SETD6 SET domain containing 6, protein lysine methyltransferase [Homo sapiens (human)] - Gene

Summary

Official Symbol: SETD6provided by HGNC
Official Full Name: SET domain containing 6, protein lysine methyltransferaseprovided by HGNC
Primary source: HGNC:HGNC:26116
See related: Ensembl:ENSG00000103037 MIM:616424; AllianceGenome:HGNC:26116
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary: This gene encodes a methyltransferase that adds a methyl group to the histone H2AZ, which is involved in nuclear receptor-dependent transcription. The protein also interacts with several endogenous proteins which are involved in nuclear hormone receptor signaling. A related pseudogene is located on chromosome 2. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
Expression: Ubiquitous expression in testis (RPKM 13.6), skin (RPKM 9.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16q21

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (58515479..58523842)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (64310621..64319075)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (58549383..58557746)

Chromosome 16 - NC_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Investigating the functional role of SETD6 in lung adenocarcinoma.
Title: Investigating the functional role of SETD6 in lung adenocarcinoma.
TWIST1 methylation by SETD6 selectively antagonizes LINC-PINT expression in glioma.
Title: TWIST1 methylation by SETD6 selectively antagonizes LINC-PINT expression in glioma.
SETD6 Regulates E2-Dependent Human Papillomavirus Transcription.
Title: SETD6 Regulates E2-Dependent Human Papillomavirus Transcription.
Structure-function conservation between the methyltransferases SETD3 and SETD6.
Title: Structure-function conservation between the methyltransferases SETD3 and SETD6.
BRD4 methylation by the methyltransferase SETD6 regulates selective transcription to control mRNA translation.
Title: BRD4 methylation by the methyltransferase SETD6 regulates selective transcription to control mRNA translation.
Silencing of SETD6 inhibits the tumorigenesis of oral squamous cell carcinoma by inhibiting methylation of PAK4 and RelA.
Title: Silencing of SETD6 inhibits the tumorigenesis of oral squamous cell carcinoma by inhibiting methylation of PAK4 and RelA.
Lysine methyltransferase SETD6 modifies histones on a glycine-lysine motif.
Title: Lysine methyltransferase SETD6 modifies histones on a glycine-lysine motif.
MiR-411 inhibits gastric cancer proliferation and migration through targeting SETD6.
Title: MiR-411 inhibits gastric cancer proliferation and migration through targeting SETD6.
Study demonstrates that SETD6 monomeric, dimeric and trimeric forms are stabilized by the methyl donor, S-adenosyl-l-methionine. SETD6 has auto-methylation activity at K39 and K179, which serves as the major auto-methylation sites with a moderate auto-methylation activity toward K372. Data support a model by which SETD6 auto-methylation and self-interaction positively regulate its enzymatic activity in vitro.
Title: Oligomerization and Auto-methylation of the Human Lysine Methyltransferase SETD6.
During mitosis SETD6 binds and methylates PLK1
Title: The methyltransferase SETD6 regulates Mitotic progression through PLK1 methylation.

Submit: New GeneRIF Correction See all GeneRIFs (19)

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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D16S2562E (e-PCR)
- UniSTS:27393

RH35951 (e-PCR)
- UniSTS:69380

D10S275 (e-PCR)
- UniSTS:147992

D16S3186 (e-PCR)
- UniSTS:17193

D16S2941 (e-PCR)
- UniSTS:7212

A002K05 (e-PCR)
- UniSTS:45133

SHGC-61172 (e-PCR)
- UniSTS:24175

RH41889 (e-PCR)
- UniSTS:47727

G43512 (e-PCR)
- UniSTS:94969

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables NF-kappaB binding	IPI Inferred from Physical Interaction more info	PubMed
enables S-adenosyl-L-methionine binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-lysine N-methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein-lysine N-methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein-lysine N-methyltransferase activity	TAS Traceable Author Statement more info

Process	Evidence Code	Pubs
involved_in negative regulation of NF-kappaB transcription factor activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in peptidyl-lysine monomethylation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of inflammatory response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in stem cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in stem cell population maintenance	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in cytosol	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: N-lysine methyltransferase SETD6

Names: SET domain-containing protein 6

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_001160305.4 → NP_001153777.1 N-lysine methyltransferase SETD6 isoform a

See identical proteins and their annotated locations for NP_001153777.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).

Source sequence(s)

AC009118

Consensus CDS

CCDS54013.1

UniProtKB/Swiss-Prot

A8K380, B5ME38, Q8TBK2, Q9H787

UniProtKB/TrEMBL

J3QT10

Related

ENSP00000219315.5, ENST00000219315.9

Conserved Domains (2) summary

pfam00856
Location:247 → 286

SET; SET domain

pfam09273
Location:338 → 465

Rubis-subs-bind; Rubisco LSMT substrate-binding
NM_024860.3 → NP_079136.2 N-lysine methyltransferase SETD6 isoform b

See identical proteins and their annotated locations for NP_079136.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an in-frame segment in the coding region, compared to variant 1. The encoded isoform (b) is shorter than isoform a.

Source sequence(s)

AC009118, AK024801, BC110433, BP338820, DA074170, GD138369

Consensus CDS

CCDS10798.1

UniProtKB/TrEMBL

J3QT10

Related

ENSP00000310082.2, ENST00000310682.6

Conserved Domains (2) summary

cd19178
Location:34 → 278

SET_SETD6; SET domain found in SET domain-containing protein 6 (SETD6) and similar proteins

pfam09273
Location:313 → 441

Rubis-subs-bind; Rubisco LSMT substrate-binding

RNA

NR_134583.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses alternate splice sites in internal exons, compared to variant 1. This variant (2) lacks two alternate internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC009118, BC110433, BP338820, DA074170, GD138369