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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

HPS6 Gene

protein-coding   GIFtS: 51
GCID: GC10P103815

Hermansky-Pudlak syndrome 6

 Explore 10 diseases affiliated with
HPS6 via our new
 Human Malady Compendium 
Biological research products
for HPS6
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Hermansky-Pudlak Syndrome 61 2     Hermansky-Pudlak Syndrome 6 Protein2
Ruby-Eye Protein Homolog2 3     Hermansky-Pudlak Syndrome-6 Protein (HPS6)2
FLJ225011     Ru3
RP11-302K17.12     RU5

External Ids:    HGNC: 188171   Entrez Gene: 798032   Ensembl: ENSG000001661897   OMIM: 6075225   UniProtKB: Q86YV93   

Export aliases for HPS6 gene to outside databases

Previous GC identifers: GC10P103058 GC10P103956 GC10P103489 GC10P097457


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for HPS6:
This intronless gene encodes a protein that may play a role in organelle biogenesis associated with melanosomes,
platelet dense granules, and lysosomes. This protein interacts with Hermansky-Pudlak syndrome 5 protein. Mutations in
this gene are associated with Hermansky-Pudlak syndrome type 6. (provided by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: HPS6_HUMAN, Q86YV9
Function: May regulate the synthesis and function of lysosomes and of highly specialized organelles, such as
melanosomes and platelet dense granules

Gene Wiki entry for HPS6


(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000010.10  NC_018921.1  NT_030059.13  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the HPS6 gene promoter:
         ER-alpha   RP58   Pax-5   Lmo2   LCR-F1   C/EBPalpha   E2F-1   E2F   ARP-1   Pax-4a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidHPS6 promoter sequence
   Search SABiosciences Chromatin IP Primers for HPS6

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat HPS6


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

Entrez Gene cytogenetic band: 10q24.32   Ensembl cytogenetic band:  10q24.32   HGNC cytogenetic band: 10q24.32

HPS6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HPS6 gene location

GeneLoc information about chromosome 10         GeneLoc Exon Structure

GeneLoc location for GC10P103815:  view genomic region     (about GC identifiers)

Start:
103,825,147 bp from pter      End:
103,827,793 bp from pter
Size:
2,647 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: HPS6_HUMAN, Q86YV9 (See protein sequence)
Recommended Name: Hermansky-Pudlak syndrome 6 protein  
Size: 775 amino acids; 82975 Da
Subunit: Component of the biogenesis of lysosome-related organelles complex-2 (or BLOC2) composed of HPS3, HPS5 and
HPS6. Directly interacts with HPS5. Interacts with biogenesis of lysosome-related organelles complex-1 (BLOC1).
Interacts with AP-3 complex. Interacts with MNAT1 (Probable)
Subcellular location: Microsome membrane. Cytoplasm, cytosol. Early endosome membrane
Sequence caution: Sequence=BAB15378.1; Type=Erroneous initiation;
Secondary accessions: Q5VV69 Q9H685

Explore the universe of human proteins at neXtProt for HPS6: NX_Q86YV9

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q86YV9

  • HPS6 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_079023.2  
    ENSEMBL proteins: 
     ENSP00000299238  

    Human Recombinant Protein Products: 
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    Uscn Proteins for HPS6

    Gene Ontology (GO): 4 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005783endoplasmic reticulum IEA--
    GO:0005792microsome ----
    GO:0005829cytosol IEA--
    GO:0031901early endosome membrane IEA--


    HPS6 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    HPS6 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR017218 BLOC-2_complex_Hps6_subunit

    Graphical View of Domain Structure for InterPro Entry Q86YV9

    ProtoNet protein and cluster: Q86YV9


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: HPS6_HUMAN, Q86YV9
    Function: May regulate the synthesis and function of lysosomes and of highly specialized organelles, such as
    melanosomes and platelet dense granules

    miRNA
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    hsa-miR-670 hsa-miR-592
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    Inhib. RNA
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    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----


    HPS6 for ontologies           About GeneDecksing


    Animal Models:
         12 MGI mutant phenotypes (inferred from 9 alleles(MGI details for Hps6):
     cardiovascular system  craniofacial  hearing/vestibular/ear  hematopoietic system  homeostasis/metabolism 
     immune system  integument  nervous system  normal  pigmentation 
     renal/urinary system  vision/eye 

