Protein:CHAT |
Protein Summary |
 Gene summary |
| Gene name: CHAT | ASpdb.0 ID: 1103 | Gene | Gene symbol | CHAT | Gene ID | 1103 |
| Gene name | choline O-acetyltransferase |
| Synonyms | CHOACTASE|CMS1A|CMS1A2|CMS6 |
| Cytomap | 10q11.23 |
| Type of gene | protein-coding |
| Description | choline O-acetyltransferaseacetyl CoA:choline O-acetyltransferasecholine acetylase |
| Modification date | 20240305 |
| UniProtAcc | P28329 |
| Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
AS Summary |
| Information of the canonical protein with experimentally identified structure from PDB (2023). |
| UniProt Acc | File name | PDB ID | Method | Resolution | Chain | Start | End |
| P28329-1 | P28329-1_2fy3_A.pdb | 2FY3 | X-ray | 2.27 | A | 126 | 727 |
| ASpdb's canonical and alternatively spliced isoform information. |
| accession_id | gene_name | canonical_id | alternative_id | canonical_length | alternative_length | canonical_start | canonical_end | type | originalSEQ | variationSEQ | alternative_start | alternative_end |
| P28329 | CHAT | P28329-1 | P28329-2 | 748 | 666 | 1 | 95 | Substitution | MGLRTAKKRGLGGGGKWKREEGGGTRGRREVRPACFLQSGGRGDPGDVGGPAGNPGCSPHPRAATRPPPLPAHTPAHTPEWCGAASAEAAEPRRA | MWPECRDEALSTV | 1 | 13 |
| P28329 | CHAT | P28329-1 | P28329-3 | 748 | 630 | 1 | 118 | Deletion | none | none | 0 | 0 |
| Multiple sequence alignment of our canonical and alternatively spliced CHAT |
| Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of CHAT |
| UniProt-id | ENSG | ENST | ENSP |
| P28329-1 | ENSG00000070748.19 | ENST00000337653.7 | ENSP00000337103.2 |
| P28329-2 | ENSG00000070748.19 | ENST00000395562.2 | ENSP00000378929.2 |
| P28329-3 | ENSG00000070748.19 | ENST00000339797.5 | ENSP00000343486.1 |
| P28329-3 | ENSG00000070748.19 | ENST00000351556.7 | ENSP00000345878.3 |
| P28329-3 | ENSG00000070748.19 | ENST00000395559.6 | ENSP00000378926.2 |
| UniProt-id | NM ID | NP ID |
| P28329-1 | NM_020549.4 | NP_065574.3 |
| P28329-2 | NM_001142933.1 | NP_001136405.1 |
| P28329-3 | NM_001142929.1 | NP_001136401.1 |
| P28329-3 | NM_001142934.1 | NP_001136406.1 |
| P28329-3 | NM_020984.3 | NP_066264.3 |
| P28329-3 | NM_020985.3 | NP_066265.3 |
| P28329-3 | NM_020986.3 | NP_066266.3 |
| Amino acid sequences of our canonical and alternatively spliced CHAT |
| accession_id | Protein sequence |
| P28329-1 | MGLRTAKKRGLGGGGKWKREEGGGTRGRREVRPACFLQSGGRGDPGDVGGPAGNPGCSPHPRAATRPPPLPAHTPAHTPEWCGAASAEAA EPRRAGPHLCIPAPGLTKTPILEKVPRKMAAKTPSSEESGLPKLPVPPLQQTLATYLQCMRHLVSEEQFRKSQAIVQQFGAPGGLGETLQ QKLLERQEKTANWVSEYWLNDMYLNNRLALPVNSSPAVIFARQHFPGTDDQLRFAASLISGVLSYKALLDSHSIPTDCAKGQLSGQPLCM KQYYGLFSSYRLPGHTQDTLVAQNSSIMPEPEHVIVACCNQFFVLDVVINFRRLSEGDLFTQLRKIVKMASNEDERLPPIGLLTSDGRSE WAEARTVLVKDSTNRDSLDMIERCICLVCLDAPGGVELSDTHRALQLLHGGGYSKNGANRWYDKSLQFVVGRDGTCGVVCEHSPFDGIVL VQCTEHLLKHVTQSSRKLIRADSVSELPAPRRLRWKCSPEIQGHLASSAEKLQRIVKNLDFIVYKFDNYGKTFIKKQKCSPDAFIQVALQ LAFYRLHRRLVPTYESASIRRFQEGRVDNIRSATPEALAFVRAVTDHKAAVPASEKLLLLKDAIRAQTAYTVMAITGMAIDNHLLALREL ARAMCKELPEMFMDETYLMSNRFVLSTSQVPTTTEMFCCYGPVVPNGYGACYNPQPETILFCISSFHSCKETSSSKFAKAVEESLIDMRD |
| P28329-2 | MWPECRDEALSTVGPHLCIPAPGLTKTPILEKVPRKMAAKTPSSEESGLPKLPVPPLQQTLATYLQCMRHLVSEEQFRKSQAIVQQFGAP GGLGETLQQKLLERQEKTANWVSEYWLNDMYLNNRLALPVNSSPAVIFARQHFPGTDDQLRFAASLISGVLSYKALLDSHSIPTDCAKGQ LSGQPLCMKQYYGLFSSYRLPGHTQDTLVAQNSSIMPEPEHVIVACCNQFFVLDVVINFRRLSEGDLFTQLRKIVKMASNEDERLPPIGL LTSDGRSEWAEARTVLVKDSTNRDSLDMIERCICLVCLDAPGGVELSDTHRALQLLHGGGYSKNGANRWYDKSLQFVVGRDGTCGVVCEH SPFDGIVLVQCTEHLLKHVTQSSRKLIRADSVSELPAPRRLRWKCSPEIQGHLASSAEKLQRIVKNLDFIVYKFDNYGKTFIKKQKCSPD AFIQVALQLAFYRLHRRLVPTYESASIRRFQEGRVDNIRSATPEALAFVRAVTDHKAAVPASEKLLLLKDAIRAQTAYTVMAITGMAIDN HLLALRELARAMCKELPEMFMDETYLMSNRFVLSTSQVPTTTEMFCCYGPVVPNGYGACYNPQPETILFCISSFHSCKETSSSKFAKAVE |
