5-Methyluridine (BioDeep_00000405731)

Main id: BioDeep_00000003091

 

PANOMIX_OTCML-2023 natural product


代谢物信息卡片


5-Methyluridine

化学式: C10H14N2O6 (258.0852)
中文名称: 5-甲基尿苷, 5-甲基尿甙
谱图信息: 最多检出来源 () 0%

分子结构信息

SMILES: CC1=CN(C(=O)NC1=O)C2C(C(C(O2)CO)O)O
InChI: InChI=1S/C10H14N2O6/c1-4-2-12(10(17)11-8(4)16)9-7(15)6(14)5(3-13)18-9/h2,5-7,9,13-15H,3H2,1H3,(H,11,16,17)/t5-,6-,7-,9-/m1/s1

描述信息

CONFIDENCE standard compound; INTERNAL_ID 320
5-Methyluridine is a is an endogenous methylated nucleoside found in human fluids.
5-Methyluridine is a is an endogenous methylated nucleoside found in human fluids.

同义名列表

2 个代谢物同义名

5-Methyluridine; 5-Methyluridine



数据库引用编号

30 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)

47 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 ADA, APOE, CDK16, MTOR, PNP, PRKAA2, PUS1, PUS10, RELA
Peripheral membrane protein 3 ADA, CDK16, MTOR
Endoplasmic reticulum membrane 1 MTOR
Nucleus 11 APOE, CDK16, CDK9, MTOR, PPARGC1A, PRKAA2, PUS1, PUS10, RELA, RFC2, TRUB1
cytosol 11 ADA, CDA, CDK16, MTOR, PNP, PPARGC1A, PRKAA2, RELA, SLC2A4, TRUB1, UPP1
dendrite 3 APOE, MTOR, PRKAA2
phagocytic vesicle 1 MTOR
trans-Golgi network 1 SLC2A4
nucleoplasm 8 CDK9, MTOR, PPARGC1A, PRKAA2, PUS1, RELA, RFC2, UPP1
Cell membrane 4 ADA, CDK16, SLC2A4, TNF
Cytoplasmic side 2 CDK16, MTOR
Multi-pass membrane protein 1 SLC2A4
Golgi apparatus membrane 1 MTOR
cell junction 1 ADA
cell surface 2 ADA, TNF
glutamatergic synapse 2 APOE, RELA
Golgi apparatus 2 APOE, PRKAA2
Golgi membrane 2 INS, MTOR
lysosomal membrane 1 MTOR
neuronal cell body 3 APOE, PRKAA2, TNF
sarcolemma 1 SLC2A4
synaptic vesicle 1 CDK16
Cytoplasm, cytosol 1 TRUB1
Cytoplasmic vesicle, secretory vesicle 1 CDK16
Lysosome 3 ADA, MTOR, RNASET2
Presynapse 1 SLC2A4
plasma membrane 5 ADA, APOE, CDK16, SLC2A4, TNF
Membrane 6 ADA, APOE, CDK9, MTOR, PRKAA2, SLC2A4
axon 1 PRKAA2
extracellular exosome 4 APOE, PNP, RNASET2, SLC2A4
Lysosome membrane 1 MTOR
endoplasmic reticulum 1 APOE
extracellular space 5 APOE, INS, PNP, RNASET2, TNF
lysosomal lumen 1 RNASET2
perinuclear region of cytoplasm 1 SLC2A4
mitochondrion 3 