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SMYD5 Gene

protein-coding   GIFtS: 49
GCID: GC02P073441

SMYD Family Member 5

(Previous name: retinoic acid induced 15)
(Previous symbol: RAI15)
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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
SMYD Family Member 51 2     ZMYND232
RAI151 2 3     Retinoic Acid Responsive2
Retinoic Acid Induced 151 2     SET And MYND Domain-Containing Protein 52
Retinoic Acid-Induced Protein 152 3     EC 2.1.1.-3
NN8-4AG2     Protein NN8-4AG3
RRG12     

External Ids:    HGNC: 162581   Entrez Gene: 103222   Ensembl: ENSG000001356327   UniProtKB: Q6GMV23   

Export aliases for SMYD5 gene to outside databases

Previous GC identifers: GC02P073399 GC02P073415 GC02P073353 GC02P073294 GC02P073177


(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 SMYD5 Gene:
SMYD5 (SMYD family member 5) is a protein-coding gene. GO annotations related to this gene include methyltransferase activity.


(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_000002.11  NT_022184.16  NC_018913.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SMYD5 gene promoter:
         HOXA9   GATA-2   NF-AT   CREB   NF-AT4   NF-AT2   deltaCREB   NF-AT3   NF-AT1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSMYD5 promoter sequence
   Search Chromatin IP Primers for SMYD5

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SMYD5


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

Entrez Gene cytogenetic band: 2p13.2   Ensembl cytogenetic band:  2p13.2   HGNC cytogenetic band: 2p12

SMYD5 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SMYD5 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02P073441:  view genomic region     (about GC identifiers)

Start:
73,441,350 bp from pter      End:
73,454,365 bp from pter
Size:
13,016 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., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: SMYD5_HUMAN, Q6GMV2 (See protein sequence)
Recommended Name: SET and MYND domain-containing protein 5  
Size: 418 amino acids; 47341 Da
Sequence caution: Sequence=AAH73806.1; Type=Erroneous initiation;
Secondary accessions: D6W5H3 Q13558

Explore the universe of human proteins at neXtProt for SMYD5: NX_Q6GMV2

Explore proteomics data for SMYD5 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See SMYD5 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_006053.2  
    ENSEMBL proteins: 
     ENSP00000388195   ENSP00000374152   ENSP00000258100   ENSP00000412587  

    SMYD5 Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for SMYD5

     
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    Search eBioscience for ELISAs for SMYD5 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    ZMYND: Zinc fingers, MYND-type

    1 InterPro protein domain:
     IPR001214 SET_dom

    Graphical View of Domain Structure for InterPro Entry Q6GMV2

    ProtoNet protein and cluster: Q6GMV2

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


    UniProtKB/Swiss-Prot: SMYD5_HUMAN, Q6GMV2
    Similarity: Belongs to the class V-like SAM-binding methyltransferase superfamily
    Similarity: Contains 1 MYND-type zinc finger
    Similarity: Contains 1 SET domain


    Find genes that share domains with SMYD5           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, 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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         Enzyme Number (IUBMB): EC 2.1.1.-1

         Gene Ontology (GO): 4 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
    GO:0005515protein binding ----
    GO:0008168methyltransferase activity IEA--
    GO:0046872metal ion binding IEA--
         
    Find genes that share ontologies with SMYD5           About GenesLikeMe


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SMYD5
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for SMYD5
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for SMYD5

    miRNA
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    miRTarBase miRNAs that target SMYD5:
    hsa-mir-125b-5p (MIRT045908)

    Block miRNA regulation of human, mouse, rat SMYD5 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SMYD5 (see all 29):
    hsa-miR-194* hsa-miR-4291 hsa-miR-875-3p hsa-miR-146a hsa-miR-15a hsa-miR-1285 hsa-miR-197 hsa-miR-124
    SwitchGear 3'UTR luciferase reporter plasmidSMYD5 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for SMYD5
    Predesigned siRNA for gene silencing in human, mouse, rat SMYD5