    HPS6 for phenotypes           About GeneDecksing


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for HPS6

    STRING Interaction Network Preview (showing 5 interactants - click image to see 9)

    5/13 Interacting proteins for HPS6 (Q86YV92, 3 ENSP000002992384) via UniProtKB, MINT, STRING, and/or I2D (see all 13)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    MNAT1P519482, 3, ENSP000002612454MINT-63851 I2D: score=5 STRING: ENSP00000261245
    KIAA0020Q153972, 3, ENSP000003809824MINT-64473 I2D: score=4 STRING: ENSP00000380982
    PIK3CBP423382, 3, ENSP000002891534MINT-8266172 I2D: score=2 STRING: ENSP00000289153
    TTC19Q6DKK22, 3, ENSP000002616474MINT-8275666 I2D: score=2 STRING: ENSP00000261647
    OSGEPQ9NPF42, 3MINT-8265146 I2D: score=2 
    About this table

    Gene Ontology (GO): 4 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006996organelle organization IEA--
    GO:0007596blood coagulation IEA--
    GO:0030318melanocyte differentiation IEA--
    GO:0043473pigmentation ----


    HPS6 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for HPS6
    Search CenterWatch for drugs/clinical trials and news about HPS6 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for HPS6 gene: 
    NM_024747.5  

    Unigene Cluster for HPS6:

    Hermansky-Pudlak syndrome 6
    Hs.125133  [show with all ESTs]
    Unigene Representative Sequence: NM_024747
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000299238(uc001kuj.3)

    miRNA
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    hsa-miR-670 hsa-miR-592
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    Inhib. RNA
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    Additional cDNA sequence: 

    AF536238.1 AK026154.1 BC009258.2 BC011594.1 BC014993.1 BC064917.1 BC080564.1 

    4 DOTS entries:

    DT.453368  DT.100035779  DT.100754955  DT.91774533 

    24/121 AceView cDNA sequences (see all 121):

    AI827286 AI470517 BU186682 BM845167 BM665182 BQ933812 T33834 AI871603 
    CB160613 AW406605 BU631093 BI793152 BC064917 BG232039 BM550132 AI921805 
    BU191786 Z41255 AI819004 AI239498 AI351205 NM_024747 BI793128 BC011594 

    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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    HPS6 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TATGGACCTG

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See HPS6 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for HPS6

    SOURCE GeneReport for Unigene cluster: Hs.125133

    UniProtKB/Swiss-Prot: HPS6_HUMAN, Q86YV9
    Tissue specificity: Ubiquitous

        SABiosciences Custom PCR Arrays for HPS6
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HPS6

    (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)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for HPS6 gene from 4/9 species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Hps61 , 5 Hermansky-Pudlak syndrome 61, 5 82.64(n)1
    82.51(a)1
      19 (38.75 cM)5
    201701  NM_176785.31  NP_789742.21 
     460034785 
    chicken
    (Gallus gallus)
    Aves HPS61 Hermansky-Pudlak syndrome 6 56.31(n)
    45.42(a)
      770328  XM_001233663.2  XP_001233664.1 
    lizard
    (Anolis carolinensis)
    Reptilia HPS66
    --
    40(a)
    1 ↔ 1
    GL343239.1(1711822-1714194)
    zebrafish
    (Danio rerio)
    Actinopterygii CU640488.16
    --
    32(a)
    1 ↔ 1
    13(29005324-29007750)


    ENSEMBL Gene Tree for HPS6 (if available)
    TreeFam Gene Tree for HPS6 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
      --

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/108 NCBI SNPs in HPS6 are shown (see all 108    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 10 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs27868471,2
    C,F,A,H,--103823135(-) CACTGC/TACCCG 1 -- us2k125Minor allele frequency- T:0.40NS EA NA WA CSA 2351
    rs1483612851,2
    --103823240(+) AAACCC/TGACCT 1 -- us2k10--------
    rs1884748071,2
    --103823370(+) CGAGAC/TTGCGC 1 -- us2k10--------
    rs49196071,2
    C,--103823374(+) attgcG/Accact 1 -- us2k1 tfbs32Minor allele frequency- A:0.00NA 4
    rs1831287561,2
    --103823423(+) ATAAAC/TAAATA 1 -- us2k10--------
    rs1421017011,2
    --103823442(+) AGGCAC/TGGTGG 1 -- us2k10--------
    rs1869194091,2
    --103823953(+) GAAGGA/GAAGAA 1 -- us2k10--------
    rs754479391,2
    F,--103824013(+) GAAAAG/TGGGAG 1 -- us2k11Minor allele frequency- T:0.03EA 120
    rs755398301,2
    C,F,--103824086(+) TGACAG/AGGTAT 1 -- us2k11Minor allele frequency- A:0.13EA 120
    rs1143222521,2
    C,F,--103824154(+) GAAGGT/CAGGGG 1 -- us2k11Minor allele frequency- C:0.03WA 118

