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    SMYD3 SET and MYND domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 64754, updated on 19-Sep-2024

    Summary

    Official Symbol
    SMYD3provided by HGNC
    Official Full Name
    SET and MYND domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:15513
    See related
    Ensembl:ENSG00000185420 MIM:608783; AllianceGenome:HGNC:15513
    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
    KMT3E; ZMYND1; ZNFN3A1; bA74P14.1
    Summary
    This gene encodes a histone methyltransferase which functions in RNA polymerase II complexes by an interaction with a specific RNA helicase. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
    Expression
    Ubiquitous expression in thyroid (RPKM 1.8), brain (RPKM 1.2) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SMYD3 in Genome Data Viewer
    Location:
    1q44
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (245749347..246507279, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (245170078..245930104, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (245912649..246670581, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene kinesin family member 26B Neighboring gene uncharacterized LOC124904571 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:245746285-245747484 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:245769345-245770175 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:245774720-245775220 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:245775221-245775721 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:245786008-245786527 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:245811797-245812310 Neighboring gene uncharacterized LOC105373265 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:245874319-245874820 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:245874821-245875320 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:245878266-245878766 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:245926173-245926700 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:245938698-245939538 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:245937857-245938697 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2850 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2851 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:245979520-245980135 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:245980136-245980750 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:246016290-246016790 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:246016791-246017291 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:246032999-246034198 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:246111472-246111972 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2852 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:246226795-246227321 Neighboring gene NANOG hESC enhancer GRCh37_chr1:246228833-246229369 Neighboring gene Sharpr-MPRA regulatory region 4643 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:246273855-246274354 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:246273353-246273854 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:246302792-246303991 Neighboring gene CRISPRi-validated SMYD3 hub enhancer Neighboring gene CRISPRi-validated SMYD3 non-hub enhancer Neighboring gene CRISPR perturbation-validated SMYD3 cis-regulatory element TAD4.SE2.HS8 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2030 Neighboring gene SMYD3 antisense RNA 1 Neighboring gene CRISPR perturbation-validated SMYD3 cis-regulatory element TAD4.SE2.HS10 Neighboring gene uncharacterized LOC124904573 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:246383465-246384417 Neighboring gene RNA, U6 small nuclear 1283, pseudogene Neighboring gene coiled-coil-helix-coiled-coil-helix domain containing 4 pseudogene 5 Neighboring gene VISTA enhancer hs2070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:246487577-246488097 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2853 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2031 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:246518331-246518956 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:246533672-246533878 Neighboring gene SMYD3 intronic transcript 1 Neighboring gene MPRA-validated peak812 silencer Neighboring gene Sharpr-MPRA regulatory region 15017 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:246591613-246592114 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:246592115-246592614 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:246612672-246613232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:246669532-246670032 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:246670033-246670533 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2034 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:246671208-246671440 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:246679947-246680127 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:246701627-246702127 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2855 Neighboring gene long intergenic non-protein coding RNA 1743 Neighboring gene transcription factor B2, mitochondrial

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Fraction of exhaled nitric oxide values in childhood are associated with 17q11.2-q12 and 17q12-q21 variants.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies new susceptibility loci for migraine.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ21080, KIAA0504, MGC104324

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables RNA polymerase II complex binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3K36 dimethyltransferase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables histone H3K4 trimethyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H4 methyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in cellular response to dexamethasone stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in establishment of protein localization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in myotube cell development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in nucleosome assembly IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    histone-lysine N-methyltransferase SMYD3
    Names
    SET and MYND domain-containing protein 3
    zinc finger MYND domain-containing protein 1
    zinc finger protein, subfamily 3A (MYND domain containing), 1
    zinc finger, MYND domain containing 1
    NP_001161212.1
    NP_001362891.1
    NP_001362892.1
    NP_001362894.1
    NP_001362895.1
    NP_073580.1
    XP_011542556.1
    XP_011542559.1
    XP_011542561.1
    XP_011542563.1
    XP_016857583.1
    XP_024304904.1
    XP_024304909.1
    XP_024304917.1
    XP_024304930.1
    XP_047283975.1
    XP_047283976.1
    XP_047283977.1
    XP_047283978.1
    XP_054194247.1
    XP_054194248.1
    XP_054194249.1
    XP_054194250.1
    XP_054194251.1
    XP_054194252.1
    XP_054194253.1
    XP_054194254.1

    NCBI Reference Sequences (RefSeq)

    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_001167740.2NP_001161212.1  histone-lysine N-methyltransferase SMYD3 isoform 1

      See identical proteins and their annotated locations for NP_001161212.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AB057595, BI916760, BP231249
      Consensus CDS
      CCDS53486.1
      UniProtKB/Swiss-Prot
      A8K0P0, B1AN38, Q86TL8, Q8N5Z6, Q96AI5, Q9H7B4
      Related
      ENSP00000419184.2, ENST00000490107.6
      Conserved Domains (2) summary
      pfam00856
      Location:201239
      SET; SET domain
      pfam01753
      Location:4987
      zf-MYND; MYND finger
    2. NM_001375962.1NP_001362891.1  histone-lysine N-methyltransferase SMYD3 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL356583, AL358859, AL445468, AL512412
      Conserved Domains (2) summary
      pfam01753
      Location:4987
      zf-MYND; MYND finger
      cl40432
      Location:5234
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
    3. NM_001375963.1NP_001362892.1  histone-lysine N-methyltransferase SMYD3 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL358859, AL445468, AL512412
      Consensus CDS
      CCDS31083.1
      Conserved Domains (2) summary
      pfam01753
      Location:128
      zf-MYND; MYND finger
      cd19203
      Location:39209
      SET_SMYD3; SET domain (including post-SET domain) found in SET and MYND domain-containing protein 3 (SMYD3) and similar proteins
    4. NM_001375965.1NP_001362894.1  histone-lysine N-methyltransferase SMYD3 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL445468, AL512412
      UniProtKB/TrEMBL
      A0A024R5P8, B3KN46
      Conserved Domains (1) summary
      cl40432
      Location:179
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
    5. NM_001375966.1NP_001362895.1  histone-lysine N-methyltransferase SMYD3 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AL445468, AL512412
      Conserved Domains (1) summary
      cl40432
      Location:976
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
    6. NM_022743.3NP_073580.1  histone-lysine N-methyltransferase SMYD3 isoform 2

