Human Gene SNX17 (uc002rkg.2) Description and Page Index
  Description: Homo sapiens sorting nexin 17 (SNX17), transcript variant 1, mRNA.
RefSeq Summary (NM_014748): 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].
Transcript (Including UTRs)
   Position: hg19 chr2:27,593,363-27,600,400 Size: 7,038 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg19 chr2:27,593,611-27,599,586 Size: 5,976 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:27,593,363-27,600,400)mRNA (may differ from genome)Protein (470 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
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neXtProtOMIMPubMedStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: SNX17_HUMAN
DESCRIPTION: RecName: Full=Sorting nexin-17;
FUNCTION: May be involved in several stages of intracellular protein trafficking. Plays a role in the sorting of endocytosed LRP1 and APP, and prevents their degradation. Required for maintenance of normal cell surface levels of APP and LRP1. Interacts with membranes containing phosphatidylinositol 3- phosphate (PtdIns(3P)).
SUBUNIT: Interacts with APP (via cytoplasmic YXNPXY motif). Interacts with KIF1B (By similarity). Interacts with the C-termini of P-selectin, PTC, LDLR, VLDLR, LRP1 and LRP8. Interacts with KRIT1 (via N-terminus).
INTERACTION: P16333:NCK1; NbExp=3; IntAct=EBI-1752620, EBI-389883; P19174:PLCG1; NbExp=2; IntAct=EBI-1752620, EBI-79387;
SUBCELLULAR LOCATION: Cytoplasm. Early endosome. Cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side.
DOMAIN: The PX domain mediates specific binding to phosphatidylinositol 3-phosphate (PtdIns(P3)). Required for association with endosomes.
SIMILARITY: Belongs to the sorting nexin family.
SIMILARITY: Contains 1 PX (phox homology) domain.
SIMILARITY: Contains 1 Ras-associating domain.
SEQUENCE CAUTION: Sequence=BAA06542.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 69.01 RPKM in Spleen
Total median expression: 2148.02 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -97.40248-0.393 Picture PostScript Text
3' UTR -327.00814-0.402 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001683 - Phox
IPR000159 - Ras-assoc

Pfam Domains:
PF00787 - PX domain

SCOP Domains:
64268 - PX domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help

3FOG
- X-ray MuPIT

3LUI
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q15036
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details  Gene DetailsGene Details 
Gene Sorter  Gene SorterGene Sorter 
  EnsemblFlyBaseWormBase 
  Protein SequenceProtein SequenceProtein Sequence 
  AlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005102 receptor binding
GO:0005515 protein binding
GO:0008022 protein C-terminus binding
GO:0008289 lipid binding
GO:0035091 phosphatidylinositol binding
GO:0050750 low-density lipoprotein particle receptor binding

Biological Process:
GO:0003279 cardiac septum development
GO:0006707 cholesterol catabolic process
GO:0006886 intracellular protein transport
GO:0006898 receptor-mediated endocytosis
GO:0007165 signal transduction
GO:0015031 protein transport
GO:0016197 endosomal transport
GO:0030100 regulation of endocytosis
GO:0035904 aorta development
GO:0060976 coronary vasculature development
GO:1990126 retrograde transport, endosome to plasma membrane

Cellular Component:
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005769 early endosome
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0030659 cytoplasmic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0032991 macromolecular complex
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  AK298620 - Homo sapiens cDNA FLJ56223 complete cds, highly similar to Sorting nexin-17.
D31764 - Homo sapiens KIAA0064 mRNA.
AK293464 - Homo sapiens cDNA FLJ53824 complete cds, highly similar to Sorting nexin-17.
AK297054 - Homo sapiens cDNA FLJ57319 complete cds, highly similar to Sorting nexin-17.
AK129689 - Homo sapiens cDNA FLJ26178 fis, clone ADG04179.
AK300144 - Homo sapiens cDNA FLJ51699 complete cds, highly similar to Sorting nexin-17.
AK222543 - Homo sapiens mRNA for sorting nexin 17 variant, clone: adSU01126.
AK298856 - Homo sapiens cDNA FLJ51047 complete cds, highly similar to Sorting nexin-17.
AK295278 - Homo sapiens cDNA FLJ61770 complete cds, highly similar to Sorting nexin-17.
AK308487 - Homo sapiens cDNA, FLJ98528.
AK307122 - Homo sapiens cDNA, FLJ97070.
AK309640 - Homo sapiens cDNA, FLJ99681.
AK293252 - Homo sapiens cDNA FLJ53821 complete cds, highly similar to Sorting nexin-17.
AK300641 - Homo sapiens cDNA FLJ51103 complete cds, highly similar to Sorting nexin-17.
BC021108 - Homo sapiens sorting nexin 17, mRNA (cDNA clone IMAGE:4622841), with apparent retained intron.
BC002524 - Homo sapiens sorting nexin 17, mRNA (cDNA clone MGC:765 IMAGE:3140610), complete cds.
BC014620 - Homo sapiens sorting nexin 17, mRNA (cDNA clone MGC:4075 IMAGE:3010648), complete cds.
AK298869 - Homo sapiens cDNA FLJ51943 complete cds, highly similar to Sorting nexin-17.
BC050590 - Homo sapiens sorting nexin 17, mRNA (cDNA clone MGC:60025 IMAGE:6044270), complete cds.
BC002610 - Homo sapiens sorting nexin 17, mRNA (cDNA clone MGC:2988 IMAGE:3143104), complete cds.
BC032320 - Homo sapiens sorting nexin 17, mRNA (cDNA clone IMAGE:5225353), containing frame-shift errors.
JD230540 - Sequence 211564 from Patent EP1572962.
AB383732 - Synthetic construct DNA, clone: pF1KSDA0064, Homo sapiens SNX17 gene for sorting nexin-17, complete cds, without stop codon, in Flexi system.
KJ892848 - Synthetic construct Homo sapiens clone ccsbBroadEn_02242 SNX17 gene, encodes complete protein.
BT007167 - Homo sapiens sorting nexin 17 mRNA, complete cds.
CR457081 - Homo sapiens full open reading frame cDNA clone RZPDo834F0711D for gene SNX17, sorting nexin 17; complete cds, incl. stopcodon.
AK316373 - Homo sapiens cDNA, FLJ79272 complete cds, highly similar to Sorting nexin-17.
JD019018 - Sequence 42 from Patent EP1572962.
JD029463 - Sequence 10487 from Patent EP1572962.
JD030058 - Sequence 11082 from Patent EP1572962.
DQ576877 - Homo sapiens piRNA piR-44989, complete sequence.
JD285332 - Sequence 266356 from Patent EP1572962.
JD316529 - Sequence 297553 from Patent EP1572962.
JD391097 - Sequence 372121 from Patent EP1572962.
JD393390 - Sequence 374414 from Patent EP1572962.
JD451004 - Sequence 432028 from Patent EP1572962.
JD508162 - Sequence 489186 from Patent EP1572962.
JD403407 - Sequence 384431 from Patent EP1572962.
JD208963 - Sequence 189987 from Patent EP1572962.
JD236158 - Sequence 217182 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: KIAA0064, NM_014748, NP_055563, Q15036, Q53HN7, Q6IAS3, SNX17_HUMAN, uc002rkg.1
UCSC ID: uc002rkg.2
RefSeq Accession: NM_014748
Protein: Q15036 (aka SNX17_HUMAN or SNXH_HUMAN)
CCDS: CCDS1750.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_014748.3
exon count: 15CDS single in 3' UTR: no RNA size: 2475
ORF size: 1413CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2897.50frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.