5-(hydroxymethyl)cytosine - Ontology Report - Rat Genome Database

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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	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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Genes (20)

5-(hydroxymethyl)cytosine

term browser

Symbol

Object Name

Qualifiers

Evidence

Notes

Source

PubMed Reference(s)

RGD Reference(s)

Position

G

ATM serine/threonine kinase

decreases methylation

5-hydroxymethylcytosine results in decreased methylation of ATM gene

NCBI chr 8:53,828,741...53,932,773
Ensembl chr 8:53,831,093...53,932,437

G

cytidine monophospho-N-acetylneuraminic acid hydroxylase

multiple interactions

[bisphenol A results in decreased methylation of CMAH intron] which results in decreased abundance of 5-hydroxymethylcytosine

NCBI chr17:40,557,161...40,642,350
Ensembl chr17:40,583,667...40,642,275

G

DNA methyltransferase 1

multiple interactions

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]

NCBI chr 8:19,440,611...19,486,659
Ensembl chr 8:19,440,611...19,486,659

G

DNA methyltransferase 3 alpha

multiple interactions

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]

NCBI chr 6:26,791,517...26,902,161
Ensembl chr 6:26,822,609...26,896,687

G

estrogen receptor 1

decreases abundance
multiple interactions

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]

NCBI chr 1:41,106,335...41,499,104
Ensembl chr 1:41,210,475...41,495,002

G

ferritin light chain 1

multiple interactions

[Chloranil results in increased abundance of 5-hydroxymethylcytosine] which results in increased expression of FTL mRNA

NCBI chr 1:95,936,387...95,938,234
Ensembl chr 1:95,936,387...95,939,725
Ensembl chr10:95,936,387...95,939,725

G

glutamate-cysteine ligase, catalytic subunit

multiple interactions

[hydroquinone affects the methylation of GCLC promoter] which results in increased abundance of 5-hydroxymethylcytosine

NCBI chr 8:78,629,899...78,668,547
Ensembl chr 8:78,630,127...78,668,544

G

GNAS complex locus

multiple interactions

[bisphenol A results in increased methylation of GNAS intron] which results in increased abundance of 5-hydroxymethylcytosine

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

G

growth factor receptor bound protein 10

multiple interactions

[bisphenol A results in increased methylation of GRB10 intron] which results in increased abundance of 5-hydroxymethylcytosine

NCBI chr14:86,495,051...86,602,800
Ensembl chr14:86,495,054...86,602,806

G

isocitrate dehydrogenase (NADP(+)) 2

decreases abundance

IDH2 protein mutant form results in decreased abundance of 5-hydroxymethylcytosine

NCBI chr 1:134,038,644...134,057,969
Ensembl chr 1:134,029,772...134,058,025

G

potassium voltage-gated channel subfamily Q member 1

multiple interactions

[bisphenol A results in decreased methylation of KCNQ1 intron] which results in decreased abundance of 5-hydroxymethylcytosine

NCBI chr 1:198,291,711...198,624,683
Ensembl chr 1:198,291,766...198,624,669

G

KLF transcription factor 14

multiple interactions

[bisphenol A results in decreased methylation of KLF14 exon] which results in decreased abundance of 5-hydroxymethylcytosine

NCBI chr 4:59,554,011...59,556,933
Ensembl chr 4:59,554,011...59,556,933

G

phosphodiesterase 10A

multiple interactions

[bisphenol A results in increased methylation of PDE10A intron] which results in increased abundance of 5-hydroxymethylcytosine

NCBI chr 1:51,765,743...52,218,086
Ensembl chr 1:51,770,132...52,216,563

G

phosphodiesterase 4D

multiple interactions

[bisphenol A results in increased methylation of PDE4D exon] which results in increased abundance of 5-hydroxymethylcytosine

NCBI chr 2:40,014,933...41,529,190
Ensembl chr 2:40,019,933...41,525,884

G

PLAG1 like zinc finger 1

multiple interactions

[bisphenol A results in increased methylation of PLAGL1 exon] which results in increased abundance of 5-hydroxymethylcytosine

NCBI chr 1:7,477,295...7,517,229
Ensembl chr 1:7,477,177...7,517,228

G

protein phosphatase 1, regulatory subunit 9A

multiple interactions

[bisphenol A results in decreased methylation of PPP1R9A intron] which results in decreased abundance of 5-hydroxymethylcytosine

NCBI chr 4:32,970,501...33,292,360
Ensembl chr 4:33,024,450...33,286,907

G

stratifin

multiple interactions

[hydroquinone affects the methylation of SFN promoter] which results in increased abundance of 5-hydroxymethylcytosine

NCBI chr 5:145,826,722...145,827,994
Ensembl chr 5:145,826,201...145,831,314

G

tet methylcytosine dioxygenase 1

multiple interactions

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]

NCBI chr20:25,761,042...25,840,926
Ensembl chr20:25,768,120...25,833,052

G

tet methylcytosine dioxygenase 2

multiple interactions
increases abundance

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]

PMID:24214992 PMID:32105160

NCBI chr 2:221,988,645...222,072,813
Ensembl chr 2:221,988,645...222,072,534

G

ubiquitin C

multiple interactions

[Chloranil results in increased abundance of 5-hydroxymethylcytosine] which results in increased expression of UBC mRNA

NCBI chr12:31,239,149...31,243,924
Ensembl chr12:31,239,152...31,243,925

Term paths to the root

Path 1
Term	Annotations
CHEBI ontology	19911
role	19854
application	19722
NMR chemical shift reference compound	18090
ammonia	17865
organic amino compound	17888
aromatic amine	15504
aminopyrimidine	2024
5-(hydroxymethyl)cytosine	20
5-(beta-D-glucosylmethyl)cytosine	0
Path 2
Term	Annotations
CHEBI ontology	19911
subatomic particle	19909
composite particle	19909
hadron	19880
baryon	19880
nucleon	19909
atomic nucleus	19880
atom	19909
main group element atom	19849
main group molecular entity	19849
s-block molecular entity	19681
hydrogen molecular entity	19662
hydrides	19167
inorganic hydride	18182
pnictogen hydride	18172
nitrogen hydride	18085
azane	17866
ammonia	17865
organic amino compound	17888
aromatic amine	15504
aminopyrimidine	2024
cytosine	1375
5-(hydroxymethyl)cytosine	20
5-(beta-D-glucosylmethyl)cytosine	0

paths to the root