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

Gene ID: 133383, updated on 2-Nov-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, Nov 2024]
Expression
Broad expression in testis (RPKM 3.4), colon (RPKM 1.3) and 25 other tissues See more
Orthologs
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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

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