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LYST Gene

protein-coding   GIFtS: 51

GC01M233890
lysosomal trafficking regulator
(Previous name: Chediak-Higashi syndrome 1 )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: CHS1)
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section

Aliases
CHS 1, 2, 3
CHS1 2, 3, 5
OTTHUMP00000059294 2
Descriptions
Beige homolog 3
Chediak-Higashi syndrome 1 1, 2
beige protein 2
lysosomal trafficking regulator 2
External Ids
HGNC: 19681
Entrez Gene: 11302
UniProtKB: Q996983
Ensembl: ENSG000001436697
Search outside databases for aliases for LYST gene

Previous GC identifer: GC01M232151

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

EntrezGene summary for LYST:
This gene is thought to encode a protein that regulates intracellular protein trafficking to and
from the lysosome. Mutations in this gene are associated with Chediak-Higashi syndrome, a rare
lysosomal storage disorder. Alternatively spliced transcript variants have been described but
their full-length nature has not been determined. [provided by RefSeq]

UniProtKB/Swiss-Prot: LYST_HUMAN, Q99698
Function: May be required for sorting endosomal resident proteins into late multivesicular
endosomes by a mechanism involving microtubules

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the LYST gene  

Entrez Gene cytogenetic band: 1q42.1-q42.2   Ensembl cytogenetic band:  1q42.3   HGNC cytogenetic band: 1q42.1-q42.2

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

GeneLoc gene densities for chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M233890:     (about GC identifiers)

Start:
233,890,964 bp from pter
End:
234,096,843 bp from pter
Size:
205,880 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000001.9  NT_004836.17  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
About This Section

UniProtKB/Swiss-Prot: LYST_HUMAN, Q99698 (See protein sequence)
Recommended Name: Lysosomal-trafficking regulator  
Size: 3801 amino acids; 429139 Da
Subunit: Interacts with CENPJ, LIP8 and ZNF521
Subcellular location: Cytoplasm (Potential)
Secondary accessions: O43274 Q5T2U9 Q96TD7 Q96TD8 Q99709 Q9H133
Alternative splicing: 3 isoforms:  Q99698-1   Q99698-2   Q99698-3   (Additional isoforms seem to exist)

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins: NP_000072.2  

    ENSEMBL proteins: 
    ENSP00000374443 ENSP00000374444 


    Human Recombinant Proteins 
    Browse Drug Discovery Central at Invitrogen for human recombinant proteins
    Browse Purified and Recombinant Proteins at Millipore
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    Browse R&D Systems for human recombinant proteins
    Browse recombinant and purified proteins available from Enzo Life Sciences
    Browse Abcam for Recombinant Proteins
    Human Recombinant Proteins from Abnova (LYST)
                    Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

    2 Gene Ontology (GO) cellular component terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737 cytoplasm IEA--
    GO:0015630 microtubule cytoskeleton IDA9606205
    About this table

    Antibodies for LYST: 
    Browse Antibodies Central at Invitrogen
    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Browse Antibodies at Sigma-Aldrich
    Browse R&D Systems for Antibodies
    Search for antibodies at Abcam and the World's Antibody Gateway (free search engine of over 150 antibody companies)
    Browse Abnova for Monoclonal and Polyclonal Antibodies
    Search Novus for antibodies for LYST

    Assays for LYST: 
    Browse Invitrogen for biochemical assays
    Browse Kits and Assays available from Millipore
    Browse R&D Systems for biochemical assays
    Browse biochemical assays available from Enzo Life Sciences

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

    5/7 InterPro domains/families (see all 7 ):
     IPR019782 WD40_repeat_2
     IPR000409 Beige_BEACH
     IPR019775 WD40_repeat_CS
     IPR001680 WD40_repeat
     IPR017986 WD40_repeat_region


       GeneDecks  LYST for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry Q99698

    ProtoNet protein and cluster: Q99698

    1 Blocks protein family: IPB000409 Beige/BEACH domain

    UniProtKB/Swiss-Prot: LYST_HUMAN, Q99698
    Similarity: Contains 1 BEACH domain
    Similarity: Contains 7 WD repeats

