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SETD3 SET domain containing 3, actin histidine methyltransferase [ Homo sapiens (human) ]

Gene ID: 84193, updated on 24-May-2020

Summary

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Official Symbol
SETD3provided by HGNC
Official Full Name
SET domain containing 3, actin histidine methyltransferaseprovided by HGNC
Primary source
HGNC:HGNC:20493
See related
Ensembl:ENSG00000183576 MIM:615671
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
hSETD3; C14orf154
Expression
Ubiquitous expression in testis (RPKM 33.6), kidney (RPKM 26.5) and 25 other tissues See more
Orthologs
mouse all

Genomic context

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See SETD3 in Genome Data Viewer
Location:
14q32.2
Exon count:
19
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 14 NC_000014.9 (99397746..99486458, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (99864083..99947228, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370660 Neighboring gene Sharpr-MPRA regulatory region 7827 Neighboring gene RNA, U6 small nuclear 91, pseudogene Neighboring gene cyclin K Neighboring gene coiled-coil domain containing 85C Neighboring gene uncharacterized LOC105370661 Neighboring gene HNF4 motif-containing MPRA enhancer 184

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. An engineered variant of SETD3 methyltransferase alters target specificity from histidine to lysine methylation. Dai S, et al. J Biol Chem, 2020 Feb 28. PMID 31911441,
  2. Structural basis for the target specificity of actin histidine methyltransferase SETD3. Dai S, et al. Nat Commun, 2019 Aug 6. PMID 31388018, Free PMC Article
  3. SETD3 is a positive regulator of DNA-damage-induced apoptosis. Abaev-Schneiderman E, et al. Cell Death Dis, 2019 Jan 25. PMID 30683849, Free PMC Article
  4. Cell cycle-dependent degradation of the methyltransferase SETD3 attenuates cell proliferation and liver tumorigenesis. Cheng X, et al. J Biol Chem, 2017 Jun 2. PMID 28442573, Free PMC Article
  5. SETD3 is regulated by a couple of microRNAs and plays opposing roles in proliferation and metastasis of hepatocellular carcinoma. Xu L, et al. Clin Sci (Lond), 2019 Oct 30. PMID 31654063

See all (29) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SETD3 is regulated by a couple of microRNAs and plays opposing roles in proliferation and metastasis of hepatocellular carcinoma.
    Title: SETD3 is regulated by a couple of microRNAs and plays opposing roles in proliferation and metastasis of hepatocellular carcinoma.
  2. Low expression of SETD3 is a reliable predictor of poor survival in colorectal cancer patients. SETD3 is a positive regulator of p53-dependent activation of DOX-induced apoptosis.
    Title: SETD3 is a positive regulator of DNA-damage-induced apoptosis.
  3. Structural analyses, supported by biochemical experiments and enzyme activity assays, indicate that the recognition and methylation of beta-actin by SETD3 are highly sequence specific, and that both SETD3 and beta-actin adopt pronounced conformational changes upon binding to each other
    Title: Structural insights into SETD3-mediated histidine methylation on β-actin.
  4. Study reports structural and molecular determinant(s) of target specificity of actin histidine vs. lysine in the active site of SETD3. To facilitate the methyl transfer reaction, SETD3 provides a local environment that promotes deprotonation of the target nitrogen N3 of histidine (and concomitant protonation of N1).
    Title: Structural basis for the target specificity of actin histidine methyltransferase SETD3.
  5. CircSETD3 inhibits the growth of HCC partly through the circSETD3/miR-421/MAPK14 pathway.
    Title: CircSETD3 (Hsa_circ_0000567) acts as a sponge for microRNA-421 inhibiting hepatocellular carcinoma growth.
  6. SETD3 protein is the actin-specific histidine N-methyltransferase.
    Title: SETD3 protein is the actin-specific histidine <i>N</i>-methyltransferase.
  7. data reveal a new SETD3-dependent methylation-based signaling pathway at chromatin that regulates VEGF expression under normoxic and hypoxic conditions.
    Title: Chromatin associated SETD3 negatively regulates VEGF expression.
  8. these data elucidated that a GSK3beta-FBXW7beta-dependent mechanism controls SETD3 protein levels during the cell cycle and attenuates its oncogenic role in liver tumorigenesis.
    Title: Cell cycle-dependent degradation of the methyltransferase SETD3 attenuates cell proliferation and liver tumorigenesis.
  9. Results show that high expression levels of SMYD2, SETD3, and NO66 in renal cell tumors. Their low expression levels were significantly associated with shorter disease-specific and disease-free survival.
    Title: Expression of histone methyltransferases as novel biomarkers for renal cell tumor diagnosis and prognostication.
  10. MAF1, RNF7 and SETD3 are identified as PCNA-associated proteins in human cells and given this interaction with PCNA, Maf1, RNF7, and SetD3 are potentially involved in DNA replication, DNA repair, or associated processes.
    Title: A fluorescent bimolecular complementation screen reveals MAF1, RNF7 and SETD3 as PCNA-associated proteins in human cells.
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

