NTMT1 N-terminal Xaa-Pro-Lys N-methyltransferase 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NTMT1provided by HGNC
Official Full Name: N-terminal Xaa-Pro-Lys N-methyltransferase 1provided by HGNC
Primary source: HGNC:HGNC:23373
See related: Ensembl:ENSG00000148335 MIM:613560; AllianceGenome:HGNC:23373
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: NRMT; NRMT1; NTM1A; AD-003; HOMT1A; C9orf32; METTL11A
Summary: The METTL11A gene encodes an N-terminal methyltransferase for the RAN (MIM 601179) guanine nucleotide exchange factor regulator of chromosome condensation 1 (RCC1; MIM 179710). METTL11A enzyme alpha-N-methylates other protein targets such as SET (MIM 600960) and RB (MIM 180200).[supplied by OMIM, Nov 2010]
Expression: Ubiquitous expression in testis (RPKM 16.4), adrenal (RPKM 9.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 9q34.11

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (129608872..129636135)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (141813472..141840743)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (132371151..132398414)

Chromosome 9 - NC_000009.12 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?

Pan-cancer analysis reveals the pro-oncogenic role of N6-methyladenosine (m6A)-regulated NTMT1 in head and neck squamous cell carcinoma.
Title: Pan-cancer analysis reveals the pro-oncogenic role of N6-methyladenosine (m6A)-regulated NTMT1 in head and neck squamous cell carcinoma.
Methyltransferase-like protein 11A promotes migration of cervical cancer cells via up-regulating ELK3.
Title: Methyltransferase-like protein 11A promotes migration of cervical cancer cells via up-regulating ELK3.
Age-related neurodegeneration and cognitive impairments of NRMT1 knockout mice are preceded by misregulation of RB and abnormal neural stem cell development.
Title: Age-related neurodegeneration and cognitive impairments of NRMT1 knockout mice are preceded by misregulation of RB and abnormal neural stem cell development.
Modulation of N-terminal methyltransferase 1 by an N(6)-methyladenosine-based epitranscriptomic mechanism.
Title: Modulation of N-terminal methyltransferase 1 by an N(6)-methyladenosine-based epitranscriptomic mechanism.
Probing the Plasticity in the Active Site of Protein N-terminal Methyltransferase 1 Using Bisubstrate Analogues.
Title: Probing the Plasticity in the Active Site of Protein N-terminal Methyltransferase 1 Using Bisubstrate Analogues.
The NRMT2 expression activates NRMT1 activity, not through priming, but by increasing its stability and substrate affinity.
Title: The N-terminal methyltransferase homologs NRMT1 and NRMT2 exhibit novel regulation of activity through heterotrimer formation.
CENP-A undergoes alpha-amino trimethylation by the enzyme NRMT in vivo.
Title: α-amino trimethylation of CENP-A by NRMT is required for full recruitment of the centromere.
NRMT1 mutants N209I (endometrial cancer) and P211S (lung cancer) alter its catalytic activity and decrease N-terminal trimethylation.
Title: Select human cancer mutants of NRMT1 alter its catalytic activity and decrease N-terminal trimethylation.
These studies position the NRMT1 knockout mouse as a useful new system for studying the effects of genomic instability and defective DNA damage repair on organismal and tissue-specific aging.
Title: NRMT1 knockout mice exhibit phenotypes associated with impaired DNA repair and premature aging.
NRMT1 adopts a core methyltransferase fold that resembles DOT1L and PRMT but not SET domain family histone methyltransferases.
Title: Molecular basis for histone N-terminal methylation by NRMT1.

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

EBI GWAS Catalog

Description
Pharmacogenomic study of side-effects for antidepressant treatment options in STAR*D. 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

SGC32655 (e-PCR)
- UniSTS:19314

RH93952 (e-PCR)
- UniSTS:91766

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables N-terminal protein N-methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables N-terminal protein N-methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in N-terminal peptidyl-alanine trimethylation	IEA Inferred from Electronic Annotation more info
involved_in N-terminal peptidyl-glycine methylation	IDA Inferred from Direct Assay more info	PubMed
involved_in N-terminal peptidyl-proline dimethylation	IDA Inferred from Direct Assay more info	PubMed
involved_in N-terminal peptidyl-serine dimethylation	IDA Inferred from Direct Assay more info	PubMed
involved_in N-terminal peptidyl-serine trimethylation	IDA Inferred from Direct Assay more info	PubMed
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in chromosome segregation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in spindle organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in spindle organization	IMP Inferred from Mutant Phenotype more info	PubMed

