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    SETD6 SET domain containing 6, protein lysine methyltransferase [ Homo sapiens (human) ]

    Gene ID: 79918, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SETD6provided by HGNC
    Official Full Name
    SET domain containing 6, protein lysine methyltransferaseprovided by HGNC
    Primary source
    HGNC:HGNC:26116
    See related
    Ensembl:ENSG00000103037 MIM:616424; AllianceGenome:HGNC:26116
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    This gene encodes a methyltransferase that adds a methyl group to the histone H2AZ, which is involved in nuclear receptor-dependent transcription. The protein also interacts with several endogenous proteins which are involved in nuclear hormone receptor signaling. A related pseudogene is located on chromosome 2. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
    Expression
    Ubiquitous expression in testis (RPKM 13.6), skin (RPKM 9.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SETD6 in Genome Data Viewer
    Location:
    16q21
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (58515479..58523842)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (64310621..64319075)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (58549383..58557746)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7550 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7551 Neighboring gene long intergenic non-protein coding RNA 2137 Neighboring gene Sharpr-MPRA regulatory region 11516 Neighboring gene Sharpr-MPRA regulatory region 12894 Neighboring gene NDRG family member 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:58521475-58521826 Neighboring gene Sharpr-MPRA regulatory region 13659 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:58529535-58530090 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:58530091-58530646 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:58533905-58534721 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:58534722-58535539 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:58535540-58536356 Neighboring gene RNA, U6 small nuclear 103, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10929 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7554 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10930 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_43903 Neighboring gene CCR4-NOT transcription complex subunit 1 Neighboring gene small nucleolar RNA, H/ACA box 46 Neighboring gene small nucleolar RNA, H/ACA box 50A

    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. SETD6 Regulates E2-Dependent Human Papillomavirus Transcription. Jose L, et al. J Virol, 2022 Nov 23. PMID 36300937, Free PMC Article
    2. A proteomic approach for the identification of novel lysine methyltransferase substrates. Levy D, et al. Epigenetics Chromatin, 2011 Oct 24. PMID 22024134, Free PMC Article
    3. SETD6 controls the expression of estrogen-responsive genes and proliferation of breast carcinoma cells. O'Neill DJ, et al. Epigenetics, 2014 Jul. PMID 24751716, Free PMC Article
    4. Lysine methyltransferase SETD6 modifies histones on a glycine-lysine motif. Binda O. Epigenetics, 2020 Jan-Feb. PMID 31370726, Free PMC Article
    5. Oligomerization and Auto-methylation of the Human Lysine Methyltransferase SETD6. Weil LE, et al. J Mol Biol, 2018 Oct 19. PMID 30189201

    See all (30) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Investigating the functional role of SETD6 in lung adenocarcinoma.
      Title: Investigating the functional role of SETD6 in lung adenocarcinoma.
    2. TWIST1 methylation by SETD6 selectively antagonizes LINC-PINT expression in glioma.
      Title: TWIST1 methylation by SETD6 selectively antagonizes LINC-PINT expression in glioma.
    3. SETD6 Regulates E2-Dependent Human Papillomavirus Transcription.
      Title: SETD6 Regulates E2-Dependent Human Papillomavirus Transcription.
    4. Structure-function conservation between the methyltransferases SETD3 and SETD6.
      Title: Structure-function conservation between the methyltransferases SETD3 and SETD6.
    5. BRD4 methylation by the methyltransferase SETD6 regulates selective transcription to control mRNA translation.
      Title: BRD4 methylation by the methyltransferase SETD6 regulates selective transcription to control mRNA translation.
    6. Silencing of SETD6 inhibits the tumorigenesis of oral squamous cell carcinoma by inhibiting methylation of PAK4 and RelA.
      Title: Silencing of SETD6 inhibits the tumorigenesis of oral squamous cell carcinoma by inhibiting methylation of PAK4 and RelA.
    7. Lysine methyltransferase SETD6 modifies histones on a glycine-lysine motif.
      Title: Lysine methyltransferase SETD6 modifies histones on a glycine-lysine motif.
    8. MiR-411 inhibits gastric cancer proliferation and migration through targeting SETD6.
      Title: MiR-411 inhibits gastric cancer proliferation and migration through targeting SETD6.
    9. Study demonstrates that SETD6 monomeric, dimeric and trimeric forms are stabilized by the methyl donor, S-adenosyl-l-methionine. SETD6 has auto-methylation activity at K39 and K179, which serves as the major auto-methylation sites with a moderate auto-methylation activity toward K372. Data support a model by which SETD6 auto-methylation and self-interaction positively regulate its enzymatic activity in vitro.
      Title: Oligomerization and Auto-methylation of the Human Lysine Methyltransferase SETD6.
    10. During mitosis SETD6 binds and methylates PLK1
      Title: The methyltransferase SETD6 regulates Mitotic progression through PLK1 methylation.
    Submit: New GeneRIF Correction See all GeneRIFs (19)

