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

Gene ID: 64754, updated on 5-Jan-2022

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
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
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Genomic context

See SMYD3 in Genome Data Viewer
Location:
1q44
Exon count:
30
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (245749342..246507279, complement)
105.20201022 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 LOC105373266 Neighboring gene uncharacterized LOC105373265 Neighboring gene uncharacterized LOC105373270 Neighboring gene uncharacterized LOC105373269 Neighboring gene Sharpr-MPRA regulatory region 4643 Neighboring gene SMYD3 antisense RNA 1 Neighboring gene RNA, U6 small nuclear 1283, pseudogene Neighboring gene coiled-coil-helix-coiled-coil-helix domain containing 4 pseudogene 5 Neighboring gene uncharacterized LOC107985599 Neighboring gene VISTA enhancer hs2070 Neighboring gene uncharacterized LOC107985726 Neighboring gene Sharpr-MPRA regulatory region 15017 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
  • 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

Associated conditions

Description Tests
Fraction of exhaled nitric oxide values in childhood are associated with 17q11.2-q12 and 17q12-q21 variants.
GeneReviews: Not available
Genome-wide meta-analysis identifies new susceptibility loci for migraine.
GeneReviews: Not available
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
GeneReviews: Not available

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

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-lysine N-methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables histone-lysine N-methyltransferase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables histone-lysine N-methyltransferase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
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 histone lysine methylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in myotube cell development IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of protein kinase activity IEA
Inferred from Electronic Annotation
more info
 
involved_in nucleosome assembly IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of peptidyl-serine phosphorylation 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
PubMed 
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_011542560.1
XP_011542561.1
XP_011542563.1
XP_016857583.1
XP_024304904.1
XP_024304909.1
XP_024304916.1
XP_024304917.1
XP_024304924.1
XP_024304930.1

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_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
    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
    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
    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: Homo sapiens Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    245749342..246507279 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024449136.1XP_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
  2. XM_017002094.2XP_016857583.1  histone-lysine N-methyltransferase SMYD3 isoform X5

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

    Conserved Domains (1) summary
    cl40432
    Location:179
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
  4. XM_011544258.2XP_011542560.1  histone-lysine N-methyltransferase SMYD3 isoform X5

    See identical proteins and their annotated locations for XP_011542560.1

    UniProtKB/TrEMBL
    B3KN46
    Conserved Domains (1) summary
    cl40432
    Location:179
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
  5. XM_011544261.3XP_011542563.1  histone-lysine N-methyltransferase SMYD3 isoform X5

    See identical proteins and their annotated locations for XP_011542563.1

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

    Conserved Domains (1) summary
    cl40432
    Location:179
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
  7. XM_011544254.2XP_011542556.1  histone-lysine N-methyltransferase SMYD3 isoform X3

    Conserved Domains (1) summary
    pfam00856
    Location:5997
    SET; SET domain
  8. XM_011544259.3XP_011542561.1  histone-lysine N-methyltransferase SMYD3 isoform X5

    See identical proteins and their annotated locations for XP_011542561.1

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

    Related
    ENST00000470510.5
    Conserved Domains (1) summary
    cl40432
    Location:179
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
  10. XM_024449156.1XP_024304924.1  histone-lysine N-methyltransferase SMYD3 isoform X5

    Conserved Domains (1) summary
    cl40432
    Location:179
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
  11. XM_011544257.1XP_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
  12. XM_024449148.1XP_024304916.1  histone-lysine N-methyltransferase SMYD3 isoform X5

    Conserved Domains (1) summary
    cl40432
    Location:179
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily
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