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CARNMT1 carnosine N-methyltransferase 1 [ Homo sapiens (human) ]

Gene ID: 138199, updated on 3-Apr-2024

Summary

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Official Symbol
CARNMT1provided by HGNC
Official Full Name
carnosine N-methyltransferase 1provided by HGNC
Primary source
HGNC:HGNC:23435
See related
Ensembl:ENSG00000156017 MIM:616552; AllianceGenome:HGNC:23435
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
C9orf41; UPF0586
Summary
The protein encoded by this gene is a methyltransferase that converts carnosine to anserine, a dipeptide found abundantly in skeletal muscle. The encoded protein can methylate other dipeptides as well. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Feb 2016]
Expression
Ubiquitous expression in thyroid (RPKM 5.8), testis (RPKM 4.9) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
9q21.13
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (74980790..75028430, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (87137362..87185022, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (77595706..77643346, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene required for meiotic nuclear division 1 homolog (S. cerevisiae) pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28468 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19951 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19952 Neighboring gene CARNMT1 antisense RNA 1 Neighboring gene chromosome 9 open reading frame 40 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:77579717-77580289 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28469 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28470 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19953 Neighboring gene nicotinamide riboside kinase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19954 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19955 Neighboring gene osteoclast stimulating factor 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:77751669-77752168

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Molecular basis for histidine N1 position-specific methylation by CARNMT1. Cao R, et al. Cell Res, 2018 Apr. PMID 29463897, Free PMC Article
  2. UPF0586 Protein C9orf41 Homolog Is Anserine-producing Methyltransferase. Drozak J, et al. J Biol Chem, 2015 Jul 10. PMID 26001783, Free PMC Article
  3. Protein array based interactome analysis of amyloid-β indicates an inhibition of protein translation. Virok DP, et al. J Proteome Res, 2011 Apr 1. PMID 21244100
  4. DNA sequence and analysis of human chromosome 9. Humphray SJ, et al. Nature, 2004 May 27. PMID 15164053, Free PMC Article
  5. SMYD3 Impedes Small Cell Lung Cancer Sensitivity to Alkylation Damage through RNF113A Methylation-Phosphorylation Cross-talk. Lukinović V, et al. Cancer Discov, 2022 Sep 2. PMID 35819319, Free PMC Article

See all (17) citations in PubMed

GeneRIFs: Gene References Into Functions

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)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ25795

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables S-adenosylmethionine-dependent methyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables carnosine N-methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables carnosine N-methyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables carnosine N-methyltransferase activity TAS
Traceable Author Statement
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein homodimerization activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in carnosine metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in carnosine metabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in carnosine metabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in histidine catabolic process TAS
Traceable Author Statement
more info
  
involved_in methylation IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol 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
carnosine N-methyltransferase
Names
UPF0586 protein C9orf41
NP_001307426.1
NP_689633.1
XP_011516525.2
XP_047278722.1
XP_054217946.1
XP_054217947.1

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)

  1. NM_001320497.2 → NP_001307426.1  carnosine N-methyltransferase isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AL158825, BC034033, BM145242, DB040199
    UniProtKB/Swiss-Prot
    Q8N4J0
    Conserved Domains (1) summary
    pfam07942
    Location:65 → 330
    N2227; N2227-like protein

  2. NM_152420.3 → NP_689633.1  carnosine N-methyltransferase isoform 1

    See identical proteins and their annotated locations for NP_689633.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
    Source sequence(s)
    AL158825, BC034033, BM145242
    Consensus CDS
    CCDS6649.1
    UniProtKB/Swiss-Prot
    Q7Z383, Q8N4J0, Q8N7C5
    Related
    ENSP00000366030.3, ENST00000376834.8
    Conserved Domains (1) summary
    pfam07942
    Location:144 → 409
    N2227; N2227-like protein

RNA

  1. NR_135282.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK299691, AL158825, BC034033, BI560441, BM145242

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    74980790..75028430 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047422766.1 → XP_047278722.1  carnosine N-methyltransferase isoform X1

  2. XM_011518223.3 → XP_011516525.2  carnosine N-methyltransferase isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    87137362..87185022 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054361971.1 → XP_054217946.1  carnosine N-methyltransferase isoform X1

  2. XM_054361972.1 → XP_054217947.1  carnosine N-methyltransferase isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N4J0.1 GenPept UniProtKB/Swiss-Prot:Q8N4J0

Gene LinkOut

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