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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
    mouse all
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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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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