    (According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
    shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
    RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (LYST)
    Browse for Gene Knock-down Tools from Millipore
    Browse Abnova for Chimera RNAi Products
                   OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_001005736

                  Applied Biosystems Silencer® siRNAs for LYST

                  Sigma-Aldrich siRNA for LYST  
                         Sigma-Aldrich shRNA Panels and shRNA for LYST  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Browse Clone Ranger at Invitrogen for clones
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_000081
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_000081
                                     untagged cDNA clones in CMV expression vector (see all 2): NM_000081 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_000081

    UniProtKB/Swiss-Prot: LYST_HUMAN, Q99698
    Function: May be required for sorting endosomal resident proteins into late multivesicular
    endosomes by a mechanism involving microtubules

    Genatlas biochemistry entry for LYST:
    putative lysosomal associated membrane protein,intracellular trafficking regulator,with two
    alternatively spliced isoforms,homologous to mouse beige and yeast VPS15

    14 MGI mutant phenotypes (inferred from 15 alleles(MGI details for Lyst):

    cellularcraniofacialhearing/vestibular/earhematopoietic systemhomeostasis/metabolism
    immune systemlimbs/digits/tailnervous systemno phenotypic analysispigmentation
    renal/urinary systemskin/coat/nailstumorigenesisvision/eye

    1 Gene Ontology (GO) molecular function term (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515 protein binding IPI11984006
    About this table

    (Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
    Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section


      --

    5/10 Gene Ontology (GO) biological process terms (links to tree view) (see all 10 ):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0015031 protein transport IEA--
    GO:0030595 leukocyte chemotaxis ISS--
    GO:0032438 melanosome organization ISS--
    GO:0032510 endosome to lysosome transport via multivesicular body sorting pathway IMP9606205
    GO:0033364 mast cell secretory granule organization ISS--
    About this table
    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
    About This Section

    Browse drugs & compounds from Enzo Life Sciences
    Browse Small Molecules at Sigma-Aldrich

    Browse Tocris compounds for LYST
    6 Novoseek chemical compound relationships for LYST gene
    Compound   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    chalcone 78.16 9 9223265 (1), 17028970 (1), 9002621 (1), 9774634 (1) (see all 6)
    chitin 69.96 17 17302816 (4), 12429521 (2), 17971081 (2), 10826699 (1) (see all 8)
    anthocyanin 47.46 1 17028970 (1)
    flavonoid 32.87 1 17028970 (1)
    histidine 12.84 1 10690356 (1)
    cholesterol 0.00 2 14657904 (1)
    About this table


    (GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView,
    non coding RNAs according to RNAdb,
    ESTs according to GeneTide,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from Invitrogen, Millipore, and/or Abnova,
    siRNAs from Applied Biosystems, Sigma-Aldrich,
    shRNA from Sigma-Aldrich, OriGene,
    Tagged/untagged cDNA clones from OriGene,
    Expression Assays from Applied Biosystems)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (LYST)
    Browse for Gene Knock-down Tools from Millipore
    Browse Abnova for Chimera RNAi Products
                   OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_001005736

                  Sigma-Aldrich siRNA for LYST  
                         Sigma-Aldrich shRNA Panels and shRNA for LYST  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_000081  

    REFSEQ mRNAs for LYST gene: 

    NM_000081.2   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_000081  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_000081
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_000081
                                     untagged cDNA clones in CMV expression vector (see all 2): NM_000081 

    Additional cDNA sequence: 

    AK307457.1 AK310790.1 AK311664.1 AL833100.1 BC020793.1 BC033098.1 BC144702.1 BX649113.1 
    L77889.1 U67615.1 U70064.1 U72192.1 U84744.1 

    18 DOTS entries:

    DT.95364459  DT.95173157  DT.100777965  DT.216563  DT.216564  DT.91843611  DT.95173154  DT.100777966 
    DT.100777967  DT.91752927  DT.40128160  DT.92427793  DT.95332360  DT.97771673  DT.97808809  DT.101974170 
    DT.95257026  DT.95354749 

