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SNX30 Gene

protein-coding   GIFtS: 47
GCID: GC09P115513

Sorting Nexin Family Member 30

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Sorting Nexin Family Member 301 2
ATG24A2
Sorting Nexin-302

External Ids:    HGNC: 236851   Entrez Gene: 4015482   Ensembl: ENSG000001481587   UniProtKB: Q5VWJ93   

Export aliases for SNX30 gene to outside databases

Previous GC identifers: GC09P112594 GC09P114519 GC09P085110


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for SNX30 Gene:
SNX30 (sorting nexin family member 30) is a protein-coding gene. GO annotations related to this gene include phosphatidylinositol binding. An important paralog of this gene is SNX7.

UniProtKB/Swiss-Prot: SNX30_HUMAN, Q5VWJ9
Function: May be involved in several stages of intracellular trafficking (By similarity)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000009.11  NT_008470.20  NC_018920.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SNX30 gene promoter:
         Max1   FOXO3   Meis-1b   YY1   MEF-2A   FOXO3a   aMEF-2   Meis-1a   c-Myc   Meis-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for SNX30

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SNX30


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 9q32   Ensembl cytogenetic band:  9q32   HGNC cytogenetic band: 9q33.1

SNX30 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SNX30 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P115513:  view genomic region     (about GC identifiers)

Start:
115,513,118 bp from pter      End:
115,643,951 bp from pter
Size:
130,834 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: SNX30_HUMAN, Q5VWJ9 (See protein sequence)
Recommended Name: Sorting nexin-30  
Size: 437 amino acids; 49677 Da

Explore the universe of human proteins at neXtProt for SNX30: NX_Q5VWJ9

Explore proteomics data for SNX30 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See SNX30 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001013012.1  
    ENSEMBL proteins: 
     ENSP00000363349   ENSP00000390454  

    SNX30 Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for SNX30

     
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    antibodies-online antibodies for SNX30 (9 products) 

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    SNX: Sorting nexins

    3 InterPro protein domains:
     IPR004148 BAR_dom
     IPR028649 SNX30
     IPR001683 Phox

    Graphical View of Domain Structure for InterPro Entry Q5VWJ9

    ProtoNet protein and cluster: Q5VWJ9

    1 Blocks protein domain: IPB001683 Phox-like

    UniProtKB/Swiss-Prot: SNX30_HUMAN, Q5VWJ9
    Similarity: Belongs to the sorting nexin family
    Similarity: Contains 1 PX (phox homology) domain


    Find genes that share domains with SNX30           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SNX30_HUMAN, Q5VWJ9
    Function: May be involved in several stages of intracellular trafficking (By similarity)

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI--
    GO:0035091phosphatidylinositol binding IBA--
         
    Find genes that share ontologies with SNX30           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for SNX30

    miRNA
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    miRTarBase miRNAs that target SNX30:
    hsa-mir-21-5p (MIRT030989)

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    Selected qRT-PCR Assays for microRNAs that regulate SNX30 (see all 112):
    hsa-miR-579 hsa-miR-3194-5p hsa-miR-520e hsa-miR-30d hsa-miR-3138 hsa-miR-30a hsa-miR-3613-3p hsa-miR-200b
    Browse SwitchGear 3'UTR luciferase reporter plasmids
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    Predesigned siRNA for gene silencing in human, mouse, rat SNX30

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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol3
    nucleus2

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm ----
    GO:0005768endosome IBA--

    Find genes that share ontologies with SNX30           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SNX30
    Interactions:

        Search GeneGlobe Interaction Network for SNX30

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for SNX30 (Q5VWJ91, 3 ENSP000003633494) via UniProtKB, MINT, STRING, and/or I2D (see all 70)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ARFGAP1Q8N6T33, ENSP000003146154I2D: score=1 STRING: ENSP00000314615
    COG3Q96JB23, ENSP000002586544I2D: score=1 STRING: ENSP00000258654
    RAB6BQ9NRW13, ENSP000002852084I2D: score=1 STRING: ENSP00000285208
    UBCP0CG483, ENSP000003448184I2D: score=1 STRING: ENSP00000344818
    VPS35Q96QK13, ENSP000002991384I2D: score=1 STRING: ENSP00000299138
    About this table

    Gene Ontology (GO): 4 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006886intracellular protein transport IBA--
    GO:0006915apoptotic process IBA--
    GO:0007154cell communication ----
    GO:0015031protein transport ----

    Find genes that share ontologies with SNX30           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for SNX30



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for SNX30 gene: 
    NM_001012994.1  

    Unigene Cluster for SNX30:

    Sorting nexin family member 30
    Hs.522350  [show with all ESTs]
    Unigene Representative Sequence: NM_001012994
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000374232(uc004bgj.4 uc004bgi.4) ENST00000416585 ENST00000604751

    miRNA
    Products:
         
    Block miRNA regulation of human, mouse, rat SNX30 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SNX30 (see all 112):
    hsa-miR-579 hsa-miR-3194-5p hsa-miR-520e hsa-miR-30d hsa-miR-3138 hsa-miR-30a hsa-miR-3613-3p hsa-miR-200b
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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      QuantiFast Probe-based Assays in human, mouse, rat SNX30

    Additional mRNA sequence: 

    AK091599.1 AK092908.1 AK126644.1 AK127013.1 AK128710.1 AK129991.1 BC014914.1 

    7 DOTS entries:

    DT.92023637  DT.113583  DT.97798459  DT.95147323  DT.121209085  DT.92060011  DT.99960599 

    Selected AceView cDNA sequences (see all 99):

    AA398365 AA401207 BF224225 AL135553 AK129991 CB151629 BQ232074 BG433378 
    BQ883111 BE882798 AA708134 AI032834 BM709668 AA399405 BQ278259 AI264632 
    BE669700 BE887539 BQ072597 CB131998 AI022371 AK128710 AA477849 BQ049375 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    SNX30 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    SNX30 Expression
    About this image

    SNX30 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SNX30 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.522350
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SNX30

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals and fungi.

