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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 8:62,724,939...62,829,040
Ensembl chr 8:53,831,093...53,932,437 		JBrowse link
G Cmah cytidine monophospho-N-acetylneuraminic acid hydroxylase multiple interactions ISO [bisphenol A results in decreased methylation of CMAH intron] which results in decreased abundance of 5-hydroxymethylcytosine CTD PMID:30044229 NCBI chr17:40,557,161...40,642,350
Ensembl chr17:40,583,667...40,642,275 		JBrowse link
G Dnmt1 DNA methyltransferase 1 multiple interactions ISO DNMT1 protein promotes the reaction [bisphenol A results in decreased abundance of 5-hydroxymethylcytosine]; DNMT1 protein promotes the reaction [bisphenol S results in decreased abundance of 5-hydroxymethylcytosine] CTD PMID:32105160 NCBI chr 8:27,716,797...27,763,405
Ensembl chr 8:19,440,611...19,486,659 		JBrowse link
G Dnmt3a DNA methyltransferase 3 alpha multiple interactions ISO DNMT3A protein promotes the reaction [bisphenol A results in decreased abundance of 5-hydroxymethylcytosine]; DNMT3A protein promotes the reaction [bisphenol S results in decreased abundance of 5-hydroxymethylcytosine] CTD PMID:32105160 NCBI chr 6:32,507,316...32,621,678
Ensembl chr 6:26,822,609...26,896,687 		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 [bisphenol A results in decreased abundance of 5-hydroxymethylcytosine]; ESR1 protein promotes the reaction [bisphenol S results in decreased abundance of 5-hydroxymethylcytosine] 		CTD PMID:32105160 NCBI chr 1:43,511,685...43,904,454
Ensembl chr 1:41,210,475...41,495,002 		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 1:105,072,858...105,074,705
Ensembl chr 1:95,936,387...95,939,725
Ensembl chr10:95,936,387...95,939,725
Ensembl chr 2:95,936,387...95,939,725 		JBrowse link
G Gclc glutamate-cysteine ligase, catalytic subunit multiple interactions ISO [hydroquinone affects the methylation of GCLC promoter] which results in increased abundance of 5-hydroxymethylcytosine CTD PMID:23940045 NCBI chr 8:87,510,251...87,548,896
Ensembl chr 8:78,630,127...78,668,544 		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 3:163,071,003...163,136,350
Ensembl chr 3:163,071,417...163,127,262
Ensembl chr 3:163,071,417...163,127,262 		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 chr14:90,708,653...90,816,399
Ensembl chr14:86,495,054...86,602,806 		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 1:143,447,925...143,467,248
Ensembl chr 1:134,029,772...134,058,025 		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 1:198,291,711...198,624,683
Ensembl chr 1:198,291,766...198,624,669 		JBrowse link
G Klf14 KLF transcription 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 4:59,554,011...59,556,933
Ensembl chr 4:59,554,011...59,556,933 		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 1:51,765,743...52,218,086
Ensembl chr 1:51,770,132...52,216,563 		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 2:41,748,337...43,262,567
Ensembl chr 2:40,019,933...41,525,884 		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 1:7,477,295...7,517,229
Ensembl chr 1:7,477,177...7,517,228 		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 4:32,970,501...33,292,360
Ensembl chr 4:33,024,450...33,286,907 		JBrowse link
G Sfn stratifin multiple interactions ISO [hydroquinone affects the methylation of SFN promoter] which results in increased abundance of 5-hydroxymethylcytosine CTD PMID:23940045 NCBI chr 5:145,826,722...145,827,994
Ensembl chr 5:145,826,201...145,831,314 		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 chr20:25,766,806...25,839,598
Ensembl chr20:25,768,120...25,833,052 		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]
bisphenol A promotes the reaction [TET2 protein results in increased abundance of 5-hydroxymethylcytosine]; bisphenol S promotes the reaction [TET2 protein results in increased abundance of 5-hydroxymethylcytosine]; TET2 protein inhibits the reaction [bisphenol A results in decreased abundance of 5-hydroxymethylcytosine]; TET2 protein inhibits the reaction [bisphenol S results in decreased abundance of 5-hydroxymethylcytosine] 		CTD PMID:24214992 PMID:32105160 NCBI chr 2:224,662,654...224,746,819
Ensembl chr 2:221,988,645...222,072,534 		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 chr12:31,239,149...31,243,924
Ensembl chr12:31,239,152...31,243,925 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  CHEBI ontology 20856
    role 20816
      application 20617
        NMR chemical shift reference compound 18453
          ammonia 18260
            organic amino compound 18260
              aromatic amine 15828
                aminopyrimidine 3807
                  5-(hydroxymethyl)cytosine 20
                    5-(beta-D-glucosylmethyl)cytosine 0
Path 2
Term Annotations click to browse term
  CHEBI ontology 20856
    subatomic particle 20854
      composite particle 20854
        hadron 20854
          baryon 20854
            nucleon 20854
              atomic nucleus 20854
                atom 20854
                  main group element atom 20777
                    main group molecular entity 20777
                      s-block molecular entity 20573
                        hydrogen molecular entity 20557
                          hydrides 19691
                            inorganic hydride 18601
                              pnictogen hydride 18587
                                nitrogen hydride 18502
                                  azane 18261
                                    ammonia 18260
                                      organic amino compound 18260
                                        aromatic amine 15828
                                          aminopyrimidine 3807
                                            cytosine 1479
                                              5-(hydroxymethyl)cytosine 20
                                                5-(beta-D-glucosylmethyl)cytosine 0
paths to the root