| P28329-3 | MAAKTPSSEESGLPKLPVPPLQQTLATYLQCMRHLVSEEQFRKSQAIVQQFGAPGGLGETLQQKLLERQEKTANWVSEYWLNDMYLNNRL ALPVNSSPAVIFARQHFPGTDDQLRFAASLISGVLSYKALLDSHSIPTDCAKGQLSGQPLCMKQYYGLFSSYRLPGHTQDTLVAQNSSIM PEPEHVIVACCNQFFVLDVVINFRRLSEGDLFTQLRKIVKMASNEDERLPPIGLLTSDGRSEWAEARTVLVKDSTNRDSLDMIERCICLV CLDAPGGVELSDTHRALQLLHGGGYSKNGANRWYDKSLQFVVGRDGTCGVVCEHSPFDGIVLVQCTEHLLKHVTQSSRKLIRADSVSELP APRRLRWKCSPEIQGHLASSAEKLQRIVKNLDFIVYKFDNYGKTFIKKQKCSPDAFIQVALQLAFYRLHRRLVPTYESASIRRFQEGRVD NIRSATPEALAFVRAVTDHKAAVPASEKLLLLKDAIRAQTAYTVMAITGMAIDNHLLALRELARAMCKELPEMFMDETYLMSNRFVLSTS QVPTTTEMFCCYGPVVPNGYGACYNPQPETILFCISSFHSCKETSSSKFAKAVEESLIDMRDLCSLLPPTESKPLATKEKATRPSQGHQP |
Protein Functional Features |
| Main function of this protein. (from UniProt) |
| CHAT (go to UniProt):P28329 |
| Retention analysis result of protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at * Minus value of BPloci means that the break pointn is located before the CDS. |
| - Retained protein feature among the 13 regional features. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| P28329 | Region | 1 | 89 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Substitution;Start=1;End=95 |
| P28329 | Region | 1 | 89 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=1;End=118 |
| P28329 | Compositional bias | 13 | 28 | Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Substitution;Start=1;End=95 |
| P28329 | Compositional bias | 13 | 28 | Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=1;End=118 |
| P28329 | Compositional bias | 61 | 75 | Note=Pro residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Substitution;Start=1;End=95 |
| P28329 | Compositional bias | 61 | 75 | Note=Pro residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=1;End=118 |
Gene Isoform Structures and Expression Levels for CHAT |
| Gene structures of our canonical and alternative spliced genes of CHAT * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Expression levels of gene isoforms across GTEx. |
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| Expression levels of gene isoforms across TCGA. |
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Protein Structures |
| PDB and CIF files of the predicted protein structures * Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format. |
| 3D view using mol* of P28329-1 |
| 3D view using mol* of P28329-2 |
| 3D view using mol* of P28329-3 |
pLDDT Score Distribution |
| pLDDT score distribution of the predicted protein structures from AlphaFold2 * AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. |
| pLDDT distribution across the protein length of P28329-1 |
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| pLDDT distribution across the protein length of P28329-2 |
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| pLDDT distribution across the protein length of P28329-3 |
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Ramachandran Plot of Protein Structures |
| Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide. |
| Ramachandran plot of P28329-1 |
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| Ramachandran plot of P28329-2 |
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Potential Active Site Information |
| The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite. |
| UniProt-id | Site score | Size | D score | Volume | Exposure | Enclosure | Contact | Phobic | Philic | Balance | Don/Acc | Residues |
| P28329-1 | 1.056 | 742 | 1.057 | 1832.649 | 0.457 | 0.781 | 1.009 | 0.685 | 1.08 | 0.634 | 0.798 | 32,33,34,35,36,37,38,39,146,152,153,198,201,202,20 3,205,206,207,208,209,210,213,214,216,245,248,254, 255,257,258,259,260,261,262,268,270,272,273,281,35 6,357,442,446,447,448,450,451,452,455,456,459,501, 504,505,508,521,525,530,531,532,533,544,549,550,55 1,552,554,555,556,557,558,560,561,566,567,568,569, 570,571,578,582,607,611,615,620,621,622,624,625,62 8,632,638,643,647,648,649,650,651,652,653,654,656, 657,658,659,660,661,662,663,664,668,670,671,672,67 3,674,675,676,684,696 |
| P28329-2 | 1.045 | 645 | 1.04 | 1865.577 | 0.501 | 0.766 | 0.982 | 0.705 | 1.103 | 0.639 | 0.72 | 1,2,70,71,115,116,118,119,120,121,123,124,125,126, 127,131,132,134,136,163,166,172,173,174,175,176,17 7,178,179,180,186,188,190,191,205,274,275,278,358, 360,363,364,365,366,368,369,370,373,374,377,419,42 2,423,426,439,448,449,450,451,454,462,466,467,468, 469,470,472,473,474,475,476,478,479,484,485,486,48 7,488,489,496,500,525,526,529,533,538,539,540,542, 543,546,547,550,556,561,565,566,567,568,569,570,57 1,572,574,575,576,577,578,579,580,581,586,588,589, 590,591,592,593,594,600,602,603,614,616 |
