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KMT5A lysine methyltransferase 5A [ Homo sapiens (human) ]

Gene ID: 387893, updated on 9-Dec-2018

Summary

Official Symbol
KMT5Aprovided by HGNC
Official Full Name
lysine methyltransferase 5Aprovided by HGNC
Primary source
HGNC:HGNC:29489
See related
Ensembl:ENSG00000183955 MIM:607240
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
Also known as
SET8; SET07; SETD8; PR-Set7; PR/SET07
Summary
The protein encoded by this gene is a protein-lysine N-methyltransferase that can monomethylate Lys-20 of histone H4 to effect transcriptional repression of some genes. The encoded protein is required for cell proliferation and plays a role in chromatin condensation. [provided by RefSeq, May 2016]
Expression
Ubiquitous expression in prostate (RPKM 17.6), esophagus (RPKM 16.8) and 25 other tissues See more
Orthologs

Genomic context

See KMT5A in Genome Data Viewer
Location:
12q24.31
Exon count:
11
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (123384116..123409356)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (123868704..123893900)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene RNA, 5S ribosomal pseudogene 375 Neighboring gene strawberry notch homolog 1 Neighboring gene uncharacterized LOC112268105 Neighboring gene microRNA 8072 Neighboring gene Rab interacting lysosomal protein like 2 Neighboring gene small nuclear ribonucleoprotein U11/U12 subunit 35 Neighboring gene Rab interacting lysosomal protein like 1

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 FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci.
NHGRI GWA Catalog
Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.
NHGRI GWA Catalog
Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
NHGRI GWA Catalog

Pathways from BioSystems

  • Cell Cycle, organism-specific biosystem (from REACTOME)
    Cell Cycle, organism-specific biosystem
    Cell Cycle
  • Cell Cycle, Mitotic, organism-specific biosystem (from REACTOME)
    Cell Cycle, Mitotic, organism-specific biosystemThe replication of the genome and the subsequent segregation of chromosomes into daughter cells are controlled by a series of events collectively known as the cell cycle. DNA replication is carried o...
  • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
    Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
  • Chromatin organization, organism-specific biosystem (from REACTOME)
    Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
  • Condensation of Prophase Chromosomes, organism-specific biosystem (from REACTOME)
    Condensation of Prophase Chromosomes, organism-specific biosystemIn mitotic prophase, the action of the condensin II complex enables initial chromosome condensation.The condensin II complex subunit NCAPD3 binds monomethylated histone H4 (H4K20me1), thereby associa...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Generic Transcription Pathway, organism-specific biosystem (from REACTOME)
    Generic Transcription Pathway, organism-specific biosystemOVERVIEW OF TRANSCRIPTION REGULATION: Detailed studies of gene transcription regulation in a wide variety of eukaryotic systems has revealed the general principles and mechanisms by which cell- or t...
  • Histone Modifications, organism-specific biosystem (from WikiPathways)
    Histone Modifications, organism-specific biosystemHistones can undergo many post-translational modifications that are involved in transcription regulation. This pathway provides an overview of various modifications for histones H3 and H4 and the en...
  • Lysine degradation, organism-specific biosystem (from KEGG)
    Lysine degradation, organism-specific biosystem
    Lysine degradation
  • Lysine degradation, conserved biosystem (from KEGG)
    Lysine degradation, conserved biosystem
    Lysine degradation
  • M Phase, organism-specific biosystem (from REACTOME)
    M Phase, organism-specific biosystemMitosis, or the M phase, involves nuclear division and cytokinesis, where two identical daughter cells are produced. Mitosis involves prophase, prometaphase, metaphase, anaphase, and telophase. Fin...
  • Mitotic Prophase, organism-specific biosystem (from REACTOME)
    Mitotic Prophase, organism-specific biosystemDuring prophase, the chromatin in the nucleus condenses, and the nucleolus disappears. Centrioles begin moving to the opposite poles or sides of the cell. Some of the fibers that extend from the cen...
  • PKMTs methylate histone lysines, organism-specific biosystem (from REACTOME)
    PKMTs methylate histone lysines, organism-specific biosystemLysine methyltransferases (KMTs) and arginine methyltransferases (RMTs) have a common mechanism of catalysis. Both families transfer a methyl group from a common donor, S-adenosyl-L-methionine (SAM),...
  • Regulation of TP53 Activity, organism-specific biosystem (from REACTOME)
    Regulation of TP53 Activity, organism-specific biosystemProtein stability and transcriptional activity of TP53 (p53) tumor suppressor are regulated by post-translational modifications that include ubiquitination, phosphorylation, acetylation, methylation,...
  • Regulation of TP53 Activity through Methylation, organism-specific biosystem (from REACTOME)
    Regulation of TP53 Activity through Methylation, organism-specific biosystemTP53 (p53) undergoes methylation on several lysine and arginine residues, which modulates its transcriptional activity.PRMT5, recruited to TP53 as part of the ATM-activated complex that includes TTC5...
  • Transcriptional Regulation by TP53, organism-specific biosystem (from REACTOME)
    Transcriptional Regulation by TP53, organism-specific biosystemThe tumor suppressor TP53 (encoded by the gene p53) is a transcription factor. Under stress conditions, it recognizes specific responsive DNA elements and thus regulates the transcription of many gen...
  • p53 pathway, organism-specific biosystem (from Pathway Interaction Database)
    p53 pathway, organism-specific biosystem
    p53 pathway