    Orthologs for SNX30 gene from Selected species (see all 17)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Snx301 , 5 sorting nexin family member 301, 5 90.31(n)1
    95.42(a)1
      4 (32.81 cM)5
    2091311  NM_172468.21  NP_766056.11 
     598058405 
    chicken
    (Gallus gallus)
    Aves SNX301 sorting nexin family member 30 77.73(n)
    87.79(a)
      427330  XM_424910.3  XP_424910.2 
    lizard
    (Anolis carolinensis)
    Reptilia SNX306
    sorting nexin family member 30
    85(a)
    1 ↔ 1
    2(57885019-57920156)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia snx301 sorting nexin family member 30 73.78(n)
    81.65(a)
      549659  NM_001016905.2  NP_001016905.1 
    zebrafish
    (Danio rerio)
    Actinopterygii snx301 sorting nexin family member 30 70.76(n)
    78.96(a)
      550496  NM_001017798.1  NP_001017798.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes SNX4(YJL036W)4
    SNX41
    Sorting nexin, involved in retrieval of late-Golgi more4
    SNX41
    43.91(n)1
    30.21(a)1
      10(378825-380096)4
    8534161, 4  NP_012498.11, 4 


    ENSEMBL Gene Tree for SNX30 (if available)
    TreeFam Gene Tree for SNX30 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SNX30 gene
    SNX72  SNX22  SNX12  SNX42  
    4 SIMAP similar genes for SNX30 using alignment to 2 protein entries:     SNX30_HUMAN (see all proteins):
    SNX7    SNX3    SNX10    SNX12

    Find genes that share paralogs with SNX30           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for SNX30 (see all 2571)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1449652571,2
    --115511216(+) TAAGAA/TTAGTA 1 -- us2k10--------
    rs1897913711,2
    --115511385(+) TTTTAA/GGTTAG 1 -- us2k10--------
    rs1808566681,2
    --115511388(+) TAGGTA/TAGGAA 1 -- us2k10--------
    rs109814971,2
    C--115511432(+) CACCCA/GCTTGT 1 -- us2k12Minor allele frequency- G:0.08CSA EA 121
    rs1838388081,2
    --115511435(+) CCACTA/TGTAGT 1 -- us2k10--------
    rs1892908261,2
    --115511525(+) CCATAC/TGGATG 1 -- us2k10--------
    rs1513213371,2
    C--115511591(+) AAAACC/TGATGT 1 -- us2k10--------
    rs21538361,2
    C,F--115511638(-) AGAAAT/GGAGTA 1 -- us2k11Minor allele frequency- G:0.06NA 120
    rs1819935831,2
    --115511655(+) ATTGTA/GCTATT 1 -- us2k10--------
    rs1859522221,2
    --115511728(+) AATGTC/GAAAGT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for SNX30 (115513118 - 115643951 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for SNX30 (see all 16):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2422302CNV Deletion17116639
    esv1549334CNV Insertion17803354
    esv995366CNV Loss20482838
    nsv8560CNV Loss18304495
    nsv825049CNV Gain20364138
    dgv262e55CNV Gain17911159
    nsv471317CNV Gain18288195
    nsv8559CNV Gain18304495
    nsv893733CNV Gain21882294
    nsv515121CNV Gain21397061

    Site Specific Mutation Identification with PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    Find genes that share disorders with SNX30           About GenesLikeMe

    Genetic Association Database (GAD): SNX30
    Human Genome Epidemiology (HuGE) Navigator: SNX30 (1 document)

    Export disorders for SNX30 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for SNX30 gene, integrated from 10 sources (see all 11):
    (articles sorted by number of sources associating them with SNX30)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Follow-up association studies of chromosome region 9q and nonsyndromic cleft lip/palate. (PubMed id 20583170)1, 4 Letra A....Vieira A.R. (Am. J. Med. Genet. A 2010)
    2. Comprehensive analysis of interactions between the Src-associated protein in mitosis of 68 kDa and the human Src-homology 3 proteome. (PubMed id 22745667)1 Asbach B....Wagner R. (PLoS ONE 2012)
    3. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    4. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)
    5. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (Sci. Signal. 2010)
    6. A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)2 Dephoure N.... Gygi S.P. (Proc. Natl. Acad. Sci. U.S.A. 2008)
    7. Identification of preferred protein interactions by phage-display of the human Src homology-3 proteome. (PubMed id 16374509)1 Kaerkkaeinen S.... Saksela K. (EMBO Rep. 2006)
    8. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
    9. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)2 Humphray S.J.... Dunham I. (Nature 2004)
    10. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 401548 HGNC: 23685 AceView: LOC401548 Ensembl:ENSG00000148158 euGenes: HUgn401548
    ECgene: SNX30 H-InvDB: SNX30

    (According to HUGE)
    About This Section

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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for SNX30 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SNX30 gene:
    Search GeneIP for patents involving SNX30

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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