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

SLN Gene

protein-coding   GIFtS: 50
GCID: GC11M107612

sarcolipin

 Explore 9 diseases affiliated with
SLN via our new
 Human Malady Compendium 
Biological research products
for SLN
    

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

Aliases
Sarcolipin1
MGC123011
MGC1258541
MGC1258551

External Ids:    HGNC: 110891   Entrez Gene: 65882   Ensembl: ENSG000001702907   OMIM: 6022035   UniProtKB: O006313   

Export aliases for SLN gene to outside databases

Previous GC identifers: GC11M109772 GC11M108934 GC11M107115 GC11M107083 GC11M103503


(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 SLN:
Sarcoplasmic reticulum Ca(2+)-ATPases are transmembrane proteins that catalyze the ATP-dependent transport of Ca(2+)
from the cytosol into the lumen of the sarcoplasmic reticulum in muscle cells. This gene encodes a small proteolipid
that regulates several sarcoplasmic reticulum Ca(2+)-ATPases. The transmembrane protein interacts with Ca(2+)-ATPases
and reduces the accumulation of Ca(2+) in the sarcoplasmic reticulum without affecting the rate of ATP hydrolysis.
(provided by RefSeq, Jul 2008)

Gene Wiki entry for SLN (Sarcolipin)


(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_000011.9  NC_018922.1  NT_033899.8  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SLN gene promoter:
         Nkx3-1   Nkx3-1 v4   MEF-2   Nkx3-1 v1   C/EBPalpha   MEF-2A   Nkx3-1 v2   Nkx3-1 v3   c-Myb   aMEF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSLN promoter sequence
   Search SABiosciences Chromatin IP Primers for SLN

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


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

Entrez Gene cytogenetic band: 11q22-q23   Ensembl cytogenetic band:  11q22.3   HGNC cytogenetic band: 11q22-q23

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

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11M107612:  view genomic region     (about GC identifiers)

Start:
107,578,101 bp from pter      End:
107,590,419 bp from pter
Size:
12,319 bases      Orientation:
minus 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: SARCO_HUMAN, O00631 (See protein sequence)
Recommended Name: Sarcolipin  
Size: 31 amino acids; 3762 Da
Subunit: Associated with calcium ATPase SERCA1
Subcellular location: Sarcoplasmic reticulum membrane; Single-pass membrane protein
1 PDB 3D structure from and Proteopedia for SLN:
1JDM (3D)    
Secondary accessions: Q6ICV3

Explore the universe of human proteins at neXtProt for SLN: NX_O00631

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_O00631

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

    REFSEQ proteins: NP_003054.1  
    ENSEMBL proteins: 
     ENSP00000435380   ENSP00000434189   ENSP00000304707  

    Human Recombinant Protein Products: 
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    Browse ProSpec Recombinant Proteins
    Uscn Proteins for SLN

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral to membrane NAS9367679
    GO:0016529sarcoplasmic reticulum IDA9575189
    GO:0033017sarcoplasmic reticulum membrane IEA--


    SLN for ontologies           About GeneDecksing



    SLN Antibody Products: 
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    Uscn ELISAs and CLIAs for SLN


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

    SLN for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR008028 Sarcolipin

    Graphical View of Domain Structure for InterPro Entry O00631

    ProtoNet protein and cluster: O00631

    1 Blocks protein family: IPB008028 Sarcolipin

    UniProtKB/Swiss-Prot: SARCO_HUMAN, O00631
    Similarity: Belongs to the sarcolipin family


    (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:
         Genatlas biochemistry entry for SLN:
    sarcolipin,low molecular weight proteolipid associated with the fast-twitch skeletal muscle sarcoplasmic reticulum Ca++
    ATPase (ATP2A1),phospholamban homolog

    miRNA
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    hsa-miR-617 hsa-miR-145 hsa-miR-590-3p hsa-miR-107 hsa-miR-103a
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    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SLN

    Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004857enzyme inhibitor activity ISS12032137
    GO:0030234enzyme regulator activity ----
    GO:0051117ATPase binding ISS12032137


