Human Gene SNX20 (uc002egk.2) Description and Page Index
  Description: Homo sapiens sorting nexin 20 (SNX20), transcript variant 1, mRNA.
RefSeq Summary (NM_182854): SNX20 interacts with the cytoplasmic domain of PSGL1 (SELPLG; MIM 600738) and cycles PSGL1 into endosomes.[supplied by OMIM, Feb 2010].
Transcript (Including UTRs)
   Position: hg19 chr16:50,706,886-50,715,264 Size: 8,379 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr16:50,707,317-50,711,437 Size: 4,121 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:50,706,886-50,715,264)mRNA (may differ from genome)Protein (316 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: SNX20_HUMAN
DESCRIPTION: RecName: Full=Sorting nexin-20; AltName: Full=Selectin ligand-interactor cytoplasmic 1;
FUNCTION: Serves as a sorting protein that cycles P-selectin glycoprotein ligand 1 (PSLG1) into endosomes with no impact on leukocytes recruitment.
SUBUNIT: Interacts with SELPLG.
INTERACTION: Q14242:SELPLG; NbExp=5; IntAct=EBI-744896, EBI-1030190;
SUBCELLULAR LOCATION: Cell membrane. Cytoplasm. Nucleus. Endosome. Endosome membrane; Peripheral membrane protein; Cytoplasmic side.
DOMAIN: The PX domain binds phosphatidylinositol 3-phosphate which is necessary for localization to the endosomes.
SIMILARITY: Belongs to the sorting nexin family.
SIMILARITY: Contains 1 PX (phox homology) domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SNX20
CDC HuGE Published Literature: SNX20
Positive Disease Associations: Inflammatory Bowel Diseases , Leprosy
Related Studies:
  1. Inflammatory Bowel Diseases
    Richard H Duerr et al. Science (New York, N.Y.) 2006, A genome-wide association study identifies IL23R as an inflammatory bowel disease gene., Science (New York, N.Y.). [PubMed 17068223]
  2. Leprosy
    , , . [PubMed 0]
  3. Leprosy
    , , . [PubMed 0]
           more ... click here to view the complete list

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 13.52 RPKM in Whole Blood
Total median expression: 55.05 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 -59.90173-0.346 Picture PostScript Text
3' UTR -136.45431-0.317 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 Q7Z614
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 BrowserNo orthologNo ortholog
Gene Details  Gene Details  
Gene Sorter  Gene Sorter  
  EnsemblFlyBase  
  Protein SequenceProtein Sequence  
  AlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0005546 phosphatidylinositol-4,5-bisphosphate binding
GO:0008289 lipid binding
GO:0032266 phosphatidylinositol-3-phosphate binding
GO:0035091 phosphatidylinositol binding

Biological Process:
GO:0015031 protein transport

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0031901 early endosome membrane


-  Descriptions from all associated GenBank mRNAs
  AK055837 - Homo sapiens cDNA FLJ31275 fis, clone KIDNE2006353.
LF385441 - JP 2014500723-A/192944: Polycomb-Associated Non-Coding RNAs.
BC027944 - Homo sapiens sorting nexin 20, mRNA (cDNA clone IMAGE:5204030).
BC063423 - Homo sapiens sorting nexin 20, mRNA (cDNA clone IMAGE:5218959), complete cds.
AK292650 - Homo sapiens cDNA FLJ76423 complete cds, highly similar to Homo sapiens selectin ligand interactor cytoplasmic-1, mRNA.
KJ900088 - Synthetic construct Homo sapiens clone ccsbBroadEn_09482 SNX20 gene, encodes complete protein.
AK292705 - Homo sapiens cDNA FLJ76579 complete cds, highly similar to Homo sapiens selectin ligand interactor cytoplasmic-1 (SLIC1), transcript variant 1, mRNA.
KJ895390 - Synthetic construct Homo sapiens clone ccsbBroadEn_04784 SNX20 gene, encodes complete protein.
LF208210 - JP 2014500723-A/15713: Polycomb-Associated Non-Coding RNAs.
AY302441 - Homo sapiens selectin ligand interactor cytoplasmic-1 (SLIC1) mRNA, complete cds.
JD308261 - Sequence 289285 from Patent EP1572962.
BC119626 - Homo sapiens sorting nexin 20, mRNA (cDNA clone IMAGE:40115502), complete cds.
BC168369 - Synthetic construct Homo sapiens clone IMAGE:100068265, MGC:195882 sorting nexin 20 (SNX20) mRNA, encodes complete protein.
JD389707 - Sequence 370731 from Patent EP1572962.
JD539612 - Sequence 520636 from Patent EP1572962.
JD390992 - Sequence 372016 from Patent EP1572962.
JD253983 - Sequence 235007 from Patent EP1572962.
JD325144 - Sequence 306168 from Patent EP1572962.
JD338183 - Sequence 319207 from Patent EP1572962.
JD209656 - Sequence 190680 from Patent EP1572962.
JD380561 - Sequence 361585 from Patent EP1572962.
MA621018 - JP 2018138019-A/192944: Polycomb-Associated Non-Coding RNAs.
MA443787 - JP 2018138019-A/15713: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K9D5, NM_182854, NP_878274, Q08E98, Q6P4H2, Q7Z614, Q8IV59, SLIC1, SNX20_HUMAN
UCSC ID: uc002egk.2
RefSeq Accession: NM_182854
Protein: Q7Z614 (aka SNX20_HUMAN)
CCDS: CCDS10745.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_182854.2
exon count: 4CDS single in 3' UTR: no RNA size: 1555
ORF size: 951CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2073.00frame 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.