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    SMYD4 SET and MYND domain containing 4 [ Homo sapiens (human) ]

    Gene ID: 114826, updated on 30-Oct-2024

    Summary

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    Official Symbol
    SMYD4provided by HGNC
    Official Full Name
    SET and MYND domain containing 4provided by HGNC
    Primary source
    HGNC:HGNC:21067
    See related
    Ensembl:ENSG00000186532 MIM:619134; AllianceGenome:HGNC:21067
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ZMYND21
    Summary
    Predicted to enable histone deacetylase binding activity. Involved in heart development. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in ovary (RPKM 3.5), fat (RPKM 3.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SMYD4 in Genome Data Viewer
    Location:
    17p13.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (1779485..1829902, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (1668185..1718627, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (1682779..1733196, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1655564-1656124 Neighboring gene serpin family F member 2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1665693-1666545 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1666546-1667398 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11456 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11457 Neighboring gene serpin family F member 1 Neighboring gene Sharpr-MPRA regulatory region 4981 Neighboring gene Sharpr-MPRA regulatory region 13179 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11458 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1734195-1734695 Neighboring gene replication protein A1 Neighboring gene SDHC pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11459 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11460 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1810454-1810962 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1810963-1811470 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:1825407-1825589 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1834946-1835511 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1835512-1836076 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:1846458-1846649 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1849416-1849974 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1851145-1851648 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1851649-1852150 Neighboring gene reticulon 4 receptor like 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1866080-1866746 Neighboring gene MPRA-validated peak2677 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr17:1879245-1879860 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1885529-1886370 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1886371-1887212 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1889733-1890236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1890237-1890738 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1894981-1895842 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1895843-1896703 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1903279-1903789 Neighboring gene uncharacterized LOC105371486 Neighboring gene uncharacterized LOC105371485 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11461

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Identification of Smyd4 as a potential tumor suppressor gene involved in breast cancer development. Hu L, et al. Cancer Res, 2009 May 1. PMID 19383909
    2. SMYD4 monomethylates PRMT5 and forms a positive feedback loop to promote hepatocellular carcinoma progression. Zhou Z, et al. Cancer Sci, 2024 May. PMID 38438251, Free PMC Article
    3. The roles of SMYD4 in epigenetic regulation of cardiac development in zebrafish. Xiao D, et al. PLoS Genet, 2018 Aug. PMID 30110327, Free PMC Article
    4. Common variants in the calcium-sensing receptor gene are associated with total serum calcium levels. O'Seaghdha CM, et al. Hum Mol Genet, 2010 Nov 1. PMID 20705733, Free PMC Article
    5. Prediction of the coding sequences of unidentified human genes. XXI. The complete sequences of 60 new cDNA clones from brain which code for large proteins. Nagase T, et al. DNA Res, 2001 Aug 31. PMID 11572484

    See all (22) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SMYD4 monomethylates PRMT5 and forms a positive feedback loop to promote hepatocellular carcinoma progression.
      Title: SMYD4 monomethylates PRMT5 and forms a positive feedback loop to promote hepatocellular carcinoma progression.
    2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    3. Smyd4, as a potential tumor suppressor, plays a critical role in breast carcinogenesis at least partly through inhibiting the expression of Pdgfr-alpha.
      Title: Identification of Smyd4 as a potential tumor suppressor gene involved in breast cancer development.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Common variants in the calcium-sensing receptor gene are associated with total serum calcium levels.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1936

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables histone deacetylase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in heart development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in heart development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    SET and MYND domain-containing protein 4

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_052928.3 → NP_443160.2  SET and MYND domain-containing protein 4

      See identical proteins and their annotated locations for NP_443160.2

      Status: VALIDATED

      Source sequence(s)
      AC130689, AK095369, AL137345, AV700545, BC035077, BM676597, CN352185, CR987176, DB219337
      Consensus CDS
      CCDS11013.1
      UniProtKB/Swiss-Prot
      Q8IYR2, Q8N1P2, Q8NAT0, Q96LV4, Q96PV2
      Related
      ENSP00000304360.7, ENST00000305513.12
      Conserved Domains (5) summary
      sd00006
      Location:68 → 96
      TPR; TPR repeat [structural motif]
      pfam00856
      Location:528 → 574
      SET; SET domain
      pfam01753
      Location:296 → 335
      zf-MYND; MYND finger
      pfam13424
      Location:660 → 726
      TPR_12; Tetratricopeptide repeat
      cl26005
      Location:72 → 237
      PLN03088; SGT1, suppressor of G2 allele of SKP1; Provisional

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      1779485..1829902 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024450560.2 → XP_024306328.1  SET and MYND domain-containing protein 4 isoform X1

      UniProtKB/Swiss-Prot
      Q8IYR2, Q8N1P2, Q8NAT0, Q96LV4, Q96PV2
      Conserved Domains (5) summary
      sd00006
      Location:68 → 96
      TPR; TPR repeat [structural motif]
      pfam00856
      Location:528 → 574
      SET; SET domain
      pfam01753
      Location:296 → 335
      zf-MYND; MYND finger
      pfam13424
      Location:660 → 726
      TPR_12; Tetratricopeptide repeat
      cl26005
      Location:72 → 237
      PLN03088; SGT1, suppressor of G2 allele of SKP1; Provisional

    2. XM_047435291.1 → XP_047291247.1  SET and MYND domain-containing protein 4 isoform X5

    3. XM_047435290.1 → XP_047291246.1  SET and MYND domain-containing protein 4 isoform X2

    4. XM_011523633.3 → XP_011521935.1  SET and MYND domain-containing protein 4 isoform X3

      Conserved Domains (4) summary
      sd00006
      Location:68 → 96
      TPR; TPR repeat [structural motif]
      pfam00856
      Location:528 → 574
      SET; SET domain
      pfam01753
      Location:296 → 335
      zf-MYND; MYND finger
      pfam13414
      Location:68 → 132
      TPR_11; TPR repeat

    5. XM_011523632.3 → XP_011521934.1  SET and MYND domain-containing protein 4 isoform X4

      Conserved Domains (4) summary
      sd00006
      Location:68 → 96
      TPR; TPR repeat [structural motif]
      pfam00856
      Location:528 → 574
      SET; SET domain
      pfam01753
      Location:296 → 335
      zf-MYND; MYND finger
      pfam13414
      Location:68 → 132
      TPR_11; TPR repeat

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      1668185..1718627 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054314942.1 → XP_054170917.1  SET and MYND domain-containing protein 4 isoform X1

    2. XM_054314945.1 → XP_054170920.1  SET and MYND domain-containing protein 4 isoform X5

    3. XM_054314943.1 → XP_054170918.1  SET and MYND domain-containing protein 4 isoform X3

    4. XM_054314944.1 → XP_054170919.1  SET and MYND domain-containing protein 4 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IYR2.3 GenPept UniProtKB/Swiss-Prot:Q8IYR2

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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