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ23027, MGC87236, DKFZp761E1415

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA polymerase II activating transcription factor binding IEA
Inferred from Electronic Annotation
more info
  
actin binding IEA
Inferred from Electronic Annotation
more info
  
histone methyltransferase activity (H3-K36 specific) IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
histone methyltransferase activity (H3-K36 specific) ISS
Inferred from Sequence or Structural Similarity
more info
  
histone methyltransferase activity (H3-K4 specific) IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
protein-histidine N-methyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
NOT protein-lysine N-methyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
transcription coactivator activity IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
transcription coactivator activity ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
actin modification IDA
Inferred from Direct Assay
more info
 PubMed 
histone H3-K36 methylation ISS
Inferred from Sequence or Structural Similarity
more info
  
histone H3-K4 methylation IEA
Inferred from Electronic Annotation
more info
  
peptidyl-histidine methylation IDA
Inferred from Direct Assay
more info
 PubMed 
peptidyl-lysine dimethylation IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
peptidyl-lysine dimethylation ISS
Inferred from Sequence or Structural Similarity
more info
  
peptidyl-lysine monomethylation IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
peptidyl-lysine monomethylation ISS
Inferred from Sequence or Structural Similarity
more info
  
NOT peptidyl-lysine trimethylation IDA
Inferred from Direct Assay
more info
 PubMed 
peptidyl-lysine trimethylation ISS
Inferred from Sequence or Structural Similarity
more info
  
positive regulation of muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
  
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
positive regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
  
regulation of uterine smooth muscle contraction ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
nuclear chromatin IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
actin-histidine N-methyltransferase
Names
SET domain containing 3
SET domain-containing protein 3
histone-lysine N-methyltransferase setd3
NP_115609.2
NP_954574.1
XP_005268184.1
XP_011535533.2
XP_011535534.1
XP_011535535.1
XP_011535536.1
XP_011535537.1
XP_016877188.1
XP_016877189.1
XP_016877190.1
XP_016877191.1

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_032233.3 → NP_115609.2  actin-histidine N-methyltransferase isoform a

    See identical proteins and their annotated locations for NP_115609.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AK026680, BC037395, BX161471, CB988965
    Consensus CDS
    CCDS9951.1
    UniProtKB/Swiss-Prot
    Q86TU7
    UniProtKB/TrEMBL
    A0A024R6K3
    Related
    ENSP00000327436.5, ENST00000331768.10
    Conserved Domains (2) summary
    pfam00856
    Location:105 → 197
    SET; SET domain
    pfam09273
    Location:353 → 475
    Rubis-subs-bind; Rubisco LSMT substrate-binding

  2. NM_199123.2 → NP_954574.1  actin-histidine N-methyltransferase isoform b

    See identical proteins and their annotated locations for NP_954574.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1, that causes a frameshift. The resulting isoform (b) is shorter and has a unique C-terminus compared to isoform a.
    Source sequence(s)
    BC009054, CB988965
    Consensus CDS
    CCDS9952.1
    UniProtKB/Swiss-Prot
    Q86TU7
    Related
    ENSP00000327910.3, ENST00000329331.7
    Conserved Domains (1) summary
    pfam00856
    Location:105 → 197
    SET; SET domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p13 Primary Assembly

