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    SETD4 SET domain containing 4 [ Homo sapiens (human) ]

    Gene ID: 54093, updated on 3-Apr-2024

    Summary

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    Official Symbol
    SETD4provided by HGNC
    Official Full Name
    SET domain containing 4provided by HGNC
    Primary source
    HGNC:HGNC:1258
    See related
    Ensembl:ENSG00000185917 AllianceGenome:HGNC:1258
    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
    C21orf18; C21orf27
    Summary
    Enables histone methyltransferase activity (H4-K20 specific). Involved in histone H4-K20 trimethylation. Located in cytosol and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in testis (RPKM 7.1), skin (RPKM 4.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SETD4 in Genome Data Viewer
    Location:
    21q22.12
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (36034541..36060526, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (34417599..34443584, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (37406839..37432824, complement)

    Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1436 Neighboring gene ribosomal protein L23a pseudogene 3 Neighboring gene ribosomal modification protein rimK like family member B pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18421 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18422 Neighboring gene SETD4 antisense RNA 1 Neighboring gene RNA, U6 small nuclear 992, pseudogene

    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. SETD4 Regulates Cell Quiescence and Catalyzes the Trimethylation of H4K20 during Diapause Formation in Artemia. Dai L, et al. Mol Cell Biol, 2017 Apr 1. PMID 28031330, Free PMC Article
    2. CBR3-AS1 Accelerates the Malignant Proliferation of Gestational Choriocarcinoma Cells by Stabilizing SETD4. Zhang Y, et al. Dis Markers, 2022. PMID 35655916, Free PMC Article
    3. SET Domain-Containing Protein 4 Epigenetically Controls Breast Cancer Stem Cell Quiescence. Ye S, et al. Cancer Res, 2019 Sep 15. PMID 31308046
    4. SET domain-containing Protein 4 (SETD4) is a Newly Identified Cytosolic and Nuclear Lysine Methyltransferase involved in Breast Cancer Cell Proliferation. Faria JA, et al. J Cancer Sci Ther, 2013 Jan 21. PMID 24738023, Free PMC Article
    5. Mapping of a novel human carbonyl reductase, CBR3, and ribosomal pseudogenes to human chromosome 21q22.2. Watanabe K, et al. Genomics, 1998 Aug 15. PMID 9740676

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SETD4 inhibits prostate cancer development by promoting H3K27me3-mediated NUPR1 transcriptional repression and cell cycle arrest.
      Title: SETD4 inhibits prostate cancer development by promoting H3K27me3-mediated NUPR1 transcriptional repression and cell cycle arrest.
    2. High SETD4 expression is associated with Breast Cancer.
      Title: SET Domain-Containing Protein 4 Epigenetically Controls Breast Cancer Stem Cell Quiescence.
    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

    EBI GWAS Catalog

    Description
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables histone H3K36 methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone H3K4 methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone H3K4 methyltransferase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables histone H3K4 monomethyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H4K20 methyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone H4K20 monomethyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H4K20me methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transcription coactivator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in chromatin remodeling ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in inflammatory response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in peptidyl-lysine monomethylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in peptidyl-lysine trimethylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of inflammatory response ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of interleukin-6 production ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of tumor necrosis factor production ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of cell proliferation in bone marrow ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    SET domain-containing protein 4
    NP_001007260.1
    NP_001007262.1
    NP_001273681.1
    NP_059134.1
    XP_011527938.1
    XP_011527939.1
    XP_011527940.1
    XP_011527941.1
    XP_011527942.1
    XP_011527945.1
    XP_011527946.1
    XP_016883894.1
    XP_024307889.1
    XP_024307890.1
    XP_047296860.1
    XP_047296861.1
    XP_047296862.1
    XP_047296863.1
    XP_047296864.1
    XP_047296865.1
    XP_047296866.1
    XP_047296867.1
    XP_054180645.1
    XP_054180646.1
    XP_054180647.1
    XP_054180648.1
    XP_054180649.1
    XP_054180650.1
    XP_054180651.1
    XP_054180652.1
    XP_054180653.1
    XP_054180654.1
    XP_054180655.1
    XP_054180656.1
    XP_054180657.1
    XP_054180658.1
    XP_054180659.1
    XP_054180660.1
    XP_054180661.1
    XP_054180662.1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001007259.3 → NP_001007260.1  SET domain-containing protein 4 isoform 2