    24/149 AceView cDNA sequences (see all 149 ):

    BQ011080 BM055408 BM055110 U70064 CK904950 BU738114 BM700528 BQ214459 
    BX649113 AW236542 BX100814 BM700370 AI683851 AI869371 BC033098 AA424769 
    BU740347 BX492438 AA486745 BU738023 AI698283 AI275101 AA360606 NM_000081 

    highest scoring ESTs for LYST:

    U70064 AI041860 N24226 BC033098 BG764384 BX646232 H99579 L77889 N25938 U67615 

    Unigene Cluster for LYST:

    Lysosomal trafficking regulator
    Hs.532411  [show with all ESTs]
    Unigene Representative Sequence: NM_000081


    GeneLoc Exon Structure

    2 Ensembl transcripts including schematic representations:
    ENST00000389793  ENST00000389794  
    (Experimental results according to 1GeneNote and GNF BioGPS,
    probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
    Expression Assays from Applied Biosystems )
    About This Section

    LYST expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for LYST

    1 / 2 / 3

    9 probe-sets matching LYST gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
    35695_at2, 3 U95-A 1 1.00 1.00 0.89 1.52 U67615 0.80 0.88 0.84 1

    35696_s_at2, 3 U95-A 1 1.00 1.00 0.75 0.50 U70064 1.00 0.90 0.95 1
    49515_at2, 3 U95-C 1 0.31 1.00 0.96 1.02 AI041860 0.80 1.00 0.91 1

    215415_s_at2, 3 U133-A 1 1.00 1.00 -- -- U70064 1.00 0.90 0.95 1

    210943_s_at2, 3 U133-A 1 1.00 1.00 -- -- U84744 0.80 0.88 0.84 1

    203518_at2, 3 U133-A 1 1.00 1.00 -- -- NM_000081 0.60 1.00 0.82 1

    215415_s_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    210943_s_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    203518_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
    GeneDecks  LYST for binary patterns associated with the probe-sets selected above  
    About GeneDecksing
    About this table    
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: --

    SOURCE GeneReport for Unigene cluster: Hs.532411

    Expression variation in blood from EXPOLDB for LYST

    UniProtKB/Swiss-Prot: LYST_HUMAN, Q99698
    Tissue specificity: Abundantly expressed in adult and fetal thymus, peripheral blood leukocytes,
    bone marrow and several regions of the adult brain

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
    About This Section


    Orthologs for LYST gene from 5/7 species (see all 7 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    LYST1   -- lysosomal trafficking regulator 90.61(n)
    90.84(a)
    479195  XM_536337.2  XP_536337.2 
    chimpanzee
    (Pan troglodytes)
    LYST1   -- lysosomal trafficking regulator 99.43(n)
    99.11(a)
    457838  XM_514288.2  XP_514288.2 
    cow
    (Bos taurus)
    LYST1   -- lysosomal trafficking regulator 90.03(n)
    90.54(a)
    281072  NM_174020.2  NP_776445.1 
    rat
    (Rattus norvegicus)
    Lyst1   -- lysosomal trafficking regulator 85.32(n)
    85.51(a)
    85419  NM_053518.1  NP_445970.1 
    mouse
    (Mus musculus)
    Lyst1, 5 13 (7.00 cM)5
    lysosomal trafficking regulator1, 5 85.2(n)1
    85.64(a)1
    171011  NM_010748.21  NP_034878.21 
     AK0421985  AK0896355  (see all 12)
    About this table        Species with no ortholog for LYST

    ENSEMBL Gene Tree for LYST
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for LYST gene
    NSMAF2  WDFY42  WDFY32  

    (According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
    About This Section