      See identical proteins and their annotated locations for NP_073580.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream translational start codon, compared to variant 1. The encoded isoform (2) is shorter at the N-terminus, compared to isoform 1.
      Source sequence(s)
      AK024733, AL356583, AL445468, AW173130
      Consensus CDS
      CCDS31083.1
      UniProtKB/Swiss-Prot
      Q9H7B4
      Related
      ENSP00000487434.1, ENST00000630181.2
      Conserved Domains (2) summary
      pfam01753
      Location:128
      zf-MYND; MYND finger
      cd19203
      Location:39209
      SET_SMYD3; SET domain (including post-SET domain) found in SET and MYND domain-containing protein 3 (SMYD3) and similar proteins

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      245749347..246507279 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047428020.1XP_047283976.1  histone-lysine N-methyltransferase SMYD3 isoform X2

    2. XM_024449136.2XP_024304904.1  histone-lysine N-methyltransferase SMYD3 isoform X2

      Conserved Domains (2) summary
      pfam01753
      Location:128
      zf-MYND; MYND finger
      cd19203
      Location:39209
      SET_SMYD3; SET domain (including post-SET domain) found in SET and MYND domain-containing protein 3 (SMYD3) and similar proteins
    3. XM_047428021.1XP_047283977.1  histone-lysine N-methyltransferase SMYD3 isoform X2

    4. XM_047428019.1XP_047283975.1  histone-lysine N-methyltransferase SMYD3 isoform X1

    5. XM_017002094.3XP_016857583.1  histone-lysine N-methyltransferase SMYD3 isoform X5

      UniProtKB/TrEMBL
      A0A024R5P8, B3KN46
      Conserved Domains (1) summary
      cl40432
      Location:179
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
    6. XM_024449162.2XP_024304930.1  histone-lysine N-methyltransferase SMYD3 isoform X5

      UniProtKB/TrEMBL
      A0A024R5P8, B3KN46
      Conserved Domains (1) summary
      cl40432
      Location:179
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
    7. XM_047428022.1XP_047283978.1  histone-lysine N-methyltransferase SMYD3 isoform X5

      UniProtKB/TrEMBL
      A0A024R5P8, B3KN46
    8. XM_011544261.4XP_011542563.1  histone-lysine N-methyltransferase SMYD3 isoform X5

      See identical proteins and their annotated locations for XP_011542563.1

      UniProtKB/TrEMBL
      A0A024R5P8, B3KN46
      Related
      ENST00000470510.5
      Conserved Domains (1) summary
      cl40432
      Location:179
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
    9. XM_024449149.2XP_024304917.1  histone-lysine N-methyltransferase SMYD3 isoform X5

      UniProtKB/TrEMBL
      A0A024R5P8, B3KN46
      Conserved Domains (1) summary
      cl40432
      Location:179
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
    10. XM_011544254.3XP_011542556.1  histone-lysine N-methyltransferase SMYD3 isoform X3

      Conserved Domains (1) summary
      pfam00856
      Location:5997
      SET; SET domain
    11. XM_011544259.4XP_011542561.1  histone-lysine N-methyltransferase SMYD3 isoform X5

      See identical proteins and their annotated locations for XP_011542561.1

      UniProtKB/TrEMBL
      A0A024R5P8, B3KN46
      Conserved Domains (1) summary
      cl40432
      Location:179
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
    12. XM_024449141.2XP_024304909.1  histone-lysine N-methyltransferase SMYD3 isoform X5

      UniProtKB/TrEMBL
      A0A024R5P8, B3KN46
      Conserved Domains (1) summary
      cl40432
      Location:179
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
    13. XM_011544257.2XP_011542559.1  histone-lysine N-methyltransferase SMYD3 isoform X4

      See identical proteins and their annotated locations for XP_011542559.1

      UniProtKB/Swiss-Prot
      Q9H7B4
      Conserved Domains (1) summary
      pfam00856
      Location:3169
      SET; SET domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      245170078..245930104 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054338273.1XP_054194248.1  histone-lysine N-methyltransferase SMYD3 isoform X2

    2. XM_054338274.1XP_054194249.1  histone-lysine N-methyltransferase SMYD3 isoform X2

    3. XM_054338275.1XP_054194250.1  histone-lysine N-methyltransferase SMYD3 isoform X2

    4. XM_054338272.1XP_054194247.1  histone-lysine N-methyltransferase SMYD3 isoform X1

    5. XM_054338277.1XP_054194252.1  histone-lysine N-methyltransferase SMYD3 isoform X5

      UniProtKB/TrEMBL
      A0A024R5P8, B3KN46
    6. XM_054338278.1XP_054194253.1  histone-lysine N-methyltransferase SMYD3 isoform X5

      UniProtKB/TrEMBL
      A0A024R5P8, B3KN46
    7. XM_054338279.1XP_054194254.1  histone-lysine N-methyltransferase SMYD3 isoform X5

      UniProtKB/TrEMBL
      A0A024R5P8, B3KN46
    8. XM_054338276.1XP_054194251.1  histone-lysine N-methyltransferase SMYD3 isoform X4