      See identical proteins and their annotated locations for NP_001007260.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and has alternatively spliced 3' terminal exon, which causes a frame-shift compared to variant 1. The resulting shorter isoform (2) has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AP000688, BC002898, BF195582
      Consensus CDS
      CCDS42923.1
      UniProtKB/Swiss-Prot
      Q9NVD3
      Related
      ENSP00000382159.2, ENST00000399208.6
      Conserved Domains (2) summary
      pfam00856
      Location:210 → 273
      SET; SET domain
      cl21457
      Location:145 → 272
      TIM_phosphate_binding; TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate ...

    2. NM_001007261.3 → NP_001007262.1  SET domain-containing protein 4 isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs at the 5' and 3' ends, contains an additional exon in the 5' region, and initiates translation from an alternate start codon compared to variant 1. The resulting isoform (4) has a shorter N-terminus and a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AB004853, AP000688, BC002898, BF195582
      Consensus CDS
      CCDS74791.1
      UniProtKB/TrEMBL
      A8MTS1
      Related
      ENSP00000382156.1, ENST00000399205.5
      Conserved Domains (2) summary
      pfam00856
      Location:186 → 249
      SET; SET domain
      cl21457
      Location:121 → 248
      TIM_phosphate_binding; TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate ...

    3. NM_001286752.2 → NP_001273681.1  SET domain-containing protein 4 isoform 3

      See identical proteins and their annotated locations for NP_001273681.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs at the 5' and 3' ends, contains an additional exon in the 5' region, and initiates translation from an alternate start codon compared to variant 1. The resulting isoform (3) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AI636385, AK095215, BC036556, DC394539
      Consensus CDS
      CCDS74792.1
      UniProtKB/Swiss-Prot
      Q9NVD3
      Related
      ENSP00000382161.1, ENST00000399212.5
      Conserved Domains (2) summary
      pfam00856
      Location:186 → 249
      SET; SET domain
      pfam09273
      Location:293 → 401
      Rubis-subs-bind; Rubisco LSMT substrate-binding

    4. NM_017438.5 → NP_059134.1  SET domain-containing protein 4 isoform 1

      See identical proteins and their annotated locations for NP_059134.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AI636385, AK001660, DC394539
      Consensus CDS
      CCDS13640.1
      UniProtKB/Swiss-Prot
      B4DT14, D3DSG2, D3DSG4, Q8NE19, Q9BU46, Q9NVD3
      Related
      ENSP00000329189.4, ENST00000332131.9
      Conserved Domains (2) summary
      pfam00856
      Location:210 → 273
      SET; SET domain
      pfam09273
      Location:317 → 425
      Rubis-subs-bind; Rubisco LSMT substrate-binding

    RNA

    1. NR_040087.3 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks an exon in the mid-region compared to variant 1. It is represented as non-coding because the use of the translational start codon, as used in variant 1, renders this transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AF391112, AI636385, DC394539
      Related
      ENST00000481477.5

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000021.9 Reference GRCh38.p14 Primary Assembly

      Range
      36034541..36060526 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011529643.2 → XP_011527945.1  SET domain-containing protein 4 isoform X2

      See identical proteins and their annotated locations for XP_011527945.1

      UniProtKB/Swiss-Prot
      Q9NVD3
      Conserved Domains (2) summary
      pfam00856
      Location:186 → 249
      SET; SET domain
      pfam09273
      Location:293 → 401
      Rubis-subs-bind; Rubisco LSMT substrate-binding

    2. XM_047440906.1 → XP_047296862.1  SET domain-containing protein 4 isoform X2

    3. XM_011529636.3 → XP_011527938.1  SET domain-containing protein 4 isoform X1

      See identical proteins and their annotated locations for XP_011527938.1

      UniProtKB/Swiss-Prot
      B4DT14, D3DSG2, D3DSG4, Q8NE19, Q9BU46, Q9NVD3
      Conserved Domains (2) summary
      pfam00856
      Location:210 → 273
      SET; SET domain
      pfam09273
      Location:317 → 425
      Rubis-subs-bind; Rubisco LSMT substrate-binding

