5-Methylcytosine (BioDeep_00000400191)

Main id: BioDeep_00000001268

 

natural product PANOMIX_OTCML-2023 BioNovoGene_Lab2019


代谢物信息卡片


2-Pyrimidinol, 4-amino-5-methyl- (9CI)

化学式: C5H7N3O (125.0589)
中文名称: 4-氨基-5-甲基-2(1H)-嘧啶酮, 5-甲基胞嘧啶, 5-甲基胞嘧啶 盐酸盐
谱图信息: 最多检出来源 Rattus norvegicus(plant) 14.26%

分子结构信息

SMILES: CC1=C(N)NC(=O)N=C1
InChI: InChI=1S/C5H7N3O/c1-3-2-7-5(9)8-4(3)6/h2H,1H3,(H3,6,7,8,9)

描述信息

A pyrimidine that is a derivative of cytosine, having a methyl group at the 5-position.
5-Methylcytosine is a well-characterized DNA modification, and is also predominantly in abundant non-coding RNAs in both prokaryotes and eukaryotes. 5-Methylcytosine in mRNA is a new epitranscriptome marker inArabidopsis, and that regulation of this modification is an integral part of gene regulatory networks underlying plant development[1].

同义名列表

5 个代谢物同义名

2-Pyrimidinol, 4-amino-5-methyl- (9CI); 5-Methylcytosine; 5-METHYLCYTOSINE HYDROCHLORIDE; 5-Methylcytosine; 5-Methylcytosine



数据库引用编号

42 个数据库交叉引用编号

分类词条

相关代谢途径

Reactome(0)

BioCyc(0)

PlantCyc(0)

代谢反应

0 个相关的代谢反应过程信息。

Reactome(0)

BioCyc(0)

WikiPathways(0)

Plant Reactome(0)

INOH(0)

PlantCyc(0)

COVID-19 Disease Map(0)

PathBank(0)

PharmGKB(0)

7 个相关的物种来源信息

在这里通过桑基图来展示出与当前的这个代谢物在我们的BioDeep知识库中具有相关联信息的其他代谢物。在这里进行关联的信息来源主要有：

  • PubMed: 来源于PubMed文献库中的文献信息，我们通过自然语言数据挖掘得到的在同一篇文献中被同时提及的相关代谢物列表，这个列表按照代谢物同时出现的文献数量降序排序，取前10个代谢物作为相关研究中关联性很高的代谢物集合展示在桑基图中。
  • NCBI Taxonomy: 通过文献数据挖掘，得到的代谢物物种来源信息关联。这个关联信息同样按照出现的次数降序排序，取前10个代谢物作为高关联度的代谢物集合展示在桑吉图上。
  • Chemical Taxonomy: 在物质分类上处于同一个分类集合中的其他代谢物
  • Chemical Reaction: 在化学反应过程中，存在为当前代谢物相关联的生化反应过程中的反应底物或者反应产物的关联代谢物信息。

点击图上的相关代谢物的名称，可以跳转到相关代谢物的信息页面。

亚细胞结构定位 关联基因列表
Cytoplasm 9 AKT1, ALYREF, DNMT3A, FTO, IDH1, TET3, TP53, TRDMT1, YBX1
Endoplasmic reticulum membrane 1 CD4
Nucleus 17 AKT1, ALYREF, DNMT1, DNMT3A, DNMT3B, FTO, MBD2, MBD4, MECP2, NOP2, TDG, TET1, TET2, TET3, TP53, TRDMT1, YBX1
cytosol 8 AKT1, ALYREF, FTO, IDH1, MBD2, MECP2, TP53, YBX1
centrosome 2 MECP2, TP53
nucleoplasm 16 AKT1, ALYREF, DNMT1, DNMT3A, DNMT3B, FTO, MBD2, MBD4, MECP2, NOP2, NSUN5, TDG, TET2, TP53, TRDMT1, YBX1
Cell membrane 2 AKT1, CD4
lamellipodium 1 AKT1
Cytoplasmic granule 1 YBX1
Synapse 1 YBX1
cell cortex 1 AKT1
glutamatergic synapse 2 AKT1, MECP2
postsynapse 2 AKT1, MECP2
Cytoplasm, cytosol 1 IDH1
plasma membrane 5 AKT1, CD4, FTO, TDG, YBX1
Membrane 3 AKT1, ALYREF, TP53
extracellular exosome 3 ALYREF, IDH1, YBX1
endoplasmic reticulum 2 TP53, YBX1
extracellular space 1 MECP2
mitochondrion 3 DNMT1, IDH1, TP53
protein-containing complex 4 AKT1, MBD2, MECP2, TP53
intracellular membrane-bounded organelle 2 FTO, YBX1
pericentric heterochromatin 1 DNMT1
Single-pass type I membrane protein 1 CD4
Secreted 1 YBX1
extracellular region 2 IDH1, YBX1
Mitochondrion matrix 1 TP53
mitochondrial matrix 1 TP53
transcription regulator complex 1 TP53
Cytoplasm, cytoskeleton, microtubule organizing center, centrosome 1 TP53
external side of plasma membrane 1 CD4
microtubule cytoskeleton 1 AKT1
nucleolus 3 NOP2, NSUN5, TP53
Cytoplasm, P-body 1 YBX1
P-body 1 YBX1
Early endosome 1 CD4
cell-cell junction 1 AKT1
vesicle 1 AKT1
heterochromatin 3 DNMT3A, MBD2, MECP2
Membrane raft 1 CD4
Cytoplasm, cytoskeleton 1 TP53
spindle 1 AKT1
Peroxisome 1 IDH1
peroxisomal matrix 1 IDH1
Nucleus, PML body 1 TP53
PML body 2 TDG, TP53
Mitochondrion intermembrane space 1 AKT1
mitochondrial intermembrane space 1 AKT1
nuclear speck 3 ALYREF, FTO, MBD4
ciliary basal body 1 AKT1
chromatin 2 MBD2, TP53
Chromosome 5 DNMT3A, MBD2, TET1, TET2, TET3
Nucleus, nucleolus 2 NOP2, NSUN5
site of double-strand break 1 TP53
female germ cell nucleus 1 DNMT1
cytoplasmic stress granule 1 YBX1
Nucleus speckle 2 ALYREF, FTO
euchromatin 1 DNMT3A
germ cell nucleus 1 TP53
replication fork 2 DNMT1, TP53
ficolin-1-rich granule lumen 1 IDH1
secretory granule lumen 1 IDH1
endoplasmic reticulum lumen 1 CD4
nuclear matrix 2 DNMT3A, TP53
transcription repressor complex 1 TP53
tertiary granule lumen 1 IDH1
XY body 1 DNMT3A
Secreted, extracellular exosome 1 YBX1
NuRD complex 1 MBD2
chromosome, centromeric region 1 DNMT3A
clathrin-coated endocytic vesicle membrane 1 CD4
ribonucleoprotein complex 1 YBX1
[Isoform 2]: Nucleus 1 TET1
[Isoform 1]: Nucleus 2 TET1, TP53
Sin3-type complex 1 TET1
U12-type spliceosomal complex 1 YBX1
female pronucleus 1 TET3
male pronucleus 1 TET3
catalytic step 2 spliceosome 1 ALYREF
CRD-mediated mRNA stability complex 1 YBX1
histone pre-mRNA 3'end processing complex 1 YBX1
T cell receptor complex 1 CD4
catalytic complex 2 DNMT3A, DNMT3B
transcription export complex 1 ALYREF


