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    SETD7 SET domain containing 7, histone lysine methyltransferase [ Homo sapiens (human) ]

    Gene ID: 80854, updated on 14-Nov-2024

    Summary

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    Official Symbol
    SETD7provided by HGNC
    Official Full Name
    SET domain containing 7, histone lysine methyltransferaseprovided by HGNC
    Primary source
    HGNC:HGNC:30412
    See related
    Ensembl:ENSG00000145391 MIM:606594; AllianceGenome:HGNC:30412
    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
    KMT7; SET7; SET9; SET7/9
    Summary
    Enables histone H3 methyltransferase activity; p53 binding activity; and protein-lysine N-methyltransferase activity. Involved in peptidyl-lysine dimethylation and peptidyl-lysine monomethylation. Acts upstream of or within DNA damage response and heterochromatin organization. Located in chromosome and nucleolus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in fat (RPKM 22.9), prostate (RPKM 16.7) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SETD7 in Genome Data Viewer
    Location:
    4q31.1
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (139492974..139556219, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (142812640..142875826, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (140414128..140477373, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA ACA64 Neighboring gene RAB33B, member RAS oncogene family Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21924 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15700 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21925 Neighboring gene RAB33B antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15701 Neighboring gene Sharpr-MPRA regulatory region 15265 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15702 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21926 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:140469419-140469605 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:140472251-140472751 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15703 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15704 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15705 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15706 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21927 Neighboring gene ferritin heavy chain 1 pseudogene 24 Neighboring gene uncharacterized LOC105377451 Neighboring gene uncharacterized LOC105377622

    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. Adverse epigenetic signatures by histone methyltransferase Set7 contribute to vascular dysfunction in patients with type 2 diabetes mellitus. Paneni F, et al. Circ Cardiovasc Genet, 2015 Feb. PMID 25472959
    2. A Common Variant in the SETD7 Gene Predicts Serum Lycopene Concentrations. D'Adamo CR, et al. Nutrients, 2016 Feb 6. PMID 26861389, Free PMC Article
    3. High expression of trimethylated histone H3 lysine 4 is associated with poor prognosis in hepatocellular carcinoma. He C, et al. Hum Pathol, 2012 Sep. PMID 22406368
    4. Non-histone Methylation of SET7/9 and its Biological Functions. Gao L, et al. Recent Pat Anticancer Drug Discov, 2022. PMID 34856916
    5. Set7/9 controls proliferation and genotoxic drug resistance of NSCLC cells. Daks A, et al. Biochem Biophys Res Commun, 2021 Oct 1. PMID 34343833

    See all (143) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SETD7 Promotes Cell Proliferation and Migration via Methylation-mediated TAF7 in Clear Cell Renal Cell Carcinoma.
      Title: SETD7 Promotes Cell Proliferation and Migration via Methylation-mediated TAF7 in Clear Cell Renal Cell Carcinoma.
    2. Epigenetic mechanism of SET7/9-mediated histone methylation modification in high glucose-induced ferroptosis in retinal pigment epithelial cells.
      Title: Epigenetic mechanism of SET7/9-mediated histone methylation modification in high glucose-induced ferroptosis in retinal pigment epithelial cells.
    3. ZKSCAN5 activates LAPTM5 expression by recruiting SETD7 to promote metastasis in pancreatic ductal adenocarcinoma.
      Title: ZKSCAN5 activates LAPTM5 expression by recruiting SETD7 to promote metastasis in pancreatic ductal adenocarcinoma.
    4. Combined SET7/9 and CDK4 inhibition act synergistically against osteosarcoma.
      Title: Combined SET7/9 and CDK4 inhibition act synergistically against osteosarcoma.
    5. Methyltransferase Set7/9 controls PARP1 expression and regulates cisplatin response of breast cancer cells.
      Title: Methyltransferase Set7/9 controls PARP1 expression and regulates cisplatin response of breast cancer cells.
    6. SET7/9-mediated methylation affects oncogenic functions of histone demethylase JMJD2A.
      Title: SET7/9-mediated methylation affects oncogenic functions of histone demethylase JMJD2A.
    7. Methylation of KRAS by SETD7 promotes KRAS degradation in non-small cell lung cancer.
      Title: Methylation of KRAS by SETD7 promotes KRAS degradation in non-small cell lung cancer.
    8. Lysine N-methyltransferase SETD7 promotes bladder cancer progression and immune escape via STAT3/PD-L1 cascade.
      Title: Lysine N-methyltransferase SETD7 promotes bladder cancer progression and immune escape via STAT3/PD-L1 cascade.
    9. SETD7 functions as a transcription repressor in prostate cancer via methylating FOXA1.
      Title: SETD7 functions as a transcription repressor in prostate cancer via methylating FOXA1.
    10. SET7 methylates the deubiquitinase OTUB1 at Lys [122] to impair its binding to E2 enzyme UBC13 and relieve its suppressive role on ferroptosis.
      Title: SET7 methylates the deubiquitinase OTUB1 at Lys (122) to impair its binding to E2 enzyme UBC13 and relieve its suppressive role on ferroptosis.
    Submit: New GeneRIF Correction See all GeneRIFs (92)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide and candidate gene association study of cigarette smoking behaviors.
    EBI GWAS Catalog