    Gene Editing
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    Clone
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    GenScript: all cDNA clones in your preferred vector: SMYD5 (NM_006062)
    Browse Sino Biological Human cDNA Clones
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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SMYD5


    (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
    extracellular2
    nucleus2
    cytosol1
    mitochondrion1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575cellular_component ND--

    Find genes that share ontologies with SMYD5           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 SMYD5
    Interactions:

        Search GeneGlobe Interaction Network for SMYD5

    STRING Interaction Network Preview (showing 5 interactants - click image to see 21)

    Selected Interacting proteins for SMYD5 (Q6GMV23 ENSP000003741524) via UniProtKB, MINT, STRING, and/or I2D (see all 31)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    DDX39BQ138383I2D: score=5 
    ENSG00000215425Q138383I2D: score=5 
    ENSG00000225073Q138383I2D: score=5 
    ENSG00000225859Q138383I2D: score=5 
    ENSG00000229496Q138383I2D: score=5 
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008150biological_process ND--

    Find genes that share ontologies with SMYD5           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 SMYD5



    (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 SMYD5 gene: 
    NM_006062.2  

    Unigene Cluster for SMYD5:

    SMYD family member 5
    Hs.631882  [show with all ESTs]
    Unigene Representative Sequence: NM_006062
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000413491 ENST00000389501(uc002siw.2 uc010yre.1) ENST00000258100
    ENST00000443900 ENST00000474652 ENST00000491204 ENST00000477038 ENST00000486518

    miRNA
    Products:
         
    Block miRNA regulation of human, mouse, rat SMYD5 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SMYD5 (see all 29):
    hsa-miR-194* hsa-miR-4291 hsa-miR-875-3p hsa-miR-146a hsa-miR-15a hsa-miR-1285 hsa-miR-197 hsa-miR-124
    SwitchGear 3'UTR luciferase reporter plasmidSMYD5 3' UTR sequence
    Inhib. RNA
    Products:
         
    OriGene RNAi products in human, mouse, rat for SMYD5
    Predesigned siRNA for gene silencing in human, mouse, rat SMYD5
    Clone
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    OriGene clones in human, mouse for SMYD5 (see all 6)
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    GenScript: all cDNA clones in your preferred vector: SMYD5 (NM_006062)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SMYD5
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for SMYD5
    Pre-validated RT2 qPCR Primer Assay in human, mouse / rat SMYD5
      QuantiTect SYBR Green Assays in human, mouse, rat SMYD5
      QuantiFast Probe-based Assays in human, mouse, rat SMYD5

    Additional mRNA sequence: 

    AK300779.1 AK301809.1 BC009484.2 BC073806.1 U50383.1 

    10 DOTS entries:

    DT.312414  DT.95366142  DT.92436136  DT.100776385  DT.100776388  DT.75103138  DT.97801940  DT.121005302 
    DT.75103137  DT.97810216 

    Selected AceView cDNA sequences (see all 129):

    BF434204 BU508174 CB140860 BU728161 AI884743 AA947499 BQ004261 CR592310 
    BU860400 CR592777 AA379041 AL550113 AW630396 BC073806 AA974233 BU539385 
    BM809072 BU931089 AA310378 CD676164 AW206927 AU121890 AI289458 AA429828 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for SMYD5 (see all 8)    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b · 4c · 4d ^ 5a · 5b ^ 6 ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14
    SP1:                          -     -                 -     -                                                           -                       -               
    SP2:                          -     -                 -     -     -                                                                                             
    SP3:                                -                 -                                                                                                         
    SP4:                          -     -                 -                                                                                                         
    SP5:                                                                                                                                                            


    ECgene alternative splicing isoforms for SMYD5

    (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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    SMYD5 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAGCCAGGTG
    SMYD5 Expression
    About this image


    SMYD5 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Skeletal Muscle (Muscoskeletal System)    fully expand to see all 2 entries
             Mononuclear Myocytes Hyoid Arch Muscles
     
     Amnion (Extraembryonic Tissues)
    SMYD5 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SMYD5 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.631882
        Custom PCR Arrays for SMYD5
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SMYD5

    (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.

