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

SMYD1 Gene

protein-coding   GIFtS: 52
GCID: GC02P088367

SET and MYND domain containing 1

 Explore 4 diseases affiliated with
SMYD1 via our new
 Human Malady Compendium 
Biological research products
for SMYD1
    

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

Aliases
SET And MYND Domain Containing 11 2     ZMYND182
BOP1 2     CD8 Beta Opposite2
KMT3D1 2     SET And MYND Domain-Containing Protein 12
ZMYND221 2     Zinc Finger, MYND Domain Containing 182

External Ids:    HGNC: 209861   Entrez Gene: 1505722   Ensembl: ENSG000001155937   OMIM: 6068465   UniProtKB: Q8NB123   

Export aliases for SMYD1 gene to outside databases

Previous GC identifers: GC02P088252 GC02P088269 GC02P088206 GC02P087289


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

UniProtKB/Swiss-Prot: SMYD1_HUMAN, Q8NB12
Function: Acts as a transcriptional repressor. Essential for cardiomyocyte differentiation and cardiac morphogenesis
(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000002.11  NC_018913.1  NT_022184.15  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SMYD1 gene promoter:
         HOXA9   HOXA9B   Elk-1   POU6F1 (c2)   GATA-1   MEF-2A   HOXA5   Meis-1a   aMEF-2   Meis-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSMYD1 promoter sequence
   Search SABiosciences Chromatin IP Primers for SMYD1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SMYD1


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

Entrez Gene cytogenetic band: 2p11.2   Ensembl cytogenetic band:  2p11.2   HGNC cytogenetic band: 2p11.1

SMYD1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SMYD1 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02P088367:  view genomic region     (about GC identifiers)

Start:
88,367,299 bp from pter      End:
88,412,906 bp from pter
Size:
45,608 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: SMYD1_HUMAN, Q8NB12 (See protein sequence)
Recommended Name: SET and MYND domain-containing protein 1  
Size: 490 amino acids; 56617 Da
Subunit: Interacts with HDAC1, HDAC2 and HDAC3 (By similarity)
Subcellular location: Cytoplasm (By similarity). Nucleus (By similarity)
Secondary accessions: A0AV30 A6NE13

Explore the universe of human proteins at neXtProt for SMYD1: NX_Q8NB12

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q8NB12

  • SMYD1 Protein expression data from MOPED and PaxDb: --
    REFSEQ proteins: NP_938015.1  
    ENSEMBL proteins: 
     ENSP00000393453   ENSP00000407888   ENSP00000387482  

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    Browse ProSpec Recombinant Proteins
    Uscn Proteins for SMYD1

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--
    GO:0005737cytoplasm IEA--


    SMYD1 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

    SMYD1 for domains           About GeneDecksing

    2 InterPro domains/families:
     IPR002893 Znf_MYND
     IPR001214 SET_dom

    Graphical View of Domain Structure for InterPro Entry Q8NB12

    ProtoNet protein and cluster: Q8NB12

    2 Blocks protein families:
    IPB001214 Nuclear protein SET
    IPB002893 Zn-finger


    UniProtKB/Swiss-Prot: SMYD1_HUMAN, Q8NB12
    Similarity: Contains 1 MYND-type zinc finger
    Similarity: Contains 1 SET domain


    (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: SMYD1_HUMAN, Q8NB12
    Function: Acts as a transcriptional repressor. Essential for cardiomyocyte differentiation and cardiac morphogenesis
    (By similarity)

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    hsa-miR-3678-3p hsa-miR-1298 hsa-miR-765 hsa-miR-3120-3p hsa-miR-888 hsa-miR-373* hsa-miR-664 hsa-miR-4261
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    Inhib. RNA
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    Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0003714transcription corepressor activity IEA--
    GO:0005515protein binding ----
    GO:0008270zinc ion binding IEA--


    SMYD1 for ontologies           About GeneDecksing


    Animal Models:
         Mouse knock-out Smyd1tm1Dsr for SMYD1
         6 MGI mutant phenotypes (inferred from 1 allele(MGI details for Smyd1):
     cardiovascular system  cellular  embryogenesis  growth/size  mortality/aging 
     muscle 

    SMYD1 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

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Heart Development
    Heart Development1.00