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

General protein information

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Preferred Names: N-terminal Xaa-Pro-Lys N-methyltransferase 1

Names: N-terminal RCC1 methyltransferase; X-Pro-Lys N-terminal protein methyltransferase 1A; alpha N-terminal protein methyltransferase 1A; methyltransferase-like protein 11A

NP_001273725.1

EC 2.1.1.244

NP_001273726.1

EC 2.1.1.244

NP_001273727.1

EC 2.1.1.244

NP_001273728.1

EC 2.1.1.244

NP_001273729.1

EC 2.1.1.244

NP_001273730.1

EC 2.1.1.244

NP_001273731.1

EC 2.1.1.244

NP_001273732.1

EC 2.1.1.244

NP_054783.2

EC 2.1.1.244

XP_047279213.1

EC 2.1.1.244

XP_047279214.1

EC 2.1.1.244

XP_047279215.1

EC 2.1.1.244

XP_047279216.1

EC 2.1.1.244

XP_047279217.1

EC 2.1.1.244

XP_054218776.1

EC 2.1.1.244

XP_054218777.1

EC 2.1.1.244

XP_054218778.1

EC 2.1.1.244

XP_054218779.1

EC 2.1.1.244

XP_054218780.1

EC 2.1.1.244

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_001286796.2 → NP_001273725.1 N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform a

See identical proteins and their annotated locations for NP_001273725.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1 through 5 all encode isoform a.

Source sequence(s)

AK298840, AL391056, AL590369, BC001396, BG468453

Consensus CDS

CCDS35160.1

UniProtKB/Swiss-Prot

A8K4J2, A8K8G7, Q5SZB9, Q9BV86, Q9UI28

Related

ENSP00000361564.1, ENST00000372486.5

Conserved Domains (1) summary

pfam05891
Location:8 → 223

Methyltransf_PK; AdoMet dependent proline di-methyltransferase
NM_001286797.2 → NP_001273726.1 N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform a

See identical proteins and their annotated locations for NP_001273726.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1 through 5 all encode isoform a.

Source sequence(s)

AK298840, AL590369, BI083998

Consensus CDS

CCDS35160.1

UniProtKB/Swiss-Prot

A8K4J2, A8K8G7, Q5SZB9, Q9BV86, Q9UI28

Related

ENSP00000478521.1, ENST00000613644.4

Conserved Domains (1) summary

pfam05891
Location:8 → 223

Methyltransf_PK; AdoMet dependent proline di-methyltransferase
NM_001286798.2 → NP_001273727.1 N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform a

See identical proteins and their annotated locations for NP_001273727.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1 through 5 all encode isoform a.

Source sequence(s)

AK298840, AL590369, BQ636193, BQ923165, CN406947

Consensus CDS

CCDS35160.1

UniProtKB/Swiss-Prot

A8K4J2, A8K8G7, Q5SZB9, Q9BV86, Q9UI28

Related

ENSP00000483489.1, ENST00000611055.4

Conserved Domains (1) summary

pfam05891
Location:8 → 223

Methyltransf_PK; AdoMet dependent proline di-methyltransferase
NM_001286799.2 → NP_001273728.1 N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform a

See identical proteins and their annotated locations for NP_001273728.1

Status: VALIDATED

Description

Transcript Variant: This variant (5) differs in the 5' UTR compared to variant 1. Variants 1 through 5 all encode isoform a.

Source sequence(s)

AK298840, AL590369, BM554138

Consensus CDS

CCDS35160.1

UniProtKB/Swiss-Prot

A8K4J2, A8K8G7, Q5SZB9, Q9BV86, Q9UI28

Related

ENSP00000361558.1, ENST00000372480.1

Conserved Domains (1) summary

pfam05891
Location:8 → 223

Methyltransf_PK; AdoMet dependent proline di-methyltransferase
NM_001286800.2 → NP_001273729.1 N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform b

See identical proteins and their annotated locations for NP_001273729.1

Status: VALIDATED

Description

Transcript Variant: This variant (6) differs in the 5' UTR, and uses an alternate splice site that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (b) has a distinct C-terminus and is shorter than isoform a. Both variants 6 and 7 encode isoform b.