    Orthologs for SMYD5 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Smyd51 , 5 SET and MYND domain containing 51, 5 87.18(n)1
    90.38(a)1
      6 (37.44 cM)5
    2321871  NM_144918.21  NP_659167.21 
     854319895 
    chicken
    (Gallus gallus)
    Aves SMYD51 SMYD family member 5 77.45(n)
    80.6(a)
      422951  NM_001012894.1  NP_001012912.1 
    lizard
    (Anolis carolinensis)
    Reptilia SMYD56
    SMYD family member 5
    84(a)
    1 ↔ 1
    GL343815.1(147-7567)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.86402 Xenopus laevis transcribed sequence with moderate similarity more 75.94(n)    BI450235.1 
    zebrafish
    (Danio rerio)
    Actinopterygii smyd51 SMYD family member 5 69.64(n)
    73.49(a)
      447875  NM_001004614.2  NP_001004614.2 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG33531 CG3353 54.24(n)
    48.34(a)
      42517  NM_142698.2  NP_650955.1 


    ENSEMBL Gene Tree for SMYD5 (if available)
    TreeFam Gene Tree for SMYD5 (if available)

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

    (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 SMYD5 (see all 336)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1808588891,2
    --73439419(+) AGGCGC/TGTGAC 1 -- us2k10--------
    rs1161511501,2
    C,F--73439633(+) CTTTCA/GTGACT 1 -- us2k11Minor allele frequency- G:0.05WA 118
    rs1146298431,2
    C--73439751(+) CTAGAA/GTGGCT 1 -- us2k10--------
    rs739442771,2
    C,F--73439775(+) CTGAGG/AGATGG 1 -- us2k12Minor allele frequency- A:0.12WA 120
    rs1138839281,2
    C,F--73439799(+) CTGCCA/CCCTGG 1 -- us2k13Minor allele frequency- C:0.07NA WA 240
    rs1138259861,2
    F--73439829(+) CCCCAG/ACTGCT 1 -- us2k11Minor allele frequency- A:0.50CSA 2
    rs1409453041,2
    C--73439955(+) TATCT-/CCCCCA 1 -- us2k10--------
    rs1381839861,2
    C--73439977(+) TATTCG/TCTCCT 1 -- us2k10--------
    rs76017421,2
    C,F--73440239(+) GCTGCC/TGTGAG 1 -- us2k16Minor allele frequency- T:0.36NA WA EA 364
    rs1496209891,2
    --73440375(+) CATAGA/GTCTGT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for SMYD5 (73441350 - 73454365 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for SMYD5:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv2776CNV Loss18451855

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SMYD5
    DNA2.0 Custom Variant and Variant Library Synthesis for SMYD5

    (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 SMYD5           About GenesLikeMe

    Genetic Association Database (GAD): SMYD5

    Export disorders for SMYD5 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 SMYD5 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with SMYD5)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Isolation of a novel retinoic acid-responsive gene by selection of genomic fragments derived from CpG-island-enriched DNA. (PubMed id 8754834)1, 2, 3 Shago M. and Giguere V. (Mol. Cell. Biol. 1996)
    2. 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. (Genome Res. 2004)
    3. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)
    4. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    5. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (amp 2011)
    6. 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)
    7. (PubMed id )2 

    (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)
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    Entrez Gene: 10322 HGNC: 16258 AceView: SMYD5 Ensembl:ENSG00000135632 euGenes: HUgn10322
    ECgene: SMYD5 H-InvDB: SMYD5

    (According to HUGE)
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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 SMYD5 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 SMYD5 gene:
    Search GeneIP for patents involving SMYD5

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



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