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

Gene ID: 54093, updated on 27-Nov-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 MIM:620995; 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 H4K20 methyltransferase activity. Predicted to be involved in several processes, including positive regulation of inflammatory response; positive regulation of macromolecule biosynthetic process; and regulation of cell proliferation in bone marrow. Located in cytosol and nucleus. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in testis (RPKM 7.1), skin (RPKM 4.7) and 25 other tissues See more
Orthologs
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (36034541..36060526, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (34417599..34443584, complement)
RS_2024_09 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. SET Domain-Containing Protein 4 Epigenetically Controls Breast Cancer Stem Cell Quiescence. Ye S, et al. Cancer Res, 2019 Sep 15. PMID 31308046
  3. SETD4 inhibits prostate cancer development by promoting H3K27me3-mediated NUPR1 transcriptional repression and cell cycle arrest. Wang C, et al. Cancer Lett, 2023 Nov 28. PMID 37879429
  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)

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 protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription coactivator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
  
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 positive regulation of inflammatory response 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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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_2024_08

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

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