N6AMT1 N-6 adenine-specific DNA methyltransferase 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: N6AMT1provided by HGNC
Official Full Name: N-6 adenine-specific DNA methyltransferase 1provided by HGNC
Primary source: HGNC:HGNC:16021
See related: Ensembl:ENSG00000156239 MIM:614553; AllianceGenome:HGNC:16021
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: KMT9; MTQ2; PrmC; HEMK2; N6AMT; PRED28; C21orf127; m.HsaHemK2P
Summary: This gene encodes an N(6)-adenine-specific DNA methyltransferase. The encoded enzyme may be involved in the methylation of release factor I during translation termination. This enzyme is also involved in converting the arsenic metabolite monomethylarsonous acid to the less toxic dimethylarsonic acid. Alternative splicing of this gene results in multiple transcript variants. A related pseudogene has been identified on chromosome 11. [provided by RefSeq, Mar 2023]
Expression: Ubiquitous expression in prostate (RPKM 1.2), ovary (RPKM 1.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 21q21.3

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	21	NC_000021.9 (28575598..28885367, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	21	NC_060945.1 (27235374..27248586, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	21	NC_000021.8 (30244513..30257689, 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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Distinct specificities of the HEMK2 protein methyltransferase in methylation of glutamine and lysine residues.
Title: Distinct specificities of the HEMK2 protein methyltransferase in methylation of glutamine and lysine residues.
Arsenic metabolism, N6AMT1 and AS3MT single nucleotide polymorphisms, and their interaction on gestational diabetes mellitus in Chinese pregnant women.
Title: Arsenic metabolism, N6AMT1 and AS3MT single nucleotide polymorphisms, and their interaction on gestational diabetes mellitus in Chinese pregnant women.
Reducing N6AMT1-mediated 6mA DNA modification promotes breast tumor progression via transcriptional repressing cell cycle inhibitors.
Title: Reducing N6AMT1-mediated 6mA DNA modification promotes breast tumor progression via transcriptional repressing cell cycle inhibitors.
KMT9 Controls Stemness and Growth of Colorectal Cancer.
Title: KMT9 Controls Stemness and Growth of Colorectal Cancer.
Structural insight into HEMK2-TRMT112-mediated glutamine methylation.
Title: Structural insight into HEMK2-TRMT112-mediated glutamine methylation.
The down-regulation of TRMT112 does not affect the N6AMT1 protein levels in cells, suggesting that the two proteins of TRMT112 network, WBSCR22 and N6AMT1, are differently regulated by their common cofactor.
Title: The Common Partner of Several Methyltransferases TRMT112 Regulates the Expression of N6AMT1 Isoforms in Mammalian Cells.
data link H4K12 methylation with KMT9-dependent regulation of androgen-independent prostate tumor cell proliferation, thereby providing a promising paradigm for the treatment of castration-resistant prostate cancer
Title: KMT9 monomethylates histone H4 lysine 12 and controls proliferation of prostate cancer cells.
The abundance of 6mA was significantly lower in cancers, accompanied by decreased N6AMT1 and increased ALKBH1 levels, and downregulation of 6mA modification levels promoted tumorigenesis. Collectively, Results demonstrate that DNA 6mA modification is extensively present in human cells and the decrease of genomic DNA 6mA promotes human tumorigenesis.
Title: N(6)-Methyladenine DNA Modification in the Human Genome.
combined effect of N6AMT1 haplotype 2_GGCCAT and As3MT haplotype 2_GCAC showed consistence with the additive significance of each haplotype on % iAs: the mean was 5.47% and 9.36% for carriers with both and null haplotypes, respectively
Title: Interactive Influence of N6AMT1 and As3MT Genetic Variations on Arsenic Metabolism in the Population of Inner Mongolia, China.
AS3MT and N6AMT1 polymorphisms and urinary arsenic metabolites (%iAs, %MMA, %DMA) in 722 subjects from an arsenic-cancer case-control study in a uniquely exposed area in northern Chile, were examined.
Title: Associations between arsenic (+3 oxidation state) methyltransferase (AS3MT) and N-6 adenine-specific DNA methyltransferase 1 (N6AMT1) polymorphisms, arsenic metabolism, and cancer risk in a chilean population.

Submit: New GeneRIF Correction See all GeneRIFs (14)

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

RH93987 (e-PCR)
- UniSTS:86332

RH80363 (e-PCR)
- UniSTS:87501

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables S-adenosyl-L-methionine binding	IDA Inferred from Direct Assay more info	PubMed
enables S-adenosylmethionine-dependent methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables arsenite methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H4K12 methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein-glutamine N-methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
NOT enables site-specific DNA-methyltransferase (adenine-specific) activity	IDA Inferred from Direct Assay more info	PubMed
enables site-specific DNA-methyltransferase (adenine-specific) activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in arsonoacetate metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in methylation	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of gene expression, epigenetic	IDA Inferred from Direct Assay more info	PubMed
involved_in peptidyl-glutamine methylation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of cell growth	IDA Inferred from Direct Assay more info	PubMed
involved_in toxin metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in transcription initiation-coupled chromatin remodeling	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in cytosol	TAS Traceable Author Statement more info
part_of eRF1 methyltransferase complex	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: methyltransferase N6AMT1

Names: HemK methyltransferase family member 2; N-6 adenine-specific DNA methyltransferase 1 (putative); N6-DNA-methyltransferase; lysine N-methyltransferase 9; methylarsonite methyltransferase N6AMT1; protein N(5)-glutamine methyltransferase

NP_037372.4

EC 2.1.1.72

NP_877426.4

EC 2.1.1.72

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_013240.6 → NP_037372.4 methyltransferase N6AMT1 isoform 1

See identical proteins and their annotated locations for NP_037372.4

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AF139682, AF227510, AMYH02037685, AW136986, BP317563, KC877845

Consensus CDS

CCDS33526.1

UniProtKB/Swiss-Prot

B2RA97, Q96F73, Q9Y5N5

Related

ENSP00000303584.5, ENST00000303775.10

Conserved Domains (1) summary

cl17173
Location:21 → 213

AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...
NM_182749.5 → NP_877426.4 methyltransferase N6AMT1 isoform 2

See identical proteins and their annotated locations for NP_877426.4

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.

Source sequence(s)

AF227510, AMYH02037685, AW136986, BC011554, BP317563, KC877845

Consensus CDS

CCDS33525.1

UniProtKB/Swiss-Prot

Q9Y5N5

Related

ENSP00000286764.4, ENST00000351429.7

Conserved Domains (1) summary

cl17173
Location:21 → 185

AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

RNA

NR_047510.3 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) contains an alternate 3' terminal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK225515, BP317563, BQ021620, BU631971