Source sequence(s)

AK298840, AL590369

Consensus CDS

CCDS69682.1

UniProtKB/Swiss-Prot

Q9BV86

Related

ENSP00000361559.3, ENST00000372481.7

Conserved Domains (1) summary

cl17173
Location:8 → 118

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_001286801.2 → NP_001273730.1 N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform b

See identical proteins and their annotated locations for NP_001273730.1

Status: VALIDATED

Description

Transcript Variant: This variant (7) differs in the 5' UTR, and uses an alternate splice site that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (b) has a distinct C-terminus and is shorter than isoform a. Both variants 6 and 7 encode isoform b.

Source sequence(s)

AK298840, AL590369, BE392289, BQ636193, HY058177

Consensus CDS

CCDS69682.1

UniProtKB/Swiss-Prot

Q9BV86

Conserved Domains (1) summary

cl17173
Location:8 → 118

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_001286802.2 → NP_001273731.1 N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform c

See identical proteins and their annotated locations for NP_001273731.1

Status: VALIDATED

Description

Transcript Variant: This variant (8) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) is shorter at the N-terminus, compared to isoform a. Both variants 8 and 9 encode isoform c.

Source sequence(s)

AK298840, AL590369, HY058177

Consensus CDS

CCDS75918.1

UniProtKB/TrEMBL

S4R338

Related

ENSP00000484447.1, ENST00000617943.4

Conserved Domains (1) summary

cl17173
Location:1 → 135

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_001286803.2 → NP_001273732.1 N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform c

See identical proteins and their annotated locations for NP_001273732.1

Status: VALIDATED

Description

Transcript Variant: This variant (9) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) is shorter at the N-terminus, compared to isoform a. Both variants 8 and 9 encode isoform c.

Source sequence(s)

AK298840, AL590369, BM009113, BQ636193

Consensus CDS

CCDS75918.1

UniProtKB/TrEMBL

S4R338

Related

ENSP00000473900.1, ENST00000482347.1

Conserved Domains (1) summary

cl17173
Location:1 → 135

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_014064.4 → NP_054783.2 N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform a

See identical proteins and their annotated locations for NP_054783.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 through 5 all encode isoform a.

Source sequence(s)

AK298840, AL590369, BC001396, BQ636193

Consensus CDS

CCDS35160.1

UniProtKB/Swiss-Prot

A8K4J2, A8K8G7, Q5SZB9, Q9BV86, Q9UI28

Related

ENSP00000361561.4, ENST00000372483.9

Conserved Domains (1) summary

pfam05891
Location:8 → 223

Methyltransf_PK; AdoMet dependent proline di-methyltransferase

RNA

NR_104596.2 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (10) contains an alternate 5' terminal exon, and uses alternate splice sites in two 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)

AK298840, AK307056, AL590369

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_000009.12 Reference GRCh38.p14 Primary Assembly

Range

129608872..129636135

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047423259.1 → XP_047279215.1 N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform X2
XM_047423258.1 → XP_047279214.1 N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform X1

UniProtKB/Swiss-Prot

A8K4J2, A8K8G7, Q5SZB9, Q9BV86, Q9UI28
XM_047423257.1 → XP_047279213.1 N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform X1

UniProtKB/Swiss-Prot

A8K4J2, A8K8G7, Q5SZB9, Q9BV86, Q9UI28
XM_047423260.1 → XP_047279216.1 N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform X2
XM_047423261.1 → XP_047279217.1 N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform X3

UniProtKB/TrEMBL

S4R338

Alternate T2T-CHM13v2.0

Genomic

NC_060933.1 Alternate T2T-CHM13v2.0

Range

141813472..141840743

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054362803.1 → XP_054218778.1 N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform X2
XM_054362802.1 → XP_054218777.1 N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform X1

UniProtKB/Swiss-Prot

A8K4J2, A8K8G7, Q5SZB9, Q9BV86, Q9UI28
XM_054362801.1 → XP_054218776.1 N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform X1

UniProtKB/Swiss-Prot

A8K4J2, A8K8G7, Q5SZB9, Q9BV86, Q9UI28
XM_054362804.1 → XP_054218779.1 N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform X2
XM_054362805.1 → XP_054218780.1 N-terminal Xaa-Pro-Lys N-methyltransferase 1 isoform X3

UniProtKB/TrEMBL

S4R338