    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)

    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

    • FLJ21148

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables NF-kappaB binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables S-adenosyl-L-methionine binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein-lysine N-methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein-lysine N-methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein-lysine N-methyltransferase activity TAS
    Traceable Author Statement
    more info
    		  
    Process Evidence Code Pubs
    involved_in negative regulation of NF-kappaB transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in peptidyl-lysine monomethylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of inflammatory response IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in stem cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in stem cell population maintenance ISS
    Inferred from Sequence or Structural Similarity
    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

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    Preferred Names
    N-lysine methyltransferase SETD6
    Names
    SET domain-containing protein 6

    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_001160305.4 → NP_001153777.1  N-lysine methyltransferase SETD6 isoform a

      See identical proteins and their annotated locations for NP_001153777.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      AC009118
      Consensus CDS
      CCDS54013.1
      UniProtKB/Swiss-Prot
      A8K380, B5ME38, Q8TBK2, Q9H787
      UniProtKB/TrEMBL
      J3QT10
      Related
      ENSP00000219315.5, ENST00000219315.9
      Conserved Domains (2) summary
      pfam00856
      Location:247 → 286
      SET; SET domain
      pfam09273
      Location:338 → 465
      Rubis-subs-bind; Rubisco LSMT substrate-binding

    2. NM_024860.3 → NP_079136.2  N-lysine methyltransferase SETD6 isoform b

      See identical proteins and their annotated locations for NP_079136.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame segment in the coding region, compared to variant 1. The encoded isoform (b) is shorter than isoform a.
      Source sequence(s)
      AC009118, AK024801, BC110433, BP338820, DA074170, GD138369
      Consensus CDS
      CCDS10798.1
      UniProtKB/TrEMBL
      J3QT10
      Related
      ENSP00000310082.2, ENST00000310682.6
      Conserved Domains (2) summary
      cd19178
      Location:34 → 278
      SET_SETD6; SET domain found in SET domain-containing protein 6 (SETD6) and similar proteins
      pfam09273
      Location:313 → 441
      Rubis-subs-bind; Rubisco LSMT substrate-binding

    RNA

    1. NR_134583.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses alternate splice sites in internal exons, compared to variant 1. This variant (2) lacks two alternate internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC009118, BC110433, BP338820, DA074170, GD138369

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      58515479..58523842
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047434664.1 → XP_047290620.1  N-lysine methyltransferase SETD6 isoform X2

      UniProtKB/TrEMBL
      H7C3N0

    2. XM_047434665.1 → XP_047290621.1  N-lysine methyltransferase SETD6 isoform X3

      UniProtKB/TrEMBL
      H7C3N0
      Related
      ENSP00000412858.1, ENST00000422445.5

    3. XM_047434663.1 → XP_047290619.1  N-lysine methyltransferase SETD6 isoform X1

      UniProtKB/TrEMBL
      E9PC53
      Related
      ENSP00000398033.1, ENST00000427443.5

    4. XM_011523336.2 → XP_011521638.1  N-lysine methyltransferase SETD6 isoform X3

      UniProtKB/TrEMBL
      H7C3N0

    5. XM_047434666.1 → XP_047290622.1  N-lysine methyltransferase SETD6 isoform X4

      UniProtKB/TrEMBL
      H7C3N0

    6. XM_047434667.1 → XP_047290623.1  N-lysine methyltransferase SETD6 isoform X5

      UniProtKB/TrEMBL
      B4DM46

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      64310621..64319075
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054313966.1 → XP_054169941.1  N-lysine methyltransferase SETD6 isoform X5

      UniProtKB/TrEMBL
      B4DM46

    2. XM_054313962.1 → XP_054169937.1  N-lysine methyltransferase SETD6 isoform X2

      UniProtKB/TrEMBL
      H7C3N0

    3. XM_054313963.1 → XP_054169938.1  N-lysine methyltransferase SETD6 isoform X3

      UniProtKB/TrEMBL
      H7C3N0

    4. XM_054313961.1 → XP_054169936.1  N-lysine methyltransferase SETD6 isoform X1

      UniProtKB/TrEMBL
      E9PC53

    5. XM_054313964.1 → XP_054169939.1  N-lysine methyltransferase SETD6 isoform X3

      UniProtKB/TrEMBL
      H7C3N0

    6. XM_054313965.1 → XP_054169940.1  N-lysine methyltransferase SETD6 isoform X4

      UniProtKB/TrEMBL
      H7C3N0
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TBK2.2 GenPept UniProtKB/Swiss-Prot:Q8TBK2

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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