    SLN for ontologies           About GeneDecksing


    Animal Models:
         Mouse knock-out Slntm1Peri for SLN
         2 MGI mutant phenotypes (inferred from 1 allele(MGI details for Sln):
     cardiovascular system  muscle 

    SLN 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:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for SLN

    STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

    4 Interacting proteins for SLN (O006313 ENSP000003047074) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ATP2A1O149833, ENSP000003495954I2D: score=2 STRING: ENSP00000349595
    PLNP266783, ENSP000003501324I2D: score=2 STRING: ENSP00000350132
    ATP2A2P166153I2D: score=1 
    --ENSP000003248924STRING: ENSP00000324892
    About this table

    Gene Ontology (GO): 5/8 biological process terms (GO ID links to tree view) (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006816calcium ion transport NAS9367679
    GO:0043086negative regulation of catalytic activity ISS12032137
    GO:0043242negative regulation of protein complex disassembly ISS12032137
    GO:0051924regulation of calcium ion transport ISS--
    GO:0090281negative regulation of calcium ion import ISS12032137


    SLN 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

    SLN for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for SLN

    1 HMDB Compound for SLN    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--
    2 Novoseek chemical compound relationships for SLN gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    calcium 47 30 9575189 (4), 17616528 (2), 16519897 (2), 18081313 (2) (see all 13)
    lipid 20.1 13 17586575 (3), 16953579 (3), 11781085 (2), 11772399 (1) (see all 6)

    Search CenterWatch for drugs/clinical trials and news about SLN / SARCO 

    (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 SLN gene: 
    NM_003063.2  

    Unigene Cluster for SLN:

    Sarcolipin
    Hs.334629  [show with all ESTs]
    Unigene Representative Sequence: BF694738
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000531293(uc001pjp.3) ENST00000525934 ENST00000305991

    miRNA
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    5 QIAGEN miScript miRNA Assays for microRNAs that regulate SLN:
    hsa-miR-617 hsa-miR-145 hsa-miR-590-3p hsa-miR-107 hsa-miR-103a
    SwitchGear 3'UTR luciferase reporter plasmidSLN 3' UTR sequence
    Inhib. RNA
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    OriGene siRNA: SLN
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat SLN
    Clone
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SLN 
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat SLN

    Additional cDNA sequence: 

    AK312097.1 BC005261.1 BC094685.1 BC104150.2 BC104185.2 BC113930.1 BC113987.1 U96094.1 

    3 DOTS entries:

    DT.215889  DT.92432410  DT.92432404 

    24/153 AceView cDNA sequences (see all 153):

    BM090813 F18591 F18810 AA112042 AW450261 BU737006 F31795 AW051121 
    BF222001 F32532 F32610 AA196050 CR450290 BG204330 BG207478 W67459 
    AJ572341 F34683 F32064 AJ346720 BM668976 BE645530 F29875 F22314 

    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

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

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

    About this image

    SLN expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    Stem Cell Differentiation: 5 LifeMap Cells 
    NameCategory
    Syncytiotrophoblast-like cells (Generation of syncyt...)
    Embryoid bodies (Two-step protocol fo...)
    Mesendoderm (Derivation and sorti...)
    Podocalyxin+, CD24+, GCTM2- (Derivation and sorti...)
    Podocalyxin+, CD24+, GCTM2 (low) (Derivation and sorti...)
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See SLN Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SLN

    SOURCE GeneReport for Unigene cluster: Hs.334629
        SABiosciences Custom PCR Arrays for SLN
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SLN

    (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 human and mouse.

    Orthologs for SLN gene from 1 species (see representative species )    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Sln5 sarcolipin   --   9 (29.24 cM) 53850251 


