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

Gene ID: 114826, updated on 10-Dec-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, Dec 2024]
Expression
Ubiquitous expression in ovary (RPKM 3.5), fat (RPKM 3.2) and 25 other tissues See more
Orthologs
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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
  • 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)

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
NP_443160.2
XP_011521934.1
XP_011521935.1
XP_024306328.1
XP_047291246.1
XP_047291247.1
XP_054170917.1
XP_054170918.1
XP_054170919.1
XP_054170920.1

NCBI Reference Sequences (RefSeq)

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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

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