文献列表

  • Navneet Kaur, Swapna Nayakoti, Natasha Brock, Nigel G Halford. Uncovering plant epigenetics: new insights into cytosine methylation in rye genomes. Journal of experimental botany. 2023 06; 74(12):3395-3398. doi: 10.1093/jxb/erad144. [PMID: 37369102]
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  • Yu Tian, Haijuan Xiao, Yanhui Yang, Pingping Zhang, Jiahui Yuan, Wei Zhang, Lijie Chen, Yibao Fan, Jinze Zhang, Huan Cheng, Tingwei Deng, Lin Yang, Weiwei Wang, Guoyong Chen, Peiqin Wang, Peng Gong, Xing Niu, Xianbin Zhang. Crosstalk between 5-methylcytosine and N6-methyladenosine machinery defines disease progression, therapeutic response and pharmacogenomic landscape in hepatocellular carcinoma. Molecular cancer. 2023 01; 22(1):5. doi: 10.1186/s12943-022-01706-6. [PMID: 36627693]
  • Xiao-Cong Zhao, Hai-Long Dong, Xiao-Lu Li, Hong-Yu Yang, Xue-Feng Chen, Liang Dai, Wen-Qiang Wu, Zhi-Jie Tan, Xing-Hua Zhang. 5-Methyl-cytosine stabilizes DNA but hinders DNA hybridization revealed by magnetic tweezers and simulations. Nucleic acids research. 2022 11; 50(21):12344-12354. doi: 10.1093/nar/gkac1122. [PMID: 36477372]
  • Sreejith Jayasree Varma, Enrica Calvani, Nana-Maria Grüning, Christoph B Messner, Nicholas Grayson, Floriana Capuano, Michael Mülleder, Markus Ralser. Global analysis of cytosine and adenine DNA modifications across the tree of life. eLife. 2022 07; 11(?):. doi: 10.7554/elife.81002. [PMID: 35900202]
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  • Wen Wang, Hengjun Huang, Hao Jiang, Chi Tian, Yisen Tang, Diwen Gan, Xiaozhen Wen, Zhenyu Song, Yuhao He, Xijun Ou, Liang Fang. A Cross-Tissue Investigation of Molecular Targets and Physiological Functions of Nsun6 Using Knockout Mice. International journal of molecular sciences. 2022 Jun; 23(12):. doi: 10.3390/ijms23126584. [PMID: 35743028]
  • Sara Gomez-Cabellos, Peter E Toorop, María Jesús Cañal, Pietro P M Iannetta, Eduardo Fernández-Pascual, Hugh W Pritchard, Anne M Visscher. Global DNA methylation and cellular 5-methylcytosine and H4 acetylated patterns in primary and secondary dormant seeds of Capsella bursa-pastoris (L.) Medik. (shepherd's purse). Protoplasma. 2022 May; 259(3):595-614. doi: 10.1007/s00709-021-01678-2. [PMID: 34212249]
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  • Shuai Wang, Hairong Xie, Fei Mao, Haiyan Wang, Shu Wang, Zhenglin Chen, Yuxia Zhang, Zhihui Xu, Jinming Xing, Zhaokang Cui, Xiquan Gao, Hongmei Jin, Jian Hua, Bo Xiong, Yufeng Wu. N4-acetyldeoxycytosine DNA modification marks euchromatin regions in Arabidopsis thaliana. Genome biology. 2022 01; 23(1):5. doi: 10.1186/s13059-021-02578-7. [PMID: 34980211]
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  • Yumei Zhang, Enen Gao, Hong Guan, Qianqian Wang, Shuo Zhang, Kexiong Liu, Fengxiang Yan, Hao Tian, Dehai Shan, Huijuan Xu, Jian Hou. Vitamin C treatment of embryos, but not donor cells, improves the cloned embryonic development in sheep. Reproduction in domestic animals = Zuchthygiene. 2020 Mar; 55(3):255-265. doi: 10.1111/rda.13606. [PMID: 31837175]
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