Human Gene SNX30 (ENST00000374232.8_4) from GENCODE V47lift37
  Description: sorting nexin family member 30 (from RefSeq NM_001012994.2)
Gencode Transcript: ENST00000374232.8_4
Gencode Gene: ENSG00000148158.17_7
Transcript (Including UTRs)
   Position: hg19 chr9:115,513,040-115,637,267 Size: 124,228 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr9:115,513,282-115,631,123 Size: 117,842 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:115,513,040-115,637,267)mRNA (may differ from genome)Protein (437 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SNX30_HUMAN
DESCRIPTION: RecName: Full=Sorting nexin-30;
FUNCTION: May be involved in several stages of intracellular trafficking (By similarity).
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

+  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: 10.29 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 193.03 RPKM



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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -153.70242-0.635 Picture PostScript Text
3' UTR -1882.306144-0.306 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
IPR004148 - BAR_dom
IPR001683 - Phox

Pfam Domains:
PF00787 - PX domain

SCOP Domains:
48340 - Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain
103657 - BAR/IMD domain-like
158414 - HP0062-like
64268 - PX domain

ModBase Predicted Comparative 3D Structure on Q5VWJ9
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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 orthologNo orthologNo orthologNo orthologNo orthologGenome Browser
Gene DetailsGene Details   Gene Details
Gene SorterGene Sorter   Gene Sorter
 RGDEnsembl  SGD
     Protein Sequence
     Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0035091 phosphatidylinositol binding

Biological Process:
GO:0006897 endocytosis
GO:0015031 protein transport
GO:0016050 vesicle organization

Cellular Component:
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0019898 extrinsic component of membrane


-  Descriptions from all associated GenBank mRNAs
  AK127013 - Homo sapiens cDNA FLJ45069 fis, clone BRAWH3026349, weakly similar to Sorting nexin 7.
AK128710 - Homo sapiens cDNA FLJ46877 fis, clone UTERU3014647.
JD449226 - Sequence 430250 from Patent EP1572962.
AK128080 - Homo sapiens cDNA FLJ46201 fis, clone TESTI4008209.
JD566618 - Sequence 547642 from Patent EP1572962.
JD145537 - Sequence 126561 from Patent EP1572962.
JD176994 - Sequence 158018 from Patent EP1572962.
JD068267 - Sequence 49291 from Patent EP1572962.
JD288188 - Sequence 269212 from Patent EP1572962.
AK129991 - Homo sapiens cDNA FLJ26481 fis, clone KDN05118.
AK126644 - Homo sapiens cDNA FLJ44686 fis, clone BRACE3011502.
DQ588692 - Homo sapiens piRNA piR-55804, complete sequence.
BC014914 - Homo sapiens cDNA clone IMAGE:3920373.
AK091599 - Homo sapiens cDNA FLJ34280 fis, clone FEBRA2003896.
AK092908 - Homo sapiens cDNA FLJ35589 fis, clone SPLEN2007498.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000374232.1, ENST00000374232.2, ENST00000374232.3, ENST00000374232.4, ENST00000374232.5, ENST00000374232.6, ENST00000374232.7, NM_001012994, Q5VWJ9, SNX30 , SNX30_HUMAN, uc318lkk.1, uc318lkk.2
UCSC ID: ENST00000374232.8_4
RefSeq Accession: NM_001012994.2
Protein: Q5VWJ9 (aka SNX30_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.