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CHEBI ONTOLOGY - ANNOTATIONS

The Chemical Entities of Biological Interest (ChEBI) ontology is downloaded weekly from EMBL-EBI at http://www.ebi.ac.uk/chebi/. The data is made available under the Creative Commons License (CC BY 3.0, http://creativecommons.org/licenses/by/3.0/). For more information see: Degtyarenko et al. (2008) ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 36, D344–D350.

Term:5-(hydroxymethyl)cytosine
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Accession:CHEBI:76792 term browser browse the term
Definition:A nucleobase analogue that is cytosine in which the hydrogen at position 5 is replaced by a hydroxymethyl group.
Synonyms:exact_synonym: 4-amino-5-(hydroxymethyl)pyrimidin-2(1H)-one
 related_synonym: 4-Amino-5-(hydroxymethyl)-2(1H)-pyrimidinone;   5-hydroxymethylcytosine;   Formula=C5H7N3O2;   InChI=1S/C5H7N3O2/c6-4-3(2-9)1-7-5(10)8-4/h1,9H,2H2,(H3,6,7,8,10);   InChIKey=RYVNIFSIEDRLSJ-UHFFFAOYSA-N;   SMILES=Nc1nc(=O)[nH]cc1CO
 xref: CAS:1123-95-1
 xref_mesh: MESH:C011865
 xref: MetaCyc:CPD-15531;   PMID:19372391;   PMID:21151123;   PMID:21778364;   PMID:24162071;   PMID:24162993;   PMID:24295785;   PMID:24315686;   PMID:24390216;   PMID:24400731;   PMID:26715454;   PMID:26753520;   PMID:26851753;   PMID:27001475;   Reaxys:125478;   Wikipedia:5-Hydroxymethylcytosine