    HapMap Linkage Disequilibrium report for HPS6 (103825147 - 103827793 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for HPS6: --
    Human Gene Mutation Database (HGMD): HPS6

    Locus Specific Mutation Databases (LSDB): HPS6

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing HPS6
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    HPS6 for disorders           About GeneDecksing

    OMIM gene information: 607522   
    OMIM disorders: 203300  
    UniProtKB/Swiss-Prot: HPS6_HUMAN, Q86YV9
  • Defects in HPS6 are the cause of Hermansky-Pudlak syndrome type 6 (HPS6) [MIM:614075]. Hermansky-Pudlak
  • syndrome (HPS) is a genetically heterogeneous, rare, autosomal recessive disorder characterized by oculocutaneous
    albinism, bleeding due to platelet storage pool deficiency, and lysosomal storage defects. This syndrome results from
    defects of diverse cytoplasmic organelles including melanosomes, platelet dense granules and lysosomes. Ceroid storage
    in the lungs is associated with pulmonary fibrosis, a common cause of premature death in individuals with HPS

    10 diseases for HPS6:    About MalaCards
    hermansky-pudlak syndrome    hermansky-pudlak syndrome 6    hermansky-pudlak syndrome 5    hermansky-pudlak syndrome 3
    platelet storage pool deficiency    oculocutaneous albinism    albinism    pulmonary fibrosis
    fibrosis    alzheimer's disease

    3 diseases from the University of Copenhagen DISEASES database for HPS6:
    Hermansky-Pudlak syndrome     Oculocutaneous albinism     Platelet storage pool deficiency

    1 Novoseek disease relationship for HPS6 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    hermansky-pudlak syndrome 94.4 1 15030569 (1)

    GeneTests: HPS6
    Hermansky-Pudlak Syndrome

    Human Genome Epidemiology (HuGE) Navigator: HPS6 (1 document)

    Export disorders for HPS6 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)
    About This Section

    PubMed articles for HPS6 gene, integrated from 9 sources (see all 23):
    (articles sorted by number of sources associating them with HPS6)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Ru2 and Ru encode mouse orthologs of the genes mutated in human Hermansky-Pudlak syndrome types 5 and 6. (PubMed id 12548288)1, 2, 3 Zhang Q.... Swank R.T. (2003)
    2. Characterization of BLOC-2, a complex containing the Hermansky-Pudlak syndrome proteins HPS3, HPS5 and HPS6. (PubMed id 15030569)1, 2, 9 Di Pietro S.M....Dell'Angelica E.C. (2004)
    3. A human protein-protein interaction network: a resource for annotating the proteome. (PubMed id 16169070)1, 2 Stelzl U.... Wanker E.E. (2005)
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    6. Clinical and cellular characterisation of Hermansky-P udlak syndrome type 6. (PubMed id 19843503)1, 9 Huizing M....Gahl W.A. (2009)
    7. Methods for quantification of in vivo changes in prote in ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (2012)
    8. Targeting protein-trafficking pathways alters melanoma treatment sensitivity. (PubMed id 22203954)1 Huang Z.M....Wei M.L. (2012)
    9. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
    10. A directed protein interaction network for investigat ing intracellular signal transduction. (PubMed id 21900206)1 Vinayagam A....Wanker E.E. (2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 79803 HGNC: 18817 AceView: HPS6 Ensembl:ENSG00000166189 euGenes: HUgn79803
    ECgene: HPS6 H-InvDB: HPS6

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for HPS6 Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/HPS6

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for HPS6 gene:
    Search GeneIP for patents involving HPS6

    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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
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