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SETD3 SET domain containing 3, actin N3(tau)-histidine methyltransferase [ Homo sapiens (human) ]

Gene ID: 84193, updated on 7-Nov-2024

Summary

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Official Symbol
SETD3provided by HGNC
Official Full Name
SET domain containing 3, actin N3(tau)-histidine methyltransferaseprovided by HGNC
Primary source
HGNC:HGNC:20493
See related
Ensembl:ENSG00000183576 MIM:615671; AllianceGenome:HGNC:20493
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
Summary
Enables protein-L-histidine N-tele-methyltransferase activity. Involved in actin modification and peptidyl-histidine methylation. Located in cytoplasm. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in testis (RPKM 33.6), kidney (RPKM 26.5) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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See SETD3 in Genome Data Viewer
Location:
14q32.2
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (99397748..99486458, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (93629309..93718026, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (99864085..99947196, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903412 Neighboring gene BCL11 transcription factor B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99677677-99678177 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99695676-99696574 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99703507-99704031 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99713148-99714044 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:99723824-99724098 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99734631-99735236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99735237-99735841 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6060 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6061 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9002 Neighboring gene uncharacterized LOC105370660 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99750257-99750979 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99784572-99785298 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99786594-99787222 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99787223-99787850 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99788913-99789673 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99798343-99799050 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99799051-99799757 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99814550-99815224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99815225-99815898 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:99827260-99827481 Neighboring gene Sharpr-MPRA regulatory region 7827 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99849405-99850263 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99860795-99861575 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99874757-99875323 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr14:99878378-99879044 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99879711-99880376 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99890523-99891386 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99891387-99892249 Neighboring gene RNA, U6 small nuclear 91, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:99946327-99946828 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6063 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9003 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99968944-99969444 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99969445-99969945 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99974643-99975198 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99977641-99978142 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99978143-99978642 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99978643-99979643 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99988085-99988644 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99988645-99989206 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99995945-99996467 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99996990-99997512 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:99997513-99998033 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:99999970-100000571 Neighboring gene coiled-coil domain containing 85C Neighboring gene uncharacterized LOC105370661 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100003689-100004280 Neighboring gene cyclin K Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100004281-100004872 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100006217-100006952 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100011369-100012103 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100017717-100018455 Neighboring gene HNF4 motif-containing MPRA enhancer 184 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100029329-100030250 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100030251-100031170 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100033011-100033930 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100035771-100036690 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100036691-100037611 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100037612-100038531 Neighboring gene VISTA enhancer hs1931 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:100045528-100046727 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100054779-100055374 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100057164-100057760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100064325-100065207 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100068739-100069392 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9004 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6065 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6066 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6067 Neighboring gene Sharpr-MPRA regulatory region 4550 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100090366-100091068 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9005 Neighboring gene HHIP like 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100118444-100118944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100118945-100119445 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100128755-100129256 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100129257-100129756 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100130377-100130920 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100130921-100131465 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9008 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100135414-100135955 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:100136897-100137496 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100137497-100138098 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100138099-100138698 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100141430-100141993 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100142557-100143120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100143121-100143683

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. SETD3 functions beyond histidine methylation. Gao R, et al. Life Sci, 2024 Nov 15. PMID 39299385
  2. 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
  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. Proteolytic Activities of Enterovirus 2A Do Not Depend on Its Interaction with SETD3. Yang X, et al. Viruses, 2022 Jun 22. PMID 35891342, Free PMC Article
  5. 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

See all (50) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Examining prestructured beta-actin peptides as substrates of histidine methyltransferase SETD3.
    Title: Examining prestructured β-actin peptides as substrates of histidine methyltransferase SETD3.
  2. SETD3 functions beyond histidine methylation.
    Title: SETD3 functions beyond histidine methylation.
  3. The EV71 2A protease occupies the central cleft of SETD3 and disrupts SETD3-actin interaction.
    Title: The EV71 2A protease occupies the central cleft of SETD3 and disrupts SETD3-actin interaction.
  4. The Role of Trp79 in beta-Actin on Histidine Methyltransferase SETD3 Catalysis.
    Title: The Role of Trp79 in β-Actin on Histidine Methyltransferase SETD3 Catalysis.
  5. CircSETD3 mediates acquired resistance to gefitinib in non-small lung cancer cells by FXR1/ECT2 pathway.
    Title: CircSETD3 mediates acquired resistance to gefitinib in non-small lung cancer cells by FXR1/ECT2 pathway.
  6. Structure-function conservation between the methyltransferases SETD3 and SETD6.
    Title: Structure-function conservation between the methyltransferases SETD3 and SETD6.
  7. Proteolytic Activities of Enterovirus 2A Do Not Depend on Its Interaction with SETD3.
    Title: Proteolytic Activities of Enterovirus 2A Do Not Depend on Its Interaction with SETD3.
  8. Importance of Ile71 in beta-actin on histidine methyltransferase SETD3 catalysis.
    Title: Importance of Ile71 in β-actin on histidine methyltransferase SETD3 catalysis.
  9. Stabilization of SETD3 by deubiquitinase USP27 enhances cell proliferation and hepatocellular carcinoma progression.
    Title: Stabilization of SETD3 by deubiquitinase USP27 enhances cell proliferation and hepatocellular carcinoma progression.
  10. The methyltransferase SETD3-mediated histidine methylation: Biological functions and potential implications in cancers.
    Title: The methyltransferase SETD3-mediated histidine methylation: Biological functions and potential implications in cancers.
Submit: New GeneRIF Correction See all GeneRIFs (24)