    1 BioSystems Pathway for SMYD1 
        Heart Development


    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SMYD1

    3 Interacting proteins for SMYD1 (Q8NB123) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HDAC3O153793I2D: score=2 
    HDAC1Q135473I2D: score=1 
    HDAC2Q927693I2D: score=1 
    About this table

    Gene Ontology (GO): 5/6 biological process terms (GO ID links to tree view) (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006338chromatin remodeling IEA--
    GO:0006351transcription, DNA-dependent IEA--
    GO:0007507heart development IEA--
    GO:0010831positive regulation of myotube differentiation IDA19783823
    GO:0045663positive regulation of myoblast differentiation IDA19783823


    SMYD1 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 SMYD1
    Search CenterWatch for drugs/clinical trials and news about SMYD1 

    (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 SMYD1 gene: 
    NM_198274.3  

    Unigene Cluster for SMYD1:

    SET and MYND domain containing 1
    Hs.516176  [show with all ESTs]
    Unigene Representative Sequence: NM_198274
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000419482(uc002ssq.2 uc002ssr.3 uc002sss.3) ENST00000444564
    ENST00000438570 ENST00000468008

    miRNA
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat SMYD1
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    hsa-miR-3678-3p hsa-miR-1298 hsa-miR-765 hsa-miR-3120-3p hsa-miR-888 hsa-miR-373* hsa-miR-664 hsa-miR-4261
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    Inhib. RNA
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    Additional cDNA sequence: 

    AF086123.1 AK022290.1 AK091724.1 AL832035.1 AY518933.1 AY518934.1 BC017915.1 BC126191.1 
    BX647878.1 

    4 DOTS entries:

    DT.306345  DT.454717  DT.100747244  DT.120946134 

    24/65 AceView cDNA sequences (see all 65):

    AA248334 AI078564 AI079318 BX500817 AI004011 AU147602 AK091724 AU121872 
    BM722342 BF060984 BF790590 CF552718 AA716121 AI420970 W95588 AI014299 
    AJ572108 BX647878 BX103184 AI015235 BQ918532 AX747145 NM_198274 F30640 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for SMYD1    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12
    SP1:              -                                                                                 
    SP2:                                                  -                                             
    SP3:                                                                                                
    SP4:              -           -     -     -     -     -     -     -     -     -     -     -         


    ECgene alternative splicing isoforms for SMYD1

    (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

    SMYD1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: AAACTGTATT

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

    About this image

    SMYD1 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    4 LifeMap In Vivo Development Anatomical Compartments/Cells 
    Tissue Anatomical Compartment CellCategory (developmental path)
    HeartMyocardiumCardiomyocytesMyocardium
    HeartPrimitive Heart TubePrimitive Heart Tube CellsMyocardium
    LimbForelimb MyotomeLimb Muscle Progenitor CellsSkeletal Muscle
    HeartHeart TubeHeart
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 2 LifeMap Cells 
    NameCategory
    DKK1-induced cells (Derivation of cardio...)
    Cardiomyocyte-like progenitor cells (Derivation of cardio...)

    Genevestigator expression for SMYD1

    SOURCE GeneReport for Unigene cluster: Hs.516176
        SABiosciences Custom PCR Arrays for SMYD1
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SMYD1

    (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 eukaryotes.

    Orthologs for SMYD1 gene from 8/26 species (see all 26)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves SMYD11 SET and MYND domain containing 1 78.69(n)
    82.06(a)
      373960  NM_204155.1  NP_989486.1 
    lizard
    (Anolis carolinensis)
    Reptilia SMYD16
    --
    81(a)
    1 ↔ 1
    6(59317803-59360113)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.18172 Xenopus laevis transcribed sequence with weak similarity more 77.51(n)    BJ073212.1 
    zebrafish
    (Danio rerio)
    Actinopterygii 570461612   -- 78.48(n)    57046161 
    fruit fly
    (Drosophila melanogaster)
    Insecta Bzd6
    Buzidau
    21(a)
    1 → many
    X(2500712-2502700)
    worm
    (Caenorhabditis elegans)
    Secernentea set-186
    set-146
    (see all 4)
    SET domain-containing protein 14
    (see all 4)
    18(a)
    18(a)
    (see all 4)
    many ↔ many
    many ↔ many
    (see all 4)
    I(10590709-10593951)
    II(10793516-10796240)
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons SDG376
    histone-lysine N-methyltransferase ASHR1
    21(a)
    possible ortholog
    2(7773328-7776683)
    rice
    (Oryza sativa)
    Liliopsida --
    zinc finger protein, putative, expressed
    21(a)
    possible ortholog
    3(28301394-28305323)


