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

Gene ID: 79918, updated on 20-Dec-2019

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
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

Genomic context

See SETD6 in Genome Data Viewer
Location:
16q21
Exon count:
8
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (58515479..58523842)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (58549383..58554431)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2137 Neighboring gene Sharpr-MPRA regulatory region 12894 Neighboring gene NDRG family member 4 Neighboring gene RNA, U6 small nuclear 103, pseudogene Neighboring gene CCR4-NOT transcription complex subunit 1 Neighboring gene small nucleolar RNA, H/ACA box 46 Neighboring gene small nucleolar RNA, H/ACA box 50A

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ21148

Gene Ontology Provided by GOA

Function Evidence Code Pubs
NF-kappaB binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
NF-kappaB binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein-lysine N-methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein-lysine N-methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
protein-lysine N-methyltransferase activity TAS
Traceable Author Statement
more info
 
Process Evidence Code Pubs
histone lysine methylation IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of NF-kappaB transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of NF-kappaB transcription factor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
peptidyl-lysine monomethylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
peptidyl-lysine monomethylation IDA
Inferred from Direct Assay
more info
PubMed 
regulation of inflammatory response IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of inflammatory response IMP
Inferred from Mutant Phenotype
more info
PubMed 
stem cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
stem cell population maintenance ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
N-lysine methyltransferase SETD6
Names
SET domain containing 6
SET domain-containing protein 6

NCBI Reference Sequences (RefSeq)

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_001160305.4NP_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
    Q8TBK2
    Related
    ENSP00000219315.4, ENST00000219315.8
    Conserved Domains (2) summary
    pfam00856
    Location:247286
    SET; SET domain
    pfam09273
    Location:338465
    Rubis-subs-bind; Rubisco LSMT substrate-binding
  2. NM_024860.3NP_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/Swiss-Prot
    Q8TBK2
    Related
    ENSP00000310082.2, ENST00000310682.6
    Conserved Domains (2) summary
    pfam00856
    Location:223262
    SET; SET domain
    pfam09273
    Location:314441
    Rubis-subs-bind; Rubisco LSMT substrate-binding

RNA

  1. 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

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p13 Primary Assembly

    Range
    58515479..58523842
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011523336.1XP_011521638.1  N-lysine methyltransferase SETD6 isoform X1

    Related
    ENSP00000412858.1, ENST00000422445.5

RNA

  1. XR_001751988.2 RNA Sequence

  2. XR_933436.2 RNA Sequence

  3. XR_933437.3 RNA Sequence

  4. XR_001751989.1 RNA Sequence

  5. XR_243429.2 RNA Sequence

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