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CHAT choline O-acetyltransferase [ Homo sapiens (human) ]

Gene ID: 1103, updated on 1-Mar-2024

Summary

Official Symbol
CHATprovided by HGNC
Official Full Name
choline O-acetyltransferaseprovided by HGNC
Primary source
HGNC:HGNC:1912
See related
Ensembl:ENSG00000070748 MIM:118490; AllianceGenome:HGNC:1912
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
CMS6; CMS1A; CMS1A2; CHOACTASE
Summary
This gene encodes an enzyme which catalyzes the biosynthesis of the neurotransmitter acetylcholine. This gene product is a characteristic feature of cholinergic neurons, and changes in these neurons may explain some of the symptoms of Alzheimer's disease. Polymorphisms in this gene have been associated with Alzheimer's disease and mild cognitive impairment. Mutations in this gene are associated with congenital myasthenic syndrome associated with episodic apnea. Multiple transcript variants encoding different isoforms have been found for this gene, and some of these variants have been shown to encode more than one isoform. [provided by RefSeq, May 2010]
Expression
Biased expression in placenta (RPKM 2.7), small intestine (RPKM 0.2) and 1 other tissue See more
Orthologs
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Genomic context

See CHAT in Genome Data Viewer
Location:
10q11.23
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (49609095..49667942)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (50457901..50516753)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (50817141..50875988)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ERCC excision repair 6, chromatin remodeling factor Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3350 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3351 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3352 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:50745676-50745864 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2363 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3353 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3354 Neighboring gene piggyBac transposable element derived 3 Neighboring gene high mobility group box 1 pseudogene 50 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:50801171-50801672 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:50801673-50802172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:50802781-50803282 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:50803283-50803782 Neighboring gene Sharpr-MPRA regulatory region 3429 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:50816693-50817488 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:50817489-50818283 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:50819328-50820224 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:50820225-50821122 Neighboring gene solute carrier family 18 member A3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:50856078-50856929 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:50856930-50857780 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:50858633-50859483 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:50897886-50898488 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr10:50898489-50899090 Neighboring gene chromosome 10 open reading frame 53 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:50965991-50966502 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:50966503-50967012 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2364 Neighboring gene oxoglutarate dehydrogenase L

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables choline O-acetyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables choline O-acetyltransferase activity TAS
Traceable Author Statement
more info
 
Process Evidence Code Pubs
involved_in acetylcholine biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in neuromuscular synaptic transmission IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in neurotransmitter transport TAS
Traceable Author Statement
more info
 
involved_in phosphatidylcholine biosynthetic process TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in cytosol TAS
Traceable Author Statement
more info
 
is_active_in neuron projection IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleus TAS
Traceable Author Statement
more info
PubMed 
located_in synapse IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
choline O-acetyltransferase
Names
acetyl CoA:choline O-acetyltransferase
choline acetylase
NP_001136401.2
NP_001136405.2
NP_001136406.2
NP_065574.4
NP_066264.4
NP_066265.4
NP_066266.4

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.

Genomic

  1. NG_011797.2 RefSeqGene

    Range
    9944..63849
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001142929.2NP_001136401.2  choline O-acetyltransferase isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (M) contains alternate 5' exon M (PMID 7616604) but uses a downstream start codon and encodes isoform 1. Transcript variants R, N1, N2, M and S encode isoform 1.
    Source sequence(s)
    AC073366
    Consensus CDS
    CCDS7233.1
    UniProtKB/TrEMBL
    B4DJJ6
    Conserved Domains (1) summary
    pfam00755
    Location:13601
    Carn_acyltransf; Choline/Carnitine o-acyltransferase
  2. NM_001142933.2NP_001136405.2  choline O-acetyltransferase isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (S) contains alternate 5' exons M and S in the 5' coding region, and uses an upstream start codon (PMID 11172068). The resulting protein (isoform 3) has a longer N-terminus compared to isoform 1.
    Source sequence(s)
    AC073366
    Consensus CDS
    CCDS44389.1
    UniProtKB/TrEMBL
    B4DJJ6
    Related
    ENSP00000378929.2, ENST00000395562.2
    Conserved Domains (1) summary
    pfam00755
    Location:49637
    Carn_acyltransf; Choline/Carnitine o-acyltransferase
  3. NM_001142934.2NP_001136406.2  choline O-acetyltransferase isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (S) contains alternate 5' exons M and S in the 5' coding region but uses a downstream start codon and encodes isoform 1 (PMID 11172068). Transcript variants R, N1, N2, M and S encode isoform 1.
    Source sequence(s)
    AC073366
    Consensus CDS
    CCDS7233.1
    UniProtKB/TrEMBL
    B4DJJ6
    Conserved Domains (1) summary
    pfam00755
    Location:13601
    Carn_acyltransf; Choline/Carnitine o-acyltransferase
  4. NM_020549.5NP_065574.4  choline O-acetyltransferase isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (M) contains alternate 5' exon M (PMID 7616604) and uses an upstream start codon. The resulting protein (isoform 2) has a longer N-terminus compared to isoform 1
    Source sequence(s)
    AC073366
    Consensus CDS
    CCDS7232.1
    UniProtKB/Swiss-Prot
    A2BDF4, A2BDF5, P28329, Q16488, Q9BQ23, Q9BQ35, Q9BQE1
    Related
    ENSP00000337103.2, ENST00000337653.7
    Conserved Domains (2) summary
    PHA03247
    Location:27138
    PHA03247; large tegument protein UL36; Provisional
    pfam00755
    Location:131719
    Carn_acyltransf; Choline/Carnitine o-acyltransferase
  5. NM_020984.4NP_066264.4  choline O-acetyltransferase isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (R) contains alternate 5' exon R (PMID 7616604) and encodes isoform 1. Transcript variants R, N1, N2, M and S encode isoform 1.
    Source sequence(s)
    AC073366
    Consensus CDS
    CCDS7233.1
    UniProtKB/TrEMBL
    B4DJJ6
    Related
    ENSP00000343486.1, ENST00000339797.5
    Conserved Domains (1) summary
    pfam00755
    Location:13601
    Carn_acyltransf; Choline/Carnitine o-acyltransferase
  6. NM_020985.4NP_066265.4  choline O-acetyltransferase isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (N1) contains alternate 5' exon N and uses an alternate splice site within alternate exon M, and encodes isoform 1 (PMID 9073174). Transcript variants R, N1, N2, M and S encode isoform 1.
    Source sequence(s)
    AC073366
    Consensus CDS
    CCDS7233.1
    UniProtKB/TrEMBL
    B4DJJ6
    Related
    ENSP00000345878.3, ENST00000351556.7
    Conserved Domains (1) summary
    pfam00755
    Location:13601
    Carn_acyltransf; Choline/Carnitine o-acyltransferase
  7. NM_020986.4NP_066266.4  choline O-acetyltransferase isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (N2) contains alternate 5' exon N and encodes isoform 1 (PMID 9073174). Transcript variants R, N1, N2, M and S encode isoform 1.
    Source sequence(s)
    AC073366
    Consensus CDS
    CCDS7233.1
    UniProtKB/TrEMBL
    B4DJJ6
    Related
    ENSP00000378926.2, ENST00000395559.6
    Conserved Domains (1) summary
    pfam00755
    Location:13601
    Carn_acyltransf; Choline/Carnitine o-acyltransferase

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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    49609095..49667942
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    50457901..50516753
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)