| P28329-3 | 1.082 | 402 | 1.08 | 1140.818 | 0.466 | 0.821 | 1.039 | 0.905 | 1.082 | 0.836 | 0.763 | 80,83,84,85,88,90,92,95,96,98,127,130,135,136,137, 139,140,141,142,143,144,150,154,163,324,328,329,33 0,332,333,334,338,403,407,412,413,414,415,418,436, 437,438,439,440,442,443,449,450,451,452,453,489,49 0,493,497,503,504,506,507,510,529,532,533,535,538, 539,540,541,542,543,544,545,550,552,553,555,566 |
Protein Structure and Feature Comparision |
| Protein Structure Comparision Using Template Modeling Scores (TM-score). |
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| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green) |
| 3D view using mol* of P28329-1_P28329-1_2fy3_A.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of P28329-1_2fy3_A_P28329-2.pdb |
| 3D view using mol* of P28329-1_2fy3_A_P28329-3.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of P28329-1_P28329-2.pdb |
| 3D view using mol* of P28329-1_P28329-3.pdb |
| Protein Feature Comparison of the protein sequendary structures among the protiens. |
| ./stats/secondary_structure/figure/P28329-1_vs_P28329-2.png |
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| ./stats/secondary_structure/figure/P28329-1_vs_P28329-3.png |
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| Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens. |
| ./stats/relative_asa/P28329-1_vs_P28329-2.png |
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| ./stats/relative_asa/P28329-1_vs_P28329-3.png |
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Protein-Protein Interaction |
| Interactors from UniProt. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| Interactors from STRING. |
| Gene name | Interactors |
Related Drugs to CHAT |
| Drugs targeting this gene/protein. (DrugBank) |
| UniProt accession | Gene name | DrugBank ID | Drug name | Drug group | Actions |
| P28329 | CHAT | DB00184 | Nicotine | approved | inhibitor |
Related Diseases to CHAT |
| Previous studies relating to the alternative splicing of CHAT and disease information from the MeSH term (PubMed) |
| Gene | PMID | Title | Abstract | MeSH ID | MeSH term |
| CHAT | 11595752 | A novel untranslated 'exon H' of the human choline acetyltransferase gene in placenta. | To investigate the existence of 5'-region(s) of human choline acetyltransferase (hChAT) mRNA in placenta we analyzed the presence or absence of ChAT 5'-untranslated regions (UTR) in human neuronal and non-neuronal cells. Total RNA from human spinal cord, placenta, cultured choriocarcinoma JEG-3 and neuroblastoma CHP126 and MC-IXC cells was reverse transcribed and used for polymerase chain reaction amplification (RT-PCR). We used a sense primer located in the 5'-flanking region, in the previously defined intronic sequence and an anti-sense primer located in the common coding exon 2 of the hChAT gene. An amplified product of 567 bp in size was obtained only in human placenta and in JEG-3 cells whereas it was absent in spinal cord, CHP126 and MC-IXC cells. It was designated 'H-type' of ChAT mRNA. Whereas CHP126 produced the R- and N-type of ChAT mRNAs, no transcript of the N-and R-type was detected in JEG-3 and human placenta. In addition, CHP126 and JEG-3 cells and placenta showed the expression of the M-type of ChAT mRNA. The identity of the amplified 567 bp product (H-type) was confirmed by Southern hybridization and sequencing. The nucleotide sequence of the amplified fragment in placenta revealed the existence of a previously unknown type of ChAT mRNA produced by alternative splicing. Using primer extension we further determined the transcription initiation site of the H-type hChAT mRNA in placenta. These results demonstrate the expression of a novel ChAT mRNA isoform in human placenta in addition to the M-type. These data may be possibly explained by the presence of a placenta specific promoter in the ChAT gene, which might be the proximal promoter P1. | D002822 | Choriocarcinoma |