    4. XM_047440904.1 → XP_047296860.1  SET domain-containing protein 4 isoform X1

      UniProtKB/Swiss-Prot
      B4DT14, D3DSG2, D3DSG4, Q8NE19, Q9BU46, Q9NVD3

    5. XM_011529640.4 → XP_011527942.1  SET domain-containing protein 4 isoform X1

      See identical proteins and their annotated locations for XP_011527942.1

      UniProtKB/Swiss-Prot
      B4DT14, D3DSG2, D3DSG4, Q8NE19, Q9BU46, Q9NVD3
      Conserved Domains (2) summary
      pfam00856
      Location:210 → 273
      SET; SET domain
      pfam09273
      Location:317 → 425
      Rubis-subs-bind; Rubisco LSMT substrate-binding

    6. XM_047440905.1 → XP_047296861.1  SET domain-containing protein 4 isoform X1

      UniProtKB/Swiss-Prot
      B4DT14, D3DSG2, D3DSG4, Q8NE19, Q9BU46, Q9NVD3

    7. XM_011529644.2 → XP_011527946.1  SET domain-containing protein 4 isoform X2

      See identical proteins and their annotated locations for XP_011527946.1

      UniProtKB/Swiss-Prot
      Q9NVD3
      Conserved Domains (2) summary
      pfam00856
      Location:186 → 249
      SET; SET domain
      pfam09273
      Location:293 → 401
      Rubis-subs-bind; Rubisco LSMT substrate-binding

    8. XM_047440907.1 → XP_047296863.1  SET domain-containing protein 4 isoform X2

    9. XM_011529637.3 → XP_011527939.1  SET domain-containing protein 4 isoform X1

      See identical proteins and their annotated locations for XP_011527939.1

      UniProtKB/Swiss-Prot
      B4DT14, D3DSG2, D3DSG4, Q8NE19, Q9BU46, Q9NVD3
      Conserved Domains (2) summary
      pfam00856
      Location:210 → 273
      SET; SET domain
      pfam09273
      Location:317 → 425
      Rubis-subs-bind; Rubisco LSMT substrate-binding

    10. XM_011529639.2 → XP_011527941.1  SET domain-containing protein 4 isoform X1

      See identical proteins and their annotated locations for XP_011527941.1

      UniProtKB/Swiss-Prot
      B4DT14, D3DSG2, D3DSG4, Q8NE19, Q9BU46, Q9NVD3
      Conserved Domains (2) summary
      pfam00856
      Location:210 → 273
      SET; SET domain
      pfam09273
      Location:317 → 425
      Rubis-subs-bind; Rubisco LSMT substrate-binding

    11. XM_011529638.3 → XP_011527940.1  SET domain-containing protein 4 isoform X1

      See identical proteins and their annotated locations for XP_011527940.1

      UniProtKB/Swiss-Prot
      B4DT14, D3DSG2, D3DSG4, Q8NE19, Q9BU46, Q9NVD3
      Related
      ENSP00000382163.1, ENST00000399215.5
      Conserved Domains (2) summary
      pfam00856
      Location:210 → 273
      SET; SET domain
      pfam09273
      Location:317 → 425
      Rubis-subs-bind; Rubisco LSMT substrate-binding

    12. XM_047440909.1 → XP_047296865.1  SET domain-containing protein 4 isoform X3

    13. XM_047440908.1 → XP_047296864.1  SET domain-containing protein 4 isoform X3

    14. XM_017028405.3 → XP_016883894.1  SET domain-containing protein 4 isoform X4

      UniProtKB/Swiss-Prot
      Q9NVD3
      Related
      ENSP00000382158.1, ENST00000399207.5
      Conserved Domains (2) summary
      pfam00856
      Location:210 → 273
      SET; SET domain
      cl21457
      Location:145 → 272
      TIM_phosphate_binding; TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate ...

