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

Summary

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, Oct 2024]
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

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_000021.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-87620 (e-PCR)
- UniSTS:37667

SHGC-13275 (e-PCR)
- UniSTS:75048

PMC156606P1 (e-PCR)
- UniSTS:271408

D8S2279 (e-PCR)
- UniSTS:473907

RH103382 (e-PCR)
- UniSTS:97708

L17971 (e-PCR)
- UniSTS:43966

SHGC-87609 (e-PCR)
- UniSTS:72130

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 peptidyl-lysine trimethylation	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

EC 2.1.1.364

NP_001007262.1

EC 2.1.1.364

NP_001273681.1

EC 2.1.1.364

NP_059134.1

EC 2.1.1.364

XP_011527938.1

EC 2.1.1.364

XP_011527939.1

EC 2.1.1.364

XP_011527940.1

EC 2.1.1.364

XP_011527941.1

EC 2.1.1.364

XP_011527942.1

EC 2.1.1.364

XP_011527945.1

EC 2.1.1.364

XP_011527946.1

EC 2.1.1.364

XP_016883894.1

EC 2.1.1.364

XP_024307889.1

EC 2.1.1.364

XP_024307890.1

EC 2.1.1.364

XP_047296860.1

EC 2.1.1.364

XP_047296861.1

EC 2.1.1.364

XP_047296862.1

EC 2.1.1.364

XP_047296863.1

EC 2.1.1.364

XP_047296864.1

EC 2.1.1.364

XP_047296865.1

EC 2.1.1.364

XP_047296866.1

EC 2.1.1.364

XP_047296867.1

EC 2.1.1.364

XP_054180645.1

EC 2.1.1.364

XP_054180646.1

EC 2.1.1.364

XP_054180647.1

EC 2.1.1.364

XP_054180648.1

EC 2.1.1.364

XP_054180649.1

EC 2.1.1.364

XP_054180650.1

EC 2.1.1.364

XP_054180651.1

EC 2.1.1.364

XP_054180652.1

EC 2.1.1.364

XP_054180653.1

EC 2.1.1.364

XP_054180654.1

EC 2.1.1.364

XP_054180655.1

EC 2.1.1.364

XP_054180656.1

EC 2.1.1.364

XP_054180657.1

EC 2.1.1.364

XP_054180658.1

EC 2.1.1.364

XP_054180659.1

EC 2.1.1.364

XP_054180660.1

EC 2.1.1.364

XP_054180661.1

EC 2.1.1.364

XP_054180662.1

EC 2.1.1.364

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)

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 ...
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 ...
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
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

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

NC_000021.9 Reference GRCh38.p14 Primary Assembly

Range

36034541..36060526 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
XM_047440906.1 → XP_047296862.1 SET domain-containing protein 4 isoform X2
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
XM_047440904.1 → XP_047296860.1 SET domain-containing protein 4 isoform X1

UniProtKB/Swiss-Prot

B4DT14, D3DSG2, D3DSG4, Q8NE19, Q9BU46, Q9NVD3
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
XM_047440905.1 → XP_047296861.1 SET domain-containing protein 4 isoform X1

UniProtKB/Swiss-Prot

B4DT14, D3DSG2, D3DSG4, Q8NE19, Q9BU46, Q9NVD3
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
XM_047440907.1 → XP_047296863.1 SET domain-containing protein 4 isoform X2
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
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
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
XM_047440909.1 → XP_047296865.1 SET domain-containing protein 4 isoform X3
XM_047440908.1 → XP_047296864.1 SET domain-containing protein 4 isoform X3
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 ...
XM_024452122.2 → XP_024307890.1 SET domain-containing protein 4 isoform X5

UniProtKB/TrEMBL

C9JWV5
XM_024452121.2 → XP_024307889.1 SET domain-containing protein 4 isoform X5

UniProtKB/TrEMBL

C9JWV5

Related

ENSP00000399998.1, ENST00000424303.5
XM_047440911.1 → XP_047296867.1 SET domain-containing protein 4 isoform X5

Related

ENSP00000396837.1, ENST00000429161.5
XM_047440910.1 → XP_047296866.1 SET domain-containing protein 4 isoform X5

RNA

XR_007067790.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060945.1 Alternate T2T-CHM13v2.0

Range

34417599..34443584 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054324677.1 → XP_054180652.1 SET domain-containing protein 4 isoform X2
XM_054324678.1 → XP_054180653.1 SET domain-containing protein 4 isoform X2
XM_054324670.1 → XP_054180645.1 SET domain-containing protein 4 isoform X1

UniProtKB/Swiss-Prot

B4DT14, D3DSG2, D3DSG4, Q8NE19, Q9BU46, Q9NVD3
XM_054324671.1 → XP_054180646.1 SET domain-containing protein 4 isoform X1

UniProtKB/Swiss-Prot

B4DT14, D3DSG2, D3DSG4, Q8NE19, Q9BU46, Q9NVD3
XM_054324673.1 → XP_054180648.1 SET domain-containing protein 4 isoform X1

UniProtKB/Swiss-Prot

B4DT14, D3DSG2, D3DSG4, Q8NE19, Q9BU46, Q9NVD3
XM_054324674.1 → XP_054180649.1 SET domain-containing protein 4 isoform X1

UniProtKB/Swiss-Prot

B4DT14, D3DSG2, D3DSG4, Q8NE19, Q9BU46, Q9NVD3
XM_054324679.1 → XP_054180654.1 SET domain-containing protein 4 isoform X2
XM_054324680.1 → XP_054180655.1 SET domain-containing protein 4 isoform X2
XM_054324672.1 → XP_054180647.1 SET domain-containing protein 4 isoform X1

UniProtKB/Swiss-Prot

B4DT14, D3DSG2, D3DSG4, Q8NE19, Q9BU46, Q9NVD3
XM_054324676.1 → XP_054180651.1 SET domain-containing protein 4 isoform X1

UniProtKB/Swiss-Prot

B4DT14, D3DSG2, D3DSG4, Q8NE19, Q9BU46, Q9NVD3
XM_054324675.1 → XP_054180650.1 SET domain-containing protein 4 isoform X1

UniProtKB/Swiss-Prot

B4DT14, D3DSG2, D3DSG4, Q8NE19, Q9BU46, Q9NVD3
XM_054324682.1 → XP_054180657.1 SET domain-containing protein 4 isoform X3
XM_054324681.1 → XP_054180656.1 SET domain-containing protein 4 isoform X3
XM_054324683.1 → XP_054180658.1 SET domain-containing protein 4 isoform X4
XM_054324685.1 → XP_054180660.1 SET domain-containing protein 4 isoform X5
XM_054324684.1 → XP_054180659.1 SET domain-containing protein 4 isoform X5
XM_054324687.1 → XP_054180662.1 SET domain-containing protein 4 isoform X5
XM_054324686.1 → XP_054180661.1 SET domain-containing protein 4 isoform X5

RNA

XR_008485339.1 RNA Sequence
XR_008485340.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

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.
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.
NM_001007262.1: Suppressed sequence

Description

NM_001007262.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.