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
histone methyltransferase activity (H4-K20 specific) TAS
Traceable Author Statement
more info
 
histone-lysine N-methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
histone-lysine N-methyltransferase activity TAS
Traceable Author Statement
more info
 
lysine N-methyltransferase activity TAS
Traceable Author Statement
more info
 
p53 binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein-lysine N-methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
transcription corepressor activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
cell cycle IEA
Inferred from Electronic Annotation
more info
 
cell division IEA
Inferred from Electronic Annotation
more info
 
histone H4-K20 methylation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
peptidyl-lysine monomethylation IDA
Inferred from Direct Assay
more info
PubMed 
regulation of DNA damage response, signal transduction by p53 class mediator IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of signal transduction by p53 class mediator TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
chromosome IEA
Inferred from Electronic Annotation
more info
 
cytosol IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
N-lysine methyltransferase KMT5A
Names
H4-K20-HMTase KMT5A
H4-K20-HMTase SETD8
H4-K20-specific histone methyltransferase
H4K20-specific histone methyltransferase splice variant Set8b
N-lysine methyltransferase SETD8
PR/SET domain containing protein 8
PR/SET domain-containing protein 07
SET domain containing (lysine methyltransferase) 8
SET domain-containing protein 8
histone-lysine N-methyltransferase KMT5A
histone-lysine N-methyltransferase SETD8
lysine (K)-specific methyltransferase 5A
lysine N-methyltransferase 5A
lysine-specific methylase 5A
NP_001311433.1
NP_001311434.1
NP_001311435.1
NP_065115.3
XP_006719457.1

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.

Genomic

  1. NG_050615.1 RefSeqGene

    Range
    5339..30576
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001324504.1NP_001311433.1  N-lysine methyltransferase KMT5A isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC137767, AC145423, BC050346, HQ259683
    UniProtKB/Swiss-Prot
    Q9NQR1
    UniProtKB/TrEMBL
    E3VVS3
    Conserved Domains (1) summary
    smart00317
    Location:194311
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
  2. NM_001324505.1NP_001311434.1  N-lysine methyltransferase KMT5A isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC137767, AC145423, BC050346
    UniProtKB/Swiss-Prot
    Q9NQR1
    Conserved Domains (1) summary
    smart00317
    Location:167284
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
  3. NM_001324506.1NP_001311435.1  N-lysine methyltransferase KMT5A isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4), as well as variant 8, encodes isoform 4.
    Source sequence(s)
    AC137767, AC145423, BC050346
    UniProtKB/Swiss-Prot
    Q9NQR1
    Conserved Domains (1) summary
    smart00317
    Location:116233
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
  4. NM_001367386.1NP_001354315.1  N-lysine methyltransferase KMT5A isoform 5

    Status: REVIEWED

    Source sequence(s)
    AC137767, AC145423, BC050346
  5. NM_001367388.1NP_001354317.1  N-lysine methyltransferase KMT5A isoform 6

    Status: REVIEWED

    Source sequence(s)
    AC137767, AC145423, BC050346
  6. NM_001367389.1NP_001354318.1  N-lysine methyltransferase KMT5A isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8), as well as variant 4, encodes isoform 4.
    Source sequence(s)
    AC137767, AC145423, BC050346
  7. NM_020382.7NP_065115.3  N-lysine methyltransferase KMT5A isoform 1

    See identical proteins and their annotated locations for NP_065115.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC137767, AC145423
    Consensus CDS
    CCDS9247.1
    UniProtKB/Swiss-Prot
    Q9NQR1
    Related
    ENSP00000384629.3, ENST00000402868.7
    Conserved Domains (1) summary
    smart00317
    Location:224341
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

RNA

  1. NR_136910.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC137767, AC145423, BC050346

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p12 Primary Assembly

    Range
    123384116..123409356
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006719394.3XP_006719457.1  N-lysine methyltransferase KMT5A isoform X1

    Conserved Domains (1) summary
    smart00317
    Location:187304
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
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