    Variation

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    See Variation Viewer (GRCh37.p13)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat HIV-1 Tat is monomethylated at lysine 71 by SETD7 (KMT7) in HEK293T and Jurkat A2 cell lines PubMed
    tat HIV-1 Tat is methylated at residue lysine 51 in its RNA-binding domain by SET7/9-KMT7 PubMed
    tat SET7/9-KMT7 binds directly to HIV-1 Tat and enhances recruitment of the Tat/P-TEFb complex to HIV-1 TAR RNA PubMed

    Go to the HIV-1, Human Interaction Database

    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

    • FLJ21193, KIAA1717

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chromatin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3 methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone H3 methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H3K4 monomethyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables p53 binding IPI
    Inferred from Physical Interaction
    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 
    Process Evidence Code Pubs
    acts_upstream_of_or_within DNA damage response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in chromatin organization NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in heterochromatin organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within heterochromatin organization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in peptidyl-lysine dimethylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in peptidyl-lysine monomethylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in response to ethanol IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in chromosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in chromosome IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleolus 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
    		  

    General protein information

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    Preferred Names
    histone-lysine N-methyltransferase SETD7
    Names
    H3-K4-HMTase SETD7
    SET domain containing 7, lysine methyltransferase
    SET domain containing lysine methyltransferase 7
    SET domain-containing protein 7
    histone H3-K4 methyltransferase SETD7
    histone H3-lysine 4-specific methyltransferase
    lysine N-methyltransferase 7
    NP_001293128.1
    NP_001293129.1
    NP_085151.1
    XP_016864150.1
    XP_054206895.1

    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_001306199.2 → NP_001293128.1  histone-lysine N-methyltransferase SETD7 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate 3' terminal exon that results in a different 3' UTR and a novel 3' coding region compared to variant 1. It encodes isoform 2, which is shorter than and has a novel C-terminus compared to isoform 1.
      Source sequence(s)
      AC114743, AI985614, AK310856
      Consensus CDS
      CCDS77961.1
      UniProtKB/TrEMBL
      D6RJA0
      Related
      ENSP00000427300.1, ENST00000506866.6
      Conserved Domains (1) summary
      smart00317
      Location:226 → 303
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

    2. NM_001306200.2 → NP_001293129.1  histone-lysine N-methyltransferase SETD7 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 3' UTR, lacks exons in the 3' coding region, and has a 3' end that extends into an intron compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC114743, BC110904
      Consensus CDS
      CCDS82956.1
      UniProtKB/TrEMBL
      B5MCZ8
      Related
      ENSP00000385913.3, ENST00000404104.7
      Conserved Domains (1) summary
      COG2849
      Location:37 → 123
      YwqK; Antitoxin component YwqK of the YwqJK toxin-antitoxin module [Defense mechanisms]

    3. NM_030648.4 → NP_085151.1  histone-lysine N-methyltransferase SETD7 isoform 1

      See identical proteins and their annotated locations for NP_085151.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC112236, AC114743
      Consensus CDS
      CCDS3748.1
      UniProtKB/Swiss-Prot
      B5WWL3, Q0VAH3, Q4W5A9, Q8WTS6, Q9C0E6
      Related
      ENSP00000274031.3, ENST00000274031.8
      Conserved Domains (2) summary
      COG2849
      Location:37 → 134
      YwqK; Antitoxin component YwqK of the YwqJK toxin-antitoxin module [Defense mechanisms]
      cd10530
      Location:208 → 337
      SET_SETD7; SET domain found in SET domain-containing protein 7 (SETD7) and similar proteins

    RNA

    1. NR_131339.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) contains an alternate internal exon, lacks alternate exons, and has a 3' end that extends into an intron compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC114743, BC066361, BC110904
      Related
      ENST00000406354.1

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      139492974..139556219 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017008661.1 → XP_016864150.1  histone-lysine N-methyltransferase SETD7 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      142812640..142875826 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054350920.1 → XP_054206895.1  histone-lysine N-methyltransferase SETD7 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WTS6.1 GenPept UniProtKB/Swiss-Prot:Q8WTS6

    Gene LinkOut

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

    Chemical Information
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