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5-(hydroxymethyl)cytosine term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Atm ATM serine/threonine kinase decreases methylation ISO 5-hydroxymethylcytosine results in decreased methylation of ATM gene CTD PMID:30990028 NCBI chr 8:58,015,938...58,119,973
Ensembl chr 8:58,015,940...58,120,045
JBrowse link
G Cmahp cytidine monophospho-N-acetylneuraminic acid hydroxylase, pseudogene multiple interactions ISO [bisphenol A results in decreased methylation of CMAH intron] which results in decreased abundance of 5-hydroxymethylcytosine CTD PMID:30044229 NCBI chr17:42,567,472...42,640,221
Ensembl chr17:42,583,945...42,640,221
JBrowse link
G Dnmt1 DNA methyltransferase 1 multiple interactions ISO DNMT1 protein promotes the reaction [bis(4-hydroxyphenyl)sulfone results in decreased abundance of 5-hydroxymethylcytosine]; DNMT1 protein promotes the reaction [bisphenol A results in decreased abundance of 5-hydroxymethylcytosine] CTD PMID:32105160 NCBI chr 8:21,922,515...21,968,495
Ensembl chr 8:21,922,515...21,968,495
JBrowse link
G Dnmt3a DNA methyltransferase 3 alpha multiple interactions ISO DNMT3A protein promotes the reaction [bis(4-hydroxyphenyl)sulfone results in decreased abundance of 5-hydroxymethylcytosine]; DNMT3A protein promotes the reaction [bisphenol A results in decreased abundance of 5-hydroxymethylcytosine] CTD PMID:32105160 NCBI chr 6:28,205,375...28,346,052
Ensembl chr 6:28,235,695...28,340,577
JBrowse link
G Esr1 estrogen receptor 1 decreases abundance
multiple interactions
ISO ESR1 protein results in decreased abundance of 5-hydroxymethylcytosine
ESR1 protein promotes the reaction [bis(4-hydroxyphenyl)sulfone results in decreased abundance of 5-hydroxymethylcytosine]; ESR1 protein promotes the reaction [bisphenol A results in decreased abundance of 5-hydroxymethylcytosine]
CTD PMID:32105160 NCBI chr 1:41,192,029...41,594,799
Ensembl chr 1:41,192,824...41,594,796
JBrowse link
G Ftl1 ferritin light chain 1 multiple interactions ISO [Chloranil results in increased abundance of 5-hydroxymethylcytosine] which results in increased expression of FTL mRNA CTD PMID:24214992 NCBI chr 1:101,448,190...101,450,034
Ensembl chr 1:101,448,346...101,449,829
JBrowse link
G Gnas GNAS complex locus multiple interactions ISO [bisphenol A results in increased methylation of GNAS intron] which results in increased abundance of 5-hydroxymethylcytosine CTD PMID:30044229 NCBI chr 3:172,374,957...172,434,988
Ensembl chr 3:172,374,957...172,428,483
Ensembl chr 3:172,374,957...172,428,483
JBrowse link
G Grb10 growth factor receptor bound protein 10 multiple interactions ISO [bisphenol A results in increased methylation of GRB10 intron] which results in increased abundance of 5-hydroxymethylcytosine CTD PMID:30044229 NCBI chr14:92,021,851...92,122,249
Ensembl chr14:92,021,851...92,117,923
JBrowse link
G Idh2 isocitrate dehydrogenase (NADP(+)) 2 decreases abundance ISO IDH2 protein mutant form results in decreased abundance of 5-hydroxymethylcytosine CTD PMID:27469509 NCBI chr 1:141,874,354...141,893,674
Ensembl chr 1:141,866,283...141,893,705
JBrowse link
G Kcnq1 potassium voltage-gated channel subfamily Q member 1 multiple interactions ISO [bisphenol A results in decreased methylation of KCNQ1 intron] which results in decreased abundance of 5-hydroxymethylcytosine CTD PMID:30044229 NCBI chr 1:216,293,087...216,630,339
Ensembl chr 1:216,293,087...216,630,339
JBrowse link
G Klf14 Kruppel-like factor 14 multiple interactions ISO [bisphenol A results in decreased methylation of KLF14 exon] which results in decreased abundance of 5-hydroxymethylcytosine CTD PMID:30044229 NCBI chr 4:58,247,876...58,250,798
Ensembl chr 4:58,247,876...58,250,798
JBrowse link
G Pde10a phosphodiesterase 10A multiple interactions ISO [bisphenol A results in increased methylation of PDE10A intron] which results in increased abundance of 5-hydroxymethylcytosine CTD PMID:30044229 NCBI chr 1:52,360,296...52,544,448
Ensembl chr 1:52,360,296...52,544,450
JBrowse link
G Pde4d phosphodiesterase 4D multiple interactions ISO [bisphenol A results in increased methylation of PDE4D exon] which results in increased abundance of 5-hydroxymethylcytosine CTD PMID:30044229 NCBI chr 2:40,219,999...41,468,551
Ensembl chr 2:40,554,146...41,464,264
JBrowse link
G Plagl1 PLAG1 like zinc finger 1 multiple interactions ISO [bisphenol A results in increased methylation of PLAGL1 exon] which results in increased abundance of 5-hydroxymethylcytosine CTD PMID:30044229 NCBI chr 1:7,219,587...7,270,169
Ensembl chr 1:7,252,349...7,259,035
JBrowse link
G Ppp1r9a protein phosphatase 1, regulatory subunit 9A multiple interactions ISO [bisphenol A results in decreased methylation of PPP1R9A intron] which results in decreased abundance of 5-hydroxymethylcytosine CTD PMID:30044229 NCBI chr 4:29,976,485...30,247,371
Ensembl chr 4:29,978,739...30,241,911
JBrowse link
G Tet1 tet methylcytosine dioxygenase 1 multiple interactions ISO TET1 protein affects the reaction [2,3,5,6-tetrachlorohydroquinone results in increased chemical synthesis of 5-hydroxymethylcytosine]; TET1 protein affects the reaction [Chloranil results in increased chemical synthesis of 5-hydroxymethylcytosine] CTD PMID:24214992 NCBI chr20:27,359,122...27,438,039
Ensembl chr20:27,366,213...27,437,427
JBrowse link
G Tet2 tet methylcytosine dioxygenase 2 multiple interactions
increases abundance
ISO TET2 protein affects the reaction [2,3,5,6-tetrachlorohydroquinone results in increased chemical synthesis of 5-hydroxymethylcytosine]; TET2 protein affects the reaction [Chloranil results in increased chemical synthesis of 5-hydroxymethylcytosine]
TET2 protein results in increased abundance of 5-hydroxymethylcytosine
bis(4-hydroxyphenyl)sulfone promotes the reaction [TET2 protein results in increased abundance of 5-hydroxymethylcytosine]; bisphenol A promotes the reaction [TET2 protein results in increased abundance of 5-hydroxymethylcytosine]; TET2 protein inhibits the reaction [bis(4-hydroxyphenyl)sulfone results in decreased abundance of 5-hydroxymethylcytosine]; TET2 protein inhibits the reaction [bisphenol A results in decreased abundance of 5-hydroxymethylcytosine]
CTD PMID:24214992, PMID:32105160 NCBI chr 2:238,719,389...238,802,975
Ensembl chr 2:238,720,835...238,803,024
JBrowse link
G Ubc ubiquitin C multiple interactions ISO [Chloranil results in increased abundance of 5-hydroxymethylcytosine] which results in increased expression of UBC mRNA CTD PMID:24214992 NCBI chr12:36,638,457...36,642,734
Ensembl chr12:36,638,457...36,642,734
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  CHEBI ontology 19787
    role 19734
      application 19393
        refrigerant 17418
          ammonia 16940
            organic amino compound 16939
              aromatic amine 13618
                aminopyrimidine 1103
                  5-(hydroxymethyl)cytosine 18
                    5-(beta-D-glucosylmethyl)cytosine 0
Path 2
Term Annotations click to browse term
  CHEBI ontology 19787
    subatomic particle 19784
      composite particle 19784
        hadron 19784
          baryon 19784
            nucleon 19784
              atomic nucleus 19784
                atom 19784
                  main group element atom 19672
                    main group molecular entity 19672
                      s-block molecular entity 19430
                        hydrogen molecular entity 19420
                          hydrides 18686
                            inorganic hydride 17411
                              pnictogen hydride 17383
                                nitrogen hydride 17224
                                  azane 16941
                                    ammonia 16940
                                      organic amino compound 16939
                                        aromatic amine 13618
                                          aminopyrimidine 1103
                                            cytosine 941
                                              5-(hydroxymethyl)cytosine 18
                                                5-(beta-D-glucosylmethyl)cytosine 0
paths to the root

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