    Range
    99397746..99486458 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011537233.2 → XP_011535535.1  actin-histidine N-methyltransferase isoform X2

    Conserved Domains (2) summary
    pfam00856
    Location:105 → 256
    SET; SET domain
    pfam09273
    Location:295 → 417
    Rubis-subs-bind; Rubisco LSMT substrate-binding

  2. XM_011537231.2 → XP_011535533.2  actin-histidine N-methyltransferase isoform X1

    UniProtKB/Swiss-Prot
    Q86TU7
    UniProtKB/TrEMBL
    A0A024R6K3
    Conserved Domains (2) summary
    pfam00856
    Location:105 → 197
    SET; SET domain
    pfam09273
    Location:353 → 475
    Rubis-subs-bind; Rubisco LSMT substrate-binding

  3. XM_005268127.3 → XP_005268184.1  actin-histidine N-methyltransferase isoform X3

    See identical proteins and their annotated locations for XP_005268184.1

    Conserved Domains (2) summary
    pfam00856
    Location:176 → 215
    SET; SET domain
    pfam09273
    Location:254 → 376
    Rubis-subs-bind; Rubisco LSMT substrate-binding

  4. XM_017021701.1 → XP_016877190.1  actin-histidine N-methyltransferase isoform X2

    Conserved Domains (2) summary
    pfam00856
    Location:105 → 256
    SET; SET domain
    pfam09273
    Location:295 → 417
    Rubis-subs-bind; Rubisco LSMT substrate-binding

  5. XM_017021702.1 → XP_016877191.1  actin-histidine N-methyltransferase isoform X4

  6. XM_011537234.1 → XP_011535536.1  actin-histidine N-methyltransferase isoform X3

    See identical proteins and their annotated locations for XP_011535536.1

    Conserved Domains (2) summary
    pfam00856
    Location:176 → 215
    SET; SET domain
    pfam09273
    Location:254 → 376
    Rubis-subs-bind; Rubisco LSMT substrate-binding

  7. XM_017021699.1 → XP_016877188.1  actin-histidine N-methyltransferase isoform X1

    UniProtKB/Swiss-Prot
    Q86TU7
    UniProtKB/TrEMBL
    A0A024R6K3
    Conserved Domains (2) summary
    pfam00856
    Location:105 → 197
    SET; SET domain
    pfam09273
    Location:353 → 475
    Rubis-subs-bind; Rubisco LSMT substrate-binding

  8. XM_011537232.3 → XP_011535534.1  actin-histidine N-methyltransferase isoform X1

    See identical proteins and their annotated locations for XP_011535534.1

    UniProtKB/Swiss-Prot
    Q86TU7
    UniProtKB/TrEMBL
    A0A024R6K3
    Conserved Domains (2) summary
    pfam00856
    Location:105 → 197
    SET; SET domain
    pfam09273
    Location:353 → 475
    Rubis-subs-bind; Rubisco LSMT substrate-binding

  9. XM_017021700.1 → XP_016877189.1  actin-histidine N-methyltransferase isoform X1

    UniProtKB/Swiss-Prot
    Q86TU7
    UniProtKB/TrEMBL
    A0A024R6K3
    Conserved Domains (2) summary
    pfam00856
    Location:105 → 197
    SET; SET domain
    pfam09273
    Location:353 → 475
    Rubis-subs-bind; Rubisco LSMT substrate-binding

  10. XM_011537235.1 → XP_011535537.1  actin-histidine N-methyltransferase isoform X5

    See identical proteins and their annotated locations for XP_011535537.1

    UniProtKB/Swiss-Prot
    Q86TU7
    Conserved Domains (1) summary
    pfam00856
    Location:105 → 197
    SET; SET domain
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q86TU7.1 GenPept UniProtKB/Swiss-Prot:Q86TU7

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