    10/962 NCBI SNPs in LYST are shown (see all 962 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 300)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 1 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs75242611,2
    A,C,F,H234040167(+) TGTTAA/CAAAAT 1 L/V mis112Minor allele frequency- C:0.04NA EU EA WA 1052
    rs75484491,2
    A,C,F,H234097264(+) GTGTAG/TGTCTA 1 -- ng314Minor allele frequency- T:0.36EU EA WA 412
    rs104656131,2
    A,C,F,H234036009(+) TTACAC/TTTGTA 1 S/N mis1 ese39Minor allele frequency- T:0.03EU EA WA NA 916
    rs37680671,2
    C,F,H234040373(+) CTAAAT/CGTAAT 1 R/H mis19Minor allele frequency- C:0.01EA EU WA 2294
    rs75410411,2
    A,C,H233989429(+) ATTGCG/ATTAGT 1 M/T mis14Minor allele frequency- A:0.00EU EA WA 418
    rs66655681,2
    C,F,H234000158(+) ATCTGC/GTGGTG 1 Q/H mis1 ese39Minor allele frequency- G:0.07EU EA WA NA 902
    rs346422411,2
    C,F233976438(+) GGGGAA/TATTTT 1 F/Y mis15Minor allele frequency- T:0.02NA EU EA WA 498
    rs127281851,2
    A,H233891901(+) TCTGCC/GTCCTG 1 -- ut314Minor allele frequency- G:0.00EU EA WA 418
    --
    rs46601171,2
    A,C234098156(+) gtggcC/Gggata 1 -- ng310--------
    rs353331951,2
    C,F233964530(+) ATTCAC/TCTTGG 1 G/D mis15Minor allele frequency- T:0.06NA EU EA WA 494
    About this table

    HapMap Linkage Disequilibrium images for LYST (up to first 250kb)

    (in which this Gene is Involved, According to OMIM, UniProtKB, Novoseek, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
    About This Section

    OMIM: 606897   disorders: 214500  

    UniProtKB/Swiss-Prot: LYST_HUMAN, Q99698

  • Defects in LYST are the cause of Chediak-Higashi syndrome (CHS) [MIM:214500]. CHS is a
    rare autosomal recessive disorder characterized by hypopigmentation, severe immunologic
    deficiency, a bleeding tendency, neurologic abnormalities, abnormal intracellular transport to and
    from the lysosome, and giant inclusion bodies in a variety of cell types. Most patients die at an
    early age unless they receive an allogeneic hematopoietic stem cell transplant (SCT)
  • 2 Novoseek disease relationships for LYST gene

    Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    chediak-higashi syndrome 95.55 13 10594238 (2), 17512928 (2), 16518687 (1), 9070932 (1) (see all 9)
    tumors 4.55 1 11504836 (1)
    About this table

    GeneTests: LYST
    Chediak-Higashi Syndrome

    Human Gene Mutation Database: LYST

    (Possibly Related Articles in Doctor's Guide)
    About This Section

      --

    (in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
    About This Section

    10/66 PubMed articles for LYST gene (see all 66 ):
    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section

     ANDOR
    Aliases
    Disorders
    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, and/or H-InvDB)
    About This Section

    Entrez Gene: 1130 HGNC: 1968 AceView: CHS1 Ensembl:ENSG00000143669 euGenes: HUgn1130
    ECgene: LYST H-InvDB: LYST
    (According to HUGE)
    About This Section

      --
    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section

    NameDescription
    LYSTbasehttp://bioinf.uta.fi/LYSTbase/
    Mutations of the LYST genehttp://www.retina-international.com/sci-news/chsmut.htm
    Albinism database (ADB)http://albinismdb.med.umn.edu/chs1mut.html
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



    Products for LYST:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



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      Invitrogen Proteins / Assays / Screening Services  Search Invitrogen catalog for LYST-related products

     Millipore Custom Antibody & Bulk Services
     Millipore Preclinical / Clinical Development Services
     Millipore Immunoassay Services
     Millipore Target Screening & Profiling Services


     Predesigned and custom siRNAs for LYST Browse antibodies at Sigma-Aldrich
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
     Lentivirus-delivered shRNAs for LYST Browse small molecules at Sigma-Aldrich
     "Your Favorite Gene" Pathwaysfeedback


      
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