    ENSEMBL Gene Tree for SMYD1 (if available)
    TreeFam Gene Tree for SMYD1 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SMYD1 gene
    SMYD42  SMYD22  SMYD32  
    3 SIMAP similar genes for SMYD1 using alignment to 4 protein entries:     SMYD1_HUMAN (see all proteins):
    DKFZp313O0925    SMYD2    SMYD3

    SMYD1 for paralogs           About GeneDecksing



    (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

    10/920 NCBI SNPs in SMYD1 are shown (see all 920    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs118911231,2
    C,F,H,--88365338(+) GTCTCA/GATCTC 1 -- us2k16Minor allele frequency- G:0.21NA 14
    rs1421397571,2
    --88365414(+) CCGGCC/TTCTTT 1 -- us2k10--------
    rs1882415741,2
    --88365516(+) AAGTTA/GTTTTG 1 -- us2k10--------
    rs1511574151,2
    --88365534(+) GTGTAC/TATCAG 1 -- us2k10--------
    rs1922587561,2
    --88365580(+) GTATTC/GTTACC 1 -- us2k10--------
    rs1848371121,2
    --88366208(+) CCTGGC/TAGCAG 1 -- us2k10--------
    rs1491768971,2
    C,--88366462(+) TCTTA-/TTA   
       TTTAT
    TTATT
    1 -- us2k10--------
    rs601210221,2
    C--88366494(+) TTATT-/TAT   
       TTATT
    AATTT
    1 -- us2k11Minor allele frequency- TATTTATT:0.00NA 2
    rs1896095721,2
    --88366529(+) GTCGCC/TCAGGC 1 -- us2k10--------
    rs1914055071,2
    --88366556(+) GATCTC/TGGCTC 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for SMYD1 (88367299 - 88412906 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for SMYD1: --

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing SMYD1
    DNA2.0 Custom Variant and Variant Library Synthesis for SMYD1

    (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.)
    About This Section

    SMYD1 for disorders           About GeneDecksing

    OMIM gene information: 606846    OMIM disorders: --

    4 diseases for SMYD1:    About MalaCards
    axenfeld-rieger syndrome    hypoplastic left heart syndrome    tetralogy of fallot    malaria

    2 diseases from the University of Copenhagen DISEASES database for SMYD1:
    Axenfeld-Rieger syndrome     Hypoplastic left heart syndrome
    Human Genome Epidemiology (HuGE) Navigator: SMYD1 (1 document)

    Export disorders for SMYD1 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 SMYD1 gene, integrated from 9 sources (see all 13):
    (articles sorted by number of sources associating them with SMYD1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. 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)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    3. Bop encodes a muscle-restricted protein containing MYND and SET domains and is essential for cardiac differentiation and morphogenesis. (PubMed id 11923873)1, 3 Gottlieb P.D....Srivastava D. (2002)
    4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (2010)
    5. SMYD1, the myogenic activator, is a direct target of serum response factor and myogenin. (PubMed id 19783823)1 Li D....Liu M. (2009)
    6. Hepatoma-derived growth factor represses SET and MYND domain containing 1 gene expression through interaction with C-terminal binding protein. (PubMed id 19162039)1 Yang J. and Everett A.D. (2009)
    7. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (2007)
    8. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)2 Hillier L.W....Wilson R.K. (2005)
    9. 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. (2002)
    10. m-Bop, a repressor protein essential for cardiogenesis, interacts with skNAC, a heart- and muscle-specific transcription factor. (PubMed id 12011100)1 Sims R.J....Gottlieb P.D. (2002)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 150572 HGNC: 20986 AceView: SMYD1 Ensembl:ENSG00000115593 euGenes: HUgn150572
    ECgene: SMYD1 H-InvDB: SMYD1

    (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 SMYD1 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 SMYD1 gene:
    Search GeneIP for patents involving SMYD1

    GeneCards and IP:
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