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

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

  • FLJ23027, MGC87236, DKFZp761E1415

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA polymerase II-specific DNA-binding transcription factor binding IEA
Inferred from Electronic Annotation
more info
  
enables actin binding IEA
Inferred from Electronic Annotation
more info
  
enables histone H3K36 methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables histone H3K36 methyltransferase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables histone H3K4 methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-L-histidine N-tele-methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein-L-histidine N-tele-methyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
NOT enables protein-lysine N-methyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables transcription coactivator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables transcription coactivator activity ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in actin modification IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in actin modification IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in chromatin remodeling IEA
Inferred from Electronic Annotation
more info
  
involved_in peptidyl-histidine methylation IDA
Inferred from Direct Assay
more info
 PubMed 
NOT involved_in peptidyl-lysine trimethylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of DNA-templated transcription ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of uterine smooth muscle contraction IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of uterine smooth muscle contraction ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in chromatin IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in 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, actin histidine methyltransferase
SET domain-containing protein 3
histone-lysine N-methyltransferase setd3
protein-L-histidine N-tele-methyltransferase
NP_115609.2
NP_954574.1
XP_011535533.2
XP_011535534.1
XP_011535535.1
XP_011535537.1
XP_016877188.1
XP_016877189.1
XP_047287761.1
XP_054232780.1
XP_054232781.1
XP_054232782.1
XP_054232783.1

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
    A0PJU3, A5PLP0, B4DZE8, Q0VAQ2, Q659C0, Q86TU7, Q86TU8, Q96GY9, Q9H5U5
    Related
    ENSP00000327436.5, ENST00000331768.10
    Conserved Domains (2) summary
    cd19176
    Location:80 → 329
    SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins
    pfam09273
    Location:350 → 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/TrEMBL
    A6NJ55, Q6NXR6
    Related
    ENSP00000327910.3, ENST00000329331.7
    Conserved Domains (1) summary
    cd19176
    Location:80 → 282
    SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) 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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    99397748..99486458 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017021699.2 → XP_016877188.1  actin-histidine N-methyltransferase isoform X1

    UniProtKB/Swiss-Prot
    A0PJU3, A5PLP0, B4DZE8, Q0VAQ2, Q659C0, Q86TU7, Q86TU8, Q96GY9, Q9H5U5
    Conserved Domains (2) summary
    cd19176
    Location:80 → 329
    SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins
    pfam09273
    Location:350 → 475
    Rubis-subs-bind; Rubisco LSMT substrate-binding

  2. XM_011537233.3 → XP_011535535.1  actin-histidine N-methyltransferase isoform X2

    Conserved Domains (2) summary
    pfam09273
    Location:292 → 417
    Rubis-subs-bind; Rubisco LSMT substrate-binding
    cd19176
    Location:80 → 271
    SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins

  3. XM_011537231.3 → XP_011535533.2  actin-histidine N-methyltransferase isoform X1

    UniProtKB/Swiss-Prot
    A0PJU3, A5PLP0, B4DZE8, Q0VAQ2, Q659C0, Q86TU7, Q86TU8, Q96GY9, Q9H5U5
    Conserved Domains (2) summary
    cd19176
    Location:80 → 329
    SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins
    pfam09273
    Location:350 → 475
    Rubis-subs-bind; Rubisco LSMT substrate-binding

  4. XM_011537232.4 → XP_011535534.1  actin-histidine N-methyltransferase isoform X1

    See identical proteins and their annotated locations for XP_011535534.1

    UniProtKB/Swiss-Prot
    A0PJU3, A5PLP0, B4DZE8, Q0VAQ2, Q659C0, Q86TU7, Q86TU8, Q96GY9, Q9H5U5
    Conserved Domains (2) summary
    cd19176
    Location:80 → 329
    SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins
    pfam09273
    Location:350 → 475
    Rubis-subs-bind; Rubisco LSMT substrate-binding

  5. XM_047431805.1 → XP_047287761.1  actin-histidine N-methyltransferase isoform X1

    UniProtKB/Swiss-Prot
    A0PJU3, A5PLP0, B4DZE8, Q0VAQ2, Q659C0, Q86TU7, Q86TU8, Q96GY9, Q9H5U5

  6. XM_017021700.2 → XP_016877189.1  actin-histidine N-methyltransferase isoform X1

    UniProtKB/Swiss-Prot
    A0PJU3, A5PLP0, B4DZE8, Q0VAQ2, Q659C0, Q86TU7, Q86TU8, Q96GY9, Q9H5U5
    Conserved Domains (2) summary
    cd19176
    Location:80 → 329
    SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins
    pfam09273
    Location:350 → 475
    Rubis-subs-bind; Rubisco LSMT substrate-binding

  7. XM_011537235.1 → XP_011535537.1  actin-histidine N-methyltransferase isoform X3

    See identical proteins and their annotated locations for XP_011535537.1

    UniProtKB/TrEMBL
    A6NJ55, Q6NXR6
    Conserved Domains (1) summary
    cd19176
    Location:80 → 282
    SET_SETD3; SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    93629309..93718026 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054376806.1 → XP_054232781.1  actin-histidine N-methyltransferase isoform X1

    UniProtKB/Swiss-Prot
    A0PJU3, A5PLP0, B4DZE8, Q0VAQ2, Q659C0, Q86TU7, Q86TU8, Q96GY9, Q9H5U5

  2. XM_054376807.1 → XP_054232782.1  actin-histidine N-methyltransferase isoform X2

  3. XM_054376805.1 → XP_054232780.1  actin-histidine N-methyltransferase isoform X1

    UniProtKB/Swiss-Prot
    A0PJU3, A5PLP0, B4DZE8, Q0VAQ2, Q659C0, Q86TU7, Q86TU8, Q96GY9, Q9H5U5

  4. XM_054376808.1 → XP_054232783.1  actin-histidine N-methyltransferase isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q86TU7.1 GenPept UniProtKB/Swiss-Prot:Q86TU7

Gene LinkOut

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