Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   

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
go back to main search page
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



show annotations for term's descendants           Sort by:
 
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 8:53,828,741...53,932,773
Ensembl chr 8:53,831,093...53,932,437
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 chr17:40,557,161...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 [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 8:19,440,611...19,486,659
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 [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 6:26,791,517...26,902,161
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 [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 1:41,106,335...41,499,104
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 1:95,936,390...95,938,234
Ensembl chr 1:95,936,387...95,939,725
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...163,136,350
Ensembl chr 3:163,071,417...163,136,350
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 chr14:86,495,054...86,602,815
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 1:134,038,644...134,057,969
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 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 4:59,554,011...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 2:40,014,933...41,529,190
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 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 chr20:25,761,042...25,840,926
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]
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 2:221,988,645...222,072,813
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 chr12:31,238,889...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 20050
    role 20001
      application 19737
        refrigerant 18086
          ammonia 17516
            organic amino compound 17516
              aromatic amine 14923
                aminopyrimidine 1603
                  5-(hydroxymethyl)cytosine 18
                    5-(beta-D-glucosylmethyl)cytosine 0
Path 2
Term Annotations click to browse term
  CHEBI ontology 20050
    subatomic particle 20048
      composite particle 20048
        hadron 20048
          baryon 20048
            nucleon 20048
              atomic nucleus 20048
                atom 20048
                  main group element atom 19948
                    main group molecular entity 19948
                      s-block molecular entity 19735
                        hydrogen molecular entity 19727
                          hydrides 19093
                            inorganic hydride 17893
                              pnictogen hydride 17876
                                nitrogen hydride 17767
                                  azane 17517
                                    ammonia 17516
                                      organic amino compound 17516
                                        aromatic amine 14923
                                          aminopyrimidine 1603
                                            cytosine 1139
                                              5-(hydroxymethyl)cytosine 18
                                                5-(beta-D-glucosylmethyl)cytosine 0
paths to the root