| CHAT | 11595752 | A novel untranslated 'exon H' of the human choline acetyltransferase gene in placenta. | To investigate the existence of 5'-region(s) of human choline acetyltransferase (hChAT) mRNA in placenta we analyzed the presence or absence of ChAT 5'-untranslated regions (UTR) in human neuronal and non-neuronal cells. Total RNA from human spinal cord, placenta, cultured choriocarcinoma JEG-3 and neuroblastoma CHP126 and MC-IXC cells was reverse transcribed and used for polymerase chain reaction amplification (RT-PCR). We used a sense primer located in the 5'-flanking region, in the previously defined intronic sequence and an anti-sense primer located in the common coding exon 2 of the hChAT gene. An amplified product of 567 bp in size was obtained only in human placenta and in JEG-3 cells whereas it was absent in spinal cord, CHP126 and MC-IXC cells. It was designated 'H-type' of ChAT mRNA. Whereas CHP126 produced the R- and N-type of ChAT mRNAs, no transcript of the N-and R-type was detected in JEG-3 and human placenta. In addition, CHP126 and JEG-3 cells and placenta showed the expression of the M-type of ChAT mRNA. The identity of the amplified 567 bp product (H-type) was confirmed by Southern hybridization and sequencing. The nucleotide sequence of the amplified fragment in placenta revealed the existence of a previously unknown type of ChAT mRNA produced by alternative splicing. Using primer extension we further determined the transcription initiation site of the H-type hChAT mRNA in placenta. These results demonstrate the expression of a novel ChAT mRNA isoform in human placenta in addition to the M-type. These data may be possibly explained by the presence of a placenta specific promoter in the ChAT gene, which might be the proximal promoter P1. | D009447 | Neuroblastoma |
| CHAT | 11595752 | A novel untranslated 'exon H' of the human choline acetyltransferase gene in placenta. | To investigate the existence of 5'-region(s) of human choline acetyltransferase (hChAT) mRNA in placenta we analyzed the presence or absence of ChAT 5'-untranslated regions (UTR) in human neuronal and non-neuronal cells. Total RNA from human spinal cord, placenta, cultured choriocarcinoma JEG-3 and neuroblastoma CHP126 and MC-IXC cells was reverse transcribed and used for polymerase chain reaction amplification (RT-PCR). We used a sense primer located in the 5'-flanking region, in the previously defined intronic sequence and an anti-sense primer located in the common coding exon 2 of the hChAT gene. An amplified product of 567 bp in size was obtained only in human placenta and in JEG-3 cells whereas it was absent in spinal cord, CHP126 and MC-IXC cells. It was designated 'H-type' of ChAT mRNA. Whereas CHP126 produced the R- and N-type of ChAT mRNAs, no transcript of the N-and R-type was detected in JEG-3 and human placenta. In addition, CHP126 and JEG-3 cells and placenta showed the expression of the M-type of ChAT mRNA. The identity of the amplified 567 bp product (H-type) was confirmed by Southern hybridization and sequencing. The nucleotide sequence of the amplified fragment in placenta revealed the existence of a previously unknown type of ChAT mRNA produced by alternative splicing. Using primer extension we further determined the transcription initiation site of the H-type hChAT mRNA in placenta. These results demonstrate the expression of a novel ChAT mRNA isoform in human placenta in addition to the M-type. These data may be possibly explained by the presence of a placenta specific promoter in the ChAT gene, which might be the proximal promoter P1. | D014594 | Uterine Neoplasms |
Clinically important variants in CHAT |
| (ClinVar, 04/20/2024) |
| accession_id | uniprot_id | gene_name | Type | Variant | Clinical_significance |
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