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SNX17 sorting nexin 17 [ Homo sapiens (human) ]

Gene ID: 9784, updated on 5-Aug-2018

Summary

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

Genomic context

See SNX17 in Genome Data Viewer
Location:
2p23.3
Exon count:
16
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 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

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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 IBA
Inferred from Biological aspect of Ancestor
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 
signaling 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
PubMed 
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
PubMed 
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 IBA
Inferred from Biological aspect of Ancestor
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-containing complex 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_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 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

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

mRNA and Protein(s)

  1. XM_017005405.2XP_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_011533203.2XP_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
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