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

SMYD5 Gene

protein-coding   GIFtS: 46
GCID: GC02P073441

SMYD Family Member 5

(Previous name: retinoic acid induced 15)
(Previous symbol: RAI15)
  Search for SMYD5
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

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

GeneCards Summary for SMYD5 Gene: 
SMYD5 (SMYD family member 5) is a protein-coding gene. GO annotations related to this gene include molecular_function and metal ion binding.


(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000002.11  NT_022184.15  NC_018913.2  
Regulatory elements:
   SABiosciences 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 SABiosciences Chromatin IP Primers for SMYD5

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

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:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q6GMV2

  • SMYD5 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    SMYD5 Protein Expression
    REFSEQ proteins: NP_006053.2  
    ENSEMBL proteins: 
     ENSP00000388195   ENSP00000374152   ENSP00000258100   ENSP00000412587  

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    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for SMYD5 

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

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

    SMYD5 for ontologies           About GeneDecksing



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


    SMYD5 for domains           About GeneDecksing


    (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,
    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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

         Enzyme Number (IUBMB): EC 2.1.1.-1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
    GO:0005515protein binding ----
    GO:0008168methyltransferase activity IEA--
    GO:0046872metal ion binding IEA--
         
    SMYD5 for ontologies           About GeneDecksing


    Animal Models:
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for SMYD5 
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    SwitchGear 3'UTR luciferase reporter plasmidSMYD5 3' UTR sequence
    Inhib. RNA
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    (Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SMYD5

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    5/11 Interacting proteins for SMYD5 (Q6GMV23 ENSP000003741524) via UniProtKB, MINT, STRING, and/or I2D (see all 11)
    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 (GO ID links to tree view):    About this table

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

    SMYD5 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, 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 SMYD5

    Search CenterWatch for drugs/clinical trials and news about 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,
    Conferences by KenesGroup, 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, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    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:
         
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    8/29 QIAGEN miScript miRNA 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:
         
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      QIAGEN 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 

    24/129 AceView cDNA sequences (see all 129):

    AA974233 AW206927 BM809072 CD676164 BQ004261 AA947499 NM_006062 AA379041 
    CR592777 CB140860 CR592310 AA310378 BC073806 BM558993 BU931089 BU728161 
    BU539385 BF434204 AU121890 AU123957 BU860400 AI289458 BU508174 BG680133 

    GeneLoc Exon Structure

    5/8 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™, 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

    SMYD5 expression in normal human tissues (normalized intensities)      SMYD5 embryonic expression: see
    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 
     5/2 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)

     -- (Gastrointestinal Tract)
             visceral organ/oral region/gland   

    See SMYD5 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SMYD5

    SOURCE GeneReport for Unigene cluster: Hs.631882
        SABiosciences 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)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for SMYD5 gene from 6/14 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
    Uncharacterized protein
    81(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 72.67(n)
    77(a)
      447875  NM_001004614.1  NP_001004614.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG33531 CG3353 54.38(n)
    47.21(a)
      42517  NM_142698.1  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)
    About This Section
      --

    (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) 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

    10/336 SNPs in SMYD5 are shown (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

    SABiosciences Cancer Mutation 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, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    SMYD5 for disorders           About MalaCards

    SMYD5 for disorders           About GeneDecksing

    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)
    About This Section

    PubMed articles for SMYD5 gene integrated from 9 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. (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. (2004)
    3. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    4. Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (2011)
    5. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (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. (2002)
    7. Hepatitis C virus core protein interacts with 14-3-3 protein and activates the kinase Raf-1. (PubMed id )2 Aoki H.... Hino O. (2000)

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

    (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 SMYD5 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 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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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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