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

    10/125 NCBI SNPs in SLN are shown (see all 125    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1498723371,2
    C,--107577649(+) ATAAC-/AATAATCA 1 -- ds50010--------
    rs1445204651,2
    --107577663(+) AATAGA/TCTATG 1 -- ds50010--------
    rs1845373511,2
    --107577671(+) ATGCTA/CCTCTT 1 -- ds50010--------
    rs112123361,2
    H--107577678(+) TCTTAG/AGGACA 1 -- ds50014Minor allele frequency- A:0.00NS EA 420
    rs1893640371,2
    --107577680(+) TTAGGA/GACATG 1 -- ds50010--------
    rs1485490671,2
    --107577758(+) TTATAA/CGATAG 1 -- ds50010--------
    rs71053971,2
    C,F,A,H,--107577778(+) TTCTTG/CTGGAT 1 -- ds500111Minor allele frequency- C:0.21NS EA NA WA CSA 785
    rs127872351,2
    H--107577785(+) GGATTC/ATAAAG 1 -- ds50014Minor allele frequency- A:0.00NS EA 418
    rs127870731,2
    H--107577788(+) TTCTAA/GAGATA 1 -- ds50014Minor allele frequency- G:0.00NS EA 412
    rs127870951,2
    H--107577831(+) TAGCCA/CGCAAT 1 -- ds50014Minor allele frequency- C:0.00NS EA 420

    HapMap Linkage Disequilibrium report for SLN (107578101 - 107590419 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for SLN
         1 CNV: 8696

    SABiosciences Cancer Mutation PCR Assays
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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

    SLN for disorders           About GeneDecksing

    OMIM gene information: 602203    OMIM disorders: --

    9 diseases for SLN:    About MalaCards
    long qt syndrome    atrial fibrillation    hypertrophic cardiomyopathy    familial hypertrophic cardiomyopathy
    congenital heart defect    tetralogy of fallot    endometriosis of uterus    dysferlinopathy
    cardiomyopathy

    1 Novoseek disease relationship for SLN gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    atrial fibrillation 10.9 4 17010328 (3), 15530144 (1)

    Human Genome Epidemiology (HuGE) Navigator: SLN (5 documents)

    Export disorders for SLN 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 SLN gene, integrated from 9 sources (see all 44):
    (articles sorted by number of sources associating them with SLN)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Characterization of the gene encoding human sarcolipin (SLN), a proteolipid associated with SERCA1: absence of structural mutations in five patients with Brody disease. (PubMed id 9367679)1, 2, 3, 9 Odermatt A.... Maclennan D.H. (1997)
    2. Structure and orientation of sarcolipin in lipid environments. (PubMed id 11781085)1, 2, 9 Mascioni A.... Veglia G. (2002)
    3. Sarcolipin regulates the activity of SERCA1, the fast-twitch skeletal muscle sarcoplasmic reticulum Ca2+-ATPase. (PubMed id 9575189)1, 9 Odermatt A....MacLennan D.H. (1998)
    4. Sarcolipin uncouples hydrolysis of ATP from accumulation of Ca2+ by the Ca2+-ATPase of skeletal-muscle sarcoplasmic reticulum. (PubMed id 11772399)1, 9 Smith W.S....Lee A.G. (2002)
    5. Sarcolipin regulates sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) by binding to transmembrane helices alone or in association with phospholamban. (PubMed id 12692302)1, 9 Asahi M....MacLennan D.H. (2003)
    6. The variation of the sarcolipin gene (SLN) in atrial fibrillation, long QT syndrome and sudden arrhythmic death syndrome. (PubMed id 17010328)1, 9 Nyberg M.T....Christiansen M. (2007)
    7. SERCA2a, phospholamban, sarcolipin, and ryanodine receptors gene expression in children with congenital heart defects. (PubMed id 17515962)1, 9 Vittorini S....Clerico A. (2007)
    8. Decreased sarcolipin protein expression and enhanced sarco(endo)plasmic reticulum Ca2+ uptake in human atrial fibrillation. (PubMed id 21640081)1 Shanmugam M....Babu G.J. (2011)
    9. Variation at the NFATC2 locus increases the risk of t hiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipr il and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1 Bailey S.D....Anand S. (2010)
    10. Gene-centric association signals for lipids and apoli poproteins identified via the HumanCVD BeadChip. (PubMed id 19913121)1 Talmud P.J.... . (2009)

    (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, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 6588 HGNC: 11089 AceView: SLN Ensembl:ENSG00000170290 euGenes: HUgn6588
    ECgene: SLN H-InvDB: SLN

    (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 SLN Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for SLN gene:
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    (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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     Regulatory tfbs in SLN promoter
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     SLN Proteins, Antibodies, CLIAs, and ELISAs
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