    15. XM_024452122.2 → XP_024307890.1  SET domain-containing protein 4 isoform X5

      UniProtKB/TrEMBL
      C9JWV5

    16. XM_024452121.2 → XP_024307889.1  SET domain-containing protein 4 isoform X5

      UniProtKB/TrEMBL
      C9JWV5
      Related
      ENSP00000399998.1, ENST00000424303.5

    17. XM_047440911.1 → XP_047296867.1  SET domain-containing protein 4 isoform X5

      Related
      ENSP00000396837.1, ENST00000429161.5

    18. XM_047440910.1 → XP_047296866.1  SET domain-containing protein 4 isoform X5

    RNA

    1. XR_007067790.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060945.1 Alternate T2T-CHM13v2.0

      Range
      34417599..34443584 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054324677.1 → XP_054180652.1  SET domain-containing protein 4 isoform X2

    2. XM_054324678.1 → XP_054180653.1  SET domain-containing protein 4 isoform X2

    3. XM_054324670.1 → XP_054180645.1  SET domain-containing protein 4 isoform X1

      UniProtKB/Swiss-Prot
      B4DT14, D3DSG2, D3DSG4, Q8NE19, Q9BU46, Q9NVD3

    4. XM_054324671.1 → XP_054180646.1  SET domain-containing protein 4 isoform X1

      UniProtKB/Swiss-Prot
      B4DT14, D3DSG2, D3DSG4, Q8NE19, Q9BU46, Q9NVD3

    5. XM_054324673.1 → XP_054180648.1  SET domain-containing protein 4 isoform X1

      UniProtKB/Swiss-Prot
      B4DT14, D3DSG2, D3DSG4, Q8NE19, Q9BU46, Q9NVD3

    6. XM_054324674.1 → XP_054180649.1  SET domain-containing protein 4 isoform X1

      UniProtKB/Swiss-Prot
      B4DT14, D3DSG2, D3DSG4, Q8NE19, Q9BU46, Q9NVD3

    7. XM_054324679.1 → XP_054180654.1  SET domain-containing protein 4 isoform X2

    8. XM_054324680.1 → XP_054180655.1  SET domain-containing protein 4 isoform X2

    9. XM_054324672.1 → XP_054180647.1  SET domain-containing protein 4 isoform X1

      UniProtKB/Swiss-Prot
      B4DT14, D3DSG2, D3DSG4, Q8NE19, Q9BU46, Q9NVD3

    10. XM_054324676.1 → XP_054180651.1  SET domain-containing protein 4 isoform X1

      UniProtKB/Swiss-Prot
      B4DT14, D3DSG2, D3DSG4, Q8NE19, Q9BU46, Q9NVD3

    11. XM_054324675.1 → XP_054180650.1  SET domain-containing protein 4 isoform X1

      UniProtKB/Swiss-Prot
      B4DT14, D3DSG2, D3DSG4, Q8NE19, Q9BU46, Q9NVD3

    12. XM_054324682.1 → XP_054180657.1  SET domain-containing protein 4 isoform X3

    13. XM_054324681.1 → XP_054180656.1  SET domain-containing protein 4 isoform X3

    14. XM_054324683.1 → XP_054180658.1  SET domain-containing protein 4 isoform X4

    15. XM_054324685.1 → XP_054180660.1  SET domain-containing protein 4 isoform X5

    16. XM_054324684.1 → XP_054180659.1  SET domain-containing protein 4 isoform X5

    17. XM_054324687.1 → XP_054180662.1  SET domain-containing protein 4 isoform X5

    18. XM_054324686.1 → XP_054180661.1  SET domain-containing protein 4 isoform X5

    RNA

    1. XR_008485339.1 RNA Sequence

    2. XR_008485340.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001007258.1: Suppressed sequence

      Description
      NM_001007258.1: This RefSeq was permanently suppressed because it contains the wrong CDS. If the correct CDS was annotated, it would be a nonsense-mediated mRNA decay (NMD) candidate.

    2. NM_001007260.1: Suppressed sequence

      Description
      NM_001007260.1: This RefSeq was permanently suppressed because it contains the wrong CDS. If the correct CDS was annotated, it would be a nonsense-mediated mRNA decay (NMD) candidate.

    3. NM_001007262.1: Suppressed sequence

      Description
      NM_001007262.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NVD3.1 GenPept UniProtKB/Swiss-Prot:Q9NVD3

    Gene LinkOut

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

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