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    SETD9 SET domain containing 9 [ Homo sapiens (human) ]

    Gene ID: 133383, updated on 28-Oct-2024

    Summary

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    Official Symbol
    SETD9provided by HGNC
    Official Full Name
    SET domain containing 9provided by HGNC
    Primary source
    HGNC:HGNC:28508
    See related
    Ensembl:ENSG00000155542 AllianceGenome:HGNC:28508
    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
    C5orf35
    Summary
    Predicted to enable lysine N-methyltransferase activity. Predicted to be involved in regulation of signal transduction by p53 class mediator. Located in mitochondrion. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Broad expression in testis (RPKM 3.4), colon (RPKM 1.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SETD9 in Genome Data Viewer
    Location:
    5q11.2
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (56909260..56928900)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (57737511..57757157)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (56205087..56224727)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene mitogen-activated protein kinase kinase kinase 1 Neighboring gene uncharacterized LOC124901214 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_86223 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:56178189-56179388 Neighboring gene uncharacterized LOC105378980 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_86245 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22573 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16024 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16025 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22574 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:56206084-56206905 Neighboring gene MIER family member 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22575 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16026 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16027 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16028 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_86248 Neighboring gene small nuclear ribonucleoprotein polypeptide B2 pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_86269 Neighboring gene Sharpr-MPRA regulatory region 15622 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22576 Neighboring gene uncharacterized LOC124900981 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16029 Neighboring gene Sharpr-MPRA regulatory region 9364

    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. Uncovering the human methyltransferasome. Petrossian TC, et al. Mol Cell Proteomics, 2011 Jan. PMID 20930037, Free PMC Article
    2. SNP variants at the MAP3K1/SETD9 locus 5q11.2 associate with somatic PIK3CA variants in breast cancers. Puzone R, et al. Eur J Hum Genet, 2017 Feb. PMID 28029147, Free PMC Article
    3. Phospho-tyrosine dependent protein-protein interaction network. Grossmann A, et al. Mol Syst Biol, 2015 Mar 26. PMID 25814554, Free PMC Article
    4. Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context. Morgenstern M, et al. Cell Metab, 2021 Dec 7. PMID 34800366, Free PMC Article
    5. Ubiquitin-mediated proteolysis of HuR by heat shock. Abdelmohsen K, et al. EMBO J, 2009 May 6. PMID 19322201, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SNP variants at the MAP3K1/SETD9 gene boundary associate with somatic PIK3CA variants in breast cancers.
      Title: SNP variants at the MAP3K1/SETD9 locus 5q11.2 associate with somatic PIK3CA variants in breast cancers.
    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

    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

    • MGC33648

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables lysine N-methyltransferase activity TAS
    Traceable Author Statement
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of signal transduction by p53 class mediator TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    located_in mitochondrion HTP PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    SET domain-containing protein 9

    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_001171990.3 → NP_001165461.1  SET domain-containing protein 9 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR and coding region, compared to variant 1, these differences result in a frameshift. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC008937, AK309152
      Consensus CDS
      CCDS93713.1
      UniProtKB/Swiss-Prot
      Q8NE22
      Related
      ENSP00000486609.1, ENST00000628593.1

    2. NM_001323018.2 → NP_001309947.1  SET domain-containing protein 9 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC008937
      Conserved Domains (1) summary
      pfam00856
      Location:235 → 268
      SET; SET domain

    3. NM_001323019.2 → NP_001309948.1  SET domain-containing protein 9 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC008937

    4. NM_001323020.2 → NP_001309949.1  SET domain-containing protein 9 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC008937

    5. NM_001323022.1 → NP_001309951.1  SET domain-containing protein 9 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC008937

    6. NM_153706.4 → NP_714917.2  SET domain-containing protein 9 isoform 1

      See identical proteins and their annotated locations for NP_714917.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC008937, BC036528
      Consensus CDS
      CCDS3972.1
      UniProtKB/Swiss-Prot
      F5H713, Q8NE22
      Related
      ENSP00000285947.2, ENST00000285947.5
      Conserved Domains (1) summary
      pfam00856
      Location:261 → 294
      SET; SET domain

    RNA

    1. NR_136555.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC008937

    2. NR_136556.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC008937
      Related
      ENST00000418299.5

    3. NR_136557.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC008937

    4. NR_136558.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC008937

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      56909260..56928900
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005248426.5 → XP_005248483.1  SET domain-containing protein 9 isoform X3

      Conserved Domains (1) summary
      pfam00856
      Location:117 → 150
      SET; SET domain

    2. XM_011543140.4 → XP_011541442.1  SET domain-containing protein 9 isoform X2

      See identical proteins and their annotated locations for XP_011541442.1

      Conserved Domains (1) summary
      pfam00856
      Location:185 → 218
      SET; SET domain

    3. XM_011543139.3 → XP_011541441.1  SET domain-containing protein 9 isoform X1

      Conserved Domains (1) summary
      pfam00856
      Location:229 → 262
      SET; SET domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      57737511..57757157
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054351571.1 → XP_054207546.1  SET domain-containing protein 9 isoform X3

    2. XM_054351570.1 → XP_054207545.1  SET domain-containing protein 9 isoform X2

    3. XM_054351569.1 → XP_054207544.1  SET domain-containing protein 9 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NE22.2 GenPept UniProtKB/Swiss-Prot:Q8NE22

    Gene LinkOut

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

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