HGNC
Primary source
HGNC:HGNC:11172
See related
Ensembl:ENSG00000028528 MIM:601272
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
VPS5; HsT17379
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 endosomal protein regulates the cell-surface expression of epidermal growth factor receptor. This protein also has a role in sorting protease-activated receptor-1 from early endosomes to lysosomes. This protein may form oligomeric complexes with family members. This gene results in three transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in thyroid (RPKM 29.5), fat (RPKM 17.2) and 25 other tissues See more
Orthologs

Genomic context

See SNX1 in Genome Data Viewer
Location:
15q22.31
Exon count:
17
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 15 NC_000015.10 (64094066..64144231)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (64386275..64436433)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928988 Neighboring gene death associated protein kinase 2 Neighboring gene cytosolic iron-sulfur assembly component 2A Neighboring gene sorting nexin 22 Neighboring gene casein kinase 1 gamma 1 Neighboring gene peptidylprolyl isomerase B Neighboring gene Sharpr-MPRA regulatory region 12494

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

  • 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...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC8664

Gene Ontology Provided by GOA

Function Evidence Code Pubs
cadherin binding HDA PubMed 
epidermal growth factor receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
insulin receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
leptin receptor 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 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein heterodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
protein heterodimerization activity NAS
Non-traceable Author Statement
more info
PubMed 
protein homodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
transferrin receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
early endosome to Golgi transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
early endosome to Golgi transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
intracellular protein transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
lamellipodium morphogenesis IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of protein catabolic process IEA
Inferred from Electronic Annotation
more info
 
receptor internalization IMP
Inferred from Mutant Phenotype
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
Golgi apparatus IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IEA
Inferred from Electronic Annotation
more info
 
early endosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
endosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endosome IDA
Inferred from Direct Assay
more info
 
endosome membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
lamellipodium IEA
Inferred from Electronic Annotation
more info
 
lysosome IDA
Inferred from Direct Assay
more info
 
membrane IDA
Inferred from Direct Assay
more info
PubMed 
protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 
retromer complex IDA
Inferred from Direct Assay
more info
PubMed 
retromer, tubulation complex IPI
Inferred from Physical Interaction
more info
PubMed 
retromer, tubulation complex NAS
Non-traceable Author Statement
more info
PubMed 
vesicle IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
sorting nexin-1
Names
sorting nexin 1A

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.

Genomic

  1. NG_029708.1 RefSeqGene

    Range
    5001..53351
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001242933.2NP_001229862.1  sorting nexin-1 isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site that causes a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (d) has a distinct and longer C-terminus, compared to isoform a.
    Source sequence(s)
    AC100840, AK128179, BX108623, DB455188
    Consensus CDS
    CCDS58371.1
    UniProtKB/Swiss-Prot
    Q13596
    Related
    ENSP00000261889.5, ENST00000261889.9
    Conserved Domains (3) summary
    cd07281
    Location:145268
    PX_SNX1; The phosphoinositide binding Phox Homology domain of Sorting Nexin 1
    pfam03700
    Location:55130
    Sorting_nexin; Sorting nexin, N-terminal domain
    cl12013
    Location:286506
    BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature
  2. NM_003099.5NP_003090.2  sorting nexin-1 isoform a

    See identical proteins and their annotated locations for NP_003090.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes isoform a.
    Source sequence(s)
    AC100840, AK291752, BX108623, DB455188
    Consensus CDS
    CCDS32266.1
    UniProtKB/Swiss-Prot
    Q13596
    Related
    ENSP00000453785.1, ENST00000559844.6
    Conserved Domains (3) summary
    cd07281
    Location:145268
    PX_SNX1; The phosphoinositide binding Phox Homology domain of Sorting Nexin 1
    cd07665
    Location:286519
    BAR_SNX1; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 1
    pfam03700
    Location:67130
    Sorting_nexin; Sorting nexin, N-terminal domain
  3. NM_148955.4NP_683758.1  sorting nexin-1 isoform b

    See identical proteins and their annotated locations for NP_683758.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame segment of the 5' coding region, compared to variant 1. It encodes a shorter isoform (b), also known as SNX1A, that is missing an internal segment compared to isoform a.
    Source sequence(s)
    AC100840, AF065484, BX108623, DB455188
    Consensus CDS
    CCDS32268.1
    UniProtKB/Swiss-Prot
    Q13596
    Related
    ENSP00000453567.1, ENST00000561026.5
    Conserved Domains (2) summary
    cd07665
    Location:221454
    BAR_SNX1; The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 1
    cl02563
    Location:91203
    PX_domain; The Phox Homology domain, a phosphoinositide binding module

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_000015.10 Reference GRCh38.p13 Primary Assembly

    Range
    64094066..64144231
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005254611.3XP_005254668.1  sorting nexin-1 isoform X1

    Conserved Domains (2) summary
    cl02563
    Location:1110
    PX_domain; The Phox Homology domain, a phosphoinositide binding module
    cl12013
    Location:128348
    BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

RNA

  1. XR_001751381.1 RNA Sequence

    Related
    ENST00000380285.7
  2. XR_001751380.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_152826.2: Suppressed sequence

    Description
    NM_152826.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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