Human Gene SNX16 (ENST00000345957.9_10) from GENCODE V47lift37
  Description: sorting nexin 16, transcript variant 5 (from RefSeq NR_145472.2)
Gencode Transcript: ENST00000345957.9_10
Gencode Gene: ENSG00000104497.15_15
Transcript (Including UTRs)
   Position: hg19 chr8:82,711,818-82,754,420 Size: 42,603 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr8:82,713,732-82,752,221 Size: 38,490 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:82,711,818-82,754,420)mRNA (may differ from genome)Protein (344 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SNX16_HUMAN
DESCRIPTION: RecName: Full=Sorting nexin-16;
FUNCTION: May be involved in several stages of intracellular trafficking. Plays a role in protein transport from early to late endosomes. Plays a role in protein transport to the lysosome. Promotes degradation of EGFR after EGF signaling. Plays a role in intracellular transport of vesicular stomatitis virus nucleocapsids from the endosome to the cytoplasm.
SUBUNIT: Homooligomer. Interacts with EGFR (By similarity).
SUBCELLULAR LOCATION: Early endosome membrane; Peripheral membrane protein; Cytoplasmic side. Late endosome membrane; Peripheral membrane protein; Cytoplasmic side. Cytoplasm (By similarity). Lysosome (By similarity).
TISSUE SPECIFICITY: Detected in placenta, lung, liver,heart and pancreas.
DOMAIN: The PX domain mediates interaction with membranes enriched in phosphatidylinositol 3-phosphate.
SIMILARITY: Belongs to the sorting nexin family.
SIMILARITY: Contains 1 PX (phox homology) domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D016604 Aflatoxin B1
  • D010634 Phenobarbital
  • D013749 Tetrachlorodibenzodioxin
  • C495626 14-deoxy-11,12-didehydroandrographolide
  • C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl
  • C014024 2,4,5,2',4',5'-hexachlorobiphenyl
  • C016403 2,4-dinitrotoluene
  • C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine
  • C021296 2-ethoxyethanol
  • C009505 4,4'-diaminodiphenylmethane
          more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 5.86 RPKM in Testis
Total median expression: 135.65 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -41.90160-0.262 Picture PostScript Text
3' UTR -367.501914-0.192 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

Pfam Domains:
PF00787 - PX domain

SCOP Domains:
64268 - PX domain

ModBase Predicted Comparative 3D Structure on P57768
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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0008289 lipid binding
GO:0035091 phosphatidylinositol binding
GO:0042802 identical protein binding

Biological Process:
GO:0006622 protein targeting to lysosome
GO:0008333 endosome to lysosome transport
GO:0015031 protein transport
GO:0045022 early endosome to late endosome transport

Cellular Component:
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005768 endosome
GO:0005769 early endosome
GO:0005770 late endosome
GO:0005829 cytosol
GO:0016020 membrane
GO:0031313 extrinsic component of endosome membrane
GO:0031901 early endosome membrane
GO:0031902 late endosome membrane
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  AL833763 - Homo sapiens mRNA; cDNA DKFZp666H147 (from clone DKFZp666H147).
JD286145 - Sequence 267169 from Patent EP1572962.
JD552651 - Sequence 533675 from Patent EP1572962.
JD509719 - Sequence 490743 from Patent EP1572962.
JD501829 - Sequence 482853 from Patent EP1572962.
JD491286 - Sequence 472310 from Patent EP1572962.
JD172202 - Sequence 153226 from Patent EP1572962.
JD333510 - Sequence 314534 from Patent EP1572962.
JD304625 - Sequence 285649 from Patent EP1572962.
AF305779 - Homo sapiens sorting nexin 16 (SNX16) mRNA, complete cds.
JD236006 - Sequence 217030 from Patent EP1572962.
JD284949 - Sequence 265973 from Patent EP1572962.
JD088034 - Sequence 69058 from Patent EP1572962.
JD553729 - Sequence 534753 from Patent EP1572962.
BC033630 - Homo sapiens sorting nexin 16, mRNA (cDNA clone MGC:44985 IMAGE:5224216), complete cds.
JD053755 - Sequence 34779 from Patent EP1572962.
JD511939 - Sequence 492963 from Patent EP1572962.
JD506767 - Sequence 487791 from Patent EP1572962.
JD501974 - Sequence 482998 from Patent EP1572962.
AK290903 - Homo sapiens cDNA FLJ75325 complete cds, highly similar to Homo sapiens sorting nexin 16 (SNX16), transcript variant 2, mRNA.
HQ448008 - Synthetic construct Homo sapiens clone IMAGE:100071378; CCSB009952_01 sorting nexin 16 (SNX16) gene, encodes complete protein.
KJ894525 - Synthetic construct Homo sapiens clone ccsbBroadEn_03919 SNX16 gene, encodes complete protein.
KJ905523 - Synthetic construct Homo sapiens clone ccsbBroadEn_15131 SNX16 gene, encodes complete protein.
CU689674 - Synthetic construct Homo sapiens gateway clone IMAGE:100020751 5' read SNX16 mRNA.
JD031919 - Sequence 12943 from Patent EP1572962.
JD021572 - Sequence 2596 from Patent EP1572962.
JD237239 - Sequence 218263 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K4D8, ENST00000345957.1, ENST00000345957.2, ENST00000345957.3, ENST00000345957.4, ENST00000345957.5, ENST00000345957.6, ENST00000345957.7, ENST00000345957.8, NR_145472, P57768, Q658L0, Q8N4U3, SNX16_HUMAN, uc317xhj.1, uc317xhj.2
UCSC ID: ENST00000345957.9_10
RefSeq Accession: NM_152836.3
Protein: P57768 (aka SNX16_HUMAN or SNXG_HUMAN)

-  Gene Model Information
  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.