Human Gene SNX4 (uc003eib.4)
  Description: Homo sapiens sorting nexin 4 (SNX4), transcript variant 1, mRNA.
RefSeq Summary (NM_003794): 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 associated with the long isoform of the leptin receptor and with receptor tyrosine kinases for platelet-derived growth factor, insulin, and epidermal growth factor in cell cultures, but its function is unknown. This protein may form oligomeric complexes with family members. Two transcript variants, one protein coding and the other non-protein coding, have been found for this gene. [provided by RefSeq, Nov 2012].
Transcript (Including UTRs)
   Position: hg19 chr3:125,165,488-125,239,058 Size: 73,571 Total Exon Count: 14 Strand: -
Coding Region
   Position: hg19 chr3:125,166,623-125,239,016 Size: 72,394 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:125,165,488-125,239,058)mRNA (may differ from genome)Protein (450 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SNX4_HUMAN
DESCRIPTION: RecName: Full=Sorting nexin-4;
FUNCTION: May be involved in several stages of intracellular trafficking. Plays a role in recycling endocytosed transferrin receptor and prevent its degradation.
SUBUNIT: Interacts with WWC1/KIBRA. Identified in a complex with WWC1/KIBRA and dynein components DYNLL1 and DYNC1I2.
SUBCELLULAR LOCATION: Early endosome membrane; Peripheral membrane protein; Cytoplasmic side. Note=Also detected on a juxtanuclear endocytic recycling compartment (ERC).
DOMAIN: The PX domain binds phosphatidylinositol 3-phosphate which is necessary for peripheral membrane localization.
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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SNX4
CDC HuGE Published Literature: SNX4

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           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: 29.26 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 532.21 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 -19.3042-0.460 Picture PostScript Text
3' UTR -248.471135-0.219 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 O95219
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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 orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005154 epidermal growth factor receptor binding
GO:0005158 insulin receptor binding
GO:0005515 protein binding
GO:0008289 lipid binding
GO:0035091 phosphatidylinositol binding
GO:1990459 transferrin receptor binding
GO:1990460 leptin receptor binding

Biological Process:
GO:0006897 endocytosis
GO:0015031 protein transport
GO:0016050 vesicle organization
GO:0032456 endocytic recycling
GO:1903595 positive regulation of histamine secretion by mast cell

Cellular Component:
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005868 cytoplasmic dynein complex
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0019898 extrinsic component of membrane
GO:0031201 SNARE complex
GO:0031901 early endosome membrane
GO:0032991 macromolecular complex


-  Descriptions from all associated GenBank mRNAs
  AF130078 - Homo sapiens clone FLB9739 PRO2637 mRNA, complete cds.
AK001835 - Homo sapiens cDNA FLJ10973 fis, clone PLACE1001092, highly similar to Sorting nexin-4.
AF065485 - Homo sapiens sorting nexin 4 mRNA, complete cds.
AK298972 - Homo sapiens cDNA FLJ50837 complete cds, highly similar to Sorting nexin-4.
BC018762 - Homo sapiens sorting nexin 4, mRNA (cDNA clone MGC:31982 IMAGE:4641014), complete cds.
DQ892131 - Synthetic construct clone IMAGE:100004761; FLH183297.01X; RZPDo839A09142D sorting nexin 4 (SNX4) gene, encodes complete protein.
KJ892606 - Synthetic construct Homo sapiens clone ccsbBroadEn_02000 SNX4 gene, encodes complete protein.
DQ895325 - Synthetic construct Homo sapiens clone IMAGE:100009785; FLH183296.01L; RZPDo839A09141D sorting nexin 4 (SNX4) gene, encodes complete protein.
AB528425 - Synthetic construct DNA, clone: pF1KB5326, Homo sapiens SNX4 gene for sorting nexin 4, without stop codon, in Flexi system.
JD552662 - Sequence 533686 from Patent EP1572962.
JD309835 - Sequence 290859 from Patent EP1572962.
JD248013 - Sequence 229037 from Patent EP1572962.
JD111259 - Sequence 92283 from Patent EP1572962.
JD288355 - Sequence 269379 from Patent EP1572962.
JD491003 - Sequence 472027 from Patent EP1572962.
JD235977 - Sequence 217001 from Patent EP1572962.
JD410940 - Sequence 391964 from Patent EP1572962.
CU676320 - Synthetic construct Homo sapiens gateway clone IMAGE:100017664 5' read SNX4 mRNA.
LF210596 - JP 2014500723-A/18099: Polycomb-Associated Non-Coding RNAs.
LF339020 - JP 2014500723-A/146523: Polycomb-Associated Non-Coding RNAs.
MA446173 - JP 2018138019-A/18099: Polycomb-Associated Non-Coding RNAs.
MA574597 - JP 2018138019-A/146523: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: B3KMH0, D3DNA3, NM_003794, NP_003785, O95219, SNX4_HUMAN, uc003eib.3
UCSC ID: uc003eib.4
RefSeq Accession: NM_003794
Protein: O95219 (aka SNX4_HUMAN)
CCDS: CCDS3032.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SNX4:
ataxias (Hereditary Ataxia Overview)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_003794.3
exon count: 14CDS single in 3' UTR: no RNA size: 2534
ORF size: 1353CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2876.00frame shift in genome: no % Coverage: 99.84
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.