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] See more...

Aliases for CARNMT1 Gene

Aliases for CARNMT1 Gene

  • Carnosine N-Methyltransferase 1 2 3 5
  • Carnosine N-Methyltransferase 3 4
  • C9orf41 3 4
  • Chromosome 9 Open Reading Frame 41 2
  • UPF0586 Protein C9orf41 3
  • EC 2.1.1.22 4
  • FLJ25795 2
  • UPF0586 3
  • CARNMT1 5

External Ids for CARNMT1 Gene

Previous HGNC Symbols for CARNMT1 Gene

  • C9orf41

Summaries for CARNMT1 Gene

Entrez Gene Summary for CARNMT1 Gene

  • 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]

GeneCards Summary for CARNMT1 Gene

CARNMT1 (Carnosine N-Methyltransferase 1) is a Protein Coding gene. Diseases associated with CARNMT1 include Hypotrichosis 4 and Mitochondrial Complex I Deficiency, Nuclear Type 1. Among its related pathways are Histidine metabolism and Viral mRNA Translation.

UniProtKB/Swiss-Prot Summary for CARNMT1 Gene

  • N-methyltransferase that catalyzes the formation of anserine (beta-alanyl-N(Pi)-methyl-L-histidine) from carnosine. Anserine, a methylated derivative of carnosine (beta-alanyl-L-histidine), is an abundant constituent of vertebrate skeletal muscles. Also methylates other L-histidine-containing di- and tripeptides such as Gly-Gly-His, Gly-His and homocarnosine (GABA-His).

Additional gene information for CARNMT1 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CARNMT1 Gene

Genomics for CARNMT1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CARNMT1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CARNMT1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CARNMT1

Genomic Locations for CARNMT1 Gene

Genomic Locations for CARNMT1 Gene
chr9:74,980,790-75,028,456
(GRCh38/hg38)
Size:
47,667 bases
Orientation:
Minus strand
chr9:77,595,936-77,643,339
(GRCh37/hg19)
Size:
47,404 bases
Orientation:
Minus strand

Genomic View for CARNMT1 Gene

Genes around CARNMT1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CARNMT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CARNMT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CARNMT1 Gene

Proteins for CARNMT1 Gene

  • Protein details for CARNMT1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N4J0-CARME_HUMAN
    Recommended name:
    Carnosine N-methyltransferase
    Protein Accession:
    Q8N4J0
    Secondary Accessions:
    • Q7Z383
    • Q8N7C5

    Protein attributes for CARNMT1 Gene

    Size:
    409 amino acids
    Molecular mass:
    47186 Da
    Quaternary structure:
    • Homodimer. Each monomer accommodates one molecule of carnosine in its active pocket (residues 313-398), precisely anchoring the histidine imidazole ring such that only N1 is exposed and deprotonated for methylation.
    SequenceCaution:
    • Sequence=BAC05369.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for CARNMT1 Gene

neXtProt entry for CARNMT1 Gene

Post-translational modifications for CARNMT1 Gene

  • Ubiquitination at Lys100
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for CARNMT1 Gene

Domains & Families for CARNMT1 Gene

Gene Families for CARNMT1 Gene

Protein Domains for CARNMT1 Gene

InterPro:
Blocks:
  • N2227-like
ProtoNet:

Suggested Antigen Peptide Sequences for CARNMT1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ58856 (B4DSD4_HUMAN)
  • UPF0586 protein C9orf41 (CI041_HUMAN)
  • Chromosome 9 open reading frame 41 (Q5T8V1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8N4J0

UniProtKB/Swiss-Prot:

CARME_HUMAN :
  • The Gly-Xaa-Gly-Xaa-Gly (GXGXG) motif binds the adenosyl part of S-adenosyl-L-methionine.
  • Belongs to the carnosine N-methyltransferase family.
Domain:
  • The Gly-Xaa-Gly-Xaa-Gly (GXGXG) motif binds the adenosyl part of S-adenosyl-L-methionine.
  • The carnosine-binding region forms hydrophobic and hydrogen bonds with carnosine, defining a flipping orientation of the imidazole ring so that N1 is present next to S-adenosyl-L-methionine for methylation.
Family:
  • Belongs to the carnosine N-methyltransferase family.
genes like me logo Genes that share domains with CARNMT1: view

Function for CARNMT1 Gene

Molecular function for CARNMT1 Gene

UniProtKB/Swiss-Prot Function:
N-methyltransferase that catalyzes the formation of anserine (beta-alanyl-N(Pi)-methyl-L-histidine) from carnosine. Anserine, a methylated derivative of carnosine (beta-alanyl-L-histidine), is an abundant constituent of vertebrate skeletal muscles. Also methylates other L-histidine-containing di- and tripeptides such as Gly-Gly-His, Gly-His and homocarnosine (GABA-His).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=carnosine + S-adenosyl-L-methionine = anserine + H(+) + S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:14205, ChEBI:CHEBI:15378, ChEBI:CHEBI:57485, ChEBI:CHEBI:57856, ChEBI:CHEBI:58445, ChEBI:CHEBI:59789; EC=2.1.1.22; Evidence={ECO:0000269|PubMed:26001783, ECO:0000269|PubMed:29463897};.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=4.959 mM for carnosine {ECO:0000269|PubMed:26001783}; KM=0.053 mM for S-adenosyl-L-methionine {ECO:0000269|PubMed:26001783}; Vmax=1.77 nmol/min/mg enzyme with carnosine as substrate {ECO:0000269|PubMed:26001783}; Note=kcat is 0.09 min(-1) for carnosine. kcat is 3.57 min(-1) for S-adenosyl-L-methionine. {ECO:0000269|PubMed:26001783}; pH dependence: Optimum pH is 7.0-7.5. {ECO:0000269|PubMed:26001783}; Temperature dependence: Optimum temperature is 50 degrees Celsius. {ECO:0000269|PubMed:26001783};

Enzyme Numbers (IUBMB) for CARNMT1 Gene

Phenotypes From GWAS Catalog for CARNMT1 Gene

Gene Ontology (GO) - Molecular Function for CARNMT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008168 methyltransferase activity IEA --
GO:0008757 S-adenosylmethionine-dependent methyltransferase activity IBA,IDA 29463897
GO:0016740 transferase activity IEA --
GO:0030735 carnosine N-methyltransferase activity TAS --
GO:0042803 protein homodimerization activity IDA 29463897
genes like me logo Genes that share ontologies with CARNMT1: view
genes like me logo Genes that share phenotypes with CARNMT1: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CARNMT1

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CARNMT1 Gene

Localization for CARNMT1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CARNMT1 Gene

Cytoplasm, cytosol. Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CARNMT1 gene
Compartment Confidence
nucleus 5
cytosol 5
cytoskeleton 2
plasma membrane 1
mitochondrion 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for CARNMT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA,IDA 26001783
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with CARNMT1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CARNMT1 Gene

Pathways & Interactions for CARNMT1 Gene

genes like me logo Genes that share pathways with CARNMT1: view

Gene Ontology (GO) - Biological Process for CARNMT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006548 histidine catabolic process TAS --
GO:0032259 methylation IEA --
GO:0035498 carnosine metabolic process IMP 29463897
genes like me logo Genes that share ontologies with CARNMT1: view

No data available for SIGNOR curated interactions for CARNMT1 Gene

Drugs & Compounds for CARNMT1 Gene

No Compound Related Data Available

Transcripts for CARNMT1 Gene

mRNA/cDNA for CARNMT1 Gene

2 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CARNMT1

Alternative Splicing Database (ASD) splice patterns (SP) for CARNMT1 Gene

No ASD Table

Relevant External Links for CARNMT1 Gene

GeneLoc Exon Structure for
CARNMT1

Expression for CARNMT1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CARNMT1

mRNA Expression by UniProt/SwissProt for CARNMT1 Gene:

Q8N4J0-CARME_HUMAN
Tissue specificity: Expressed at higher level in kidney. Expressed at lower level in brain and skeletal muscle.

Evidence on tissue expression from TISSUES for CARNMT1 Gene

  • Nervous system(4.4)
  • Muscle(2.2)
genes like me logo Genes that share expression patterns with CARNMT1: view

No data available for mRNA expression in normal human tissues , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for CARNMT1 Gene

Orthologs for CARNMT1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for CARNMT1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia C9orf41 31
  • 100 (a)
OneToOne
C9H9orf41 30
  • 99.92 (n)
Dog
(Canis familiaris)
Mammalia C9orf41 31
  • 97 (a)
OneToOne
C1H9orf41 30
  • 95.49 (n)
Cow
(Bos Taurus)
Mammalia C9orf41 31
  • 96 (a)
OneToOne
C8H9orf41 30
  • 94.46 (n)
Rat
(Rattus norvegicus)
Mammalia RGD1311863 30
  • 92.48 (n)
Mouse
(Mus musculus)
Mammalia 2410127L17Rik 30 31
  • 92.21 (n)
OneToOne
Carnmt1 17
Oppossum
(Monodelphis domestica)
Mammalia C9orf41 31
  • 83 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia C9orf41 31
  • 76 (a)
OneToOne
Chicken
(Gallus gallus)
Aves CZH9ORF41 30 31
  • 84.35 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia C9orf41 31
  • 74 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia c9orf41 30
  • 75.48 (n)
Str.7522 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.5307 30
Zebrafish
(Danio rerio)
Actinopterygii C5H9orf41 31
  • 68 (a)
OneToOne
zgc:112985 30
  • 67.75 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007115 30
  • 52.63 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG11596 30 31
  • 49.81 (n)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea Y48E1C.2 30 31
  • 49.8 (n)
OneToOne
K. Lactis Yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C13750g 30
  • 47.26 (n)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes YNL092W 30
  • 46.12 (n)
-- 31
  • 28 (a)
OneToOne
-- 33
A. gosspyii yeast
(Eremothecium gossypii)
Saccharomycetes AGOS_ACL085C 30
  • 43.66 (n)
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT2G32170 30
  • 54.55 (n)
Soybean
(Glycine max)
eudicotyledons Gma.12593 30
Rice
(Oryza sativa)
Liliopsida Os05g0511300 30
  • 56.13 (n)
Os.17049 30
Barley
(Hordeum vulgare)
Liliopsida Hv.3236 30
Wheat
(Triticum aestivum)
Liliopsida Ta.11407 30
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPBC1778.07 30
  • 49.1 (n)
Bread mold
(Neurospora crassa)
Ascomycetes NCU03692 30
  • 46.05 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 46 (a)
OneToOne
Species where no ortholog for CARNMT1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for CARNMT1 Gene

ENSEMBL:
Gene Tree for CARNMT1 (if available)
TreeFam:
Gene Tree for CARNMT1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CARNMT1: view image

Paralogs for CARNMT1 Gene

No data available for Paralogs for CARNMT1 Gene

Variants for CARNMT1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CARNMT1 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
782145 Benign: not provided 74,998,623(-) A/G NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for CARNMT1 Gene

Structural Variations from Database of Genomic Variants (DGV) for CARNMT1 Gene

Variant ID Type Subtype PubMed ID
esv3620712 CNV loss 21293372

Variation tolerance for CARNMT1 Gene

Residual Variation Intolerance Score: 16.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.62; 13.39% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CARNMT1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CARNMT1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CARNMT1 Gene

Disorders for CARNMT1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for CARNMT1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
hypotrichosis 4
  • hypt4
mitochondrial complex i deficiency, nuclear type 1
  • mc1dn1
- elite association - COSMIC cancer census association via MalaCards
genes like me logo Genes that share disorders with CARNMT1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CARNMT1 Gene

Publications for CARNMT1 Gene

  1. UPF0586 Protein C9orf41 Homolog Is Anserine-producing Methyltransferase. (PMID: 26001783) Drozak J … de Heer E (The Journal of biological chemistry 2015) 2 3 4
  2. Molecular basis for histidine N1 position-specific methylation by CARNMT1. (PMID: 29463897) Cao R … Li H (Cell research 2018) 3 4
  3. DNA sequence and analysis of human chromosome 9. (PMID: 15164053) Humphray SJ … Dunham I (Nature 2004) 3 4
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4

Products for CARNMT1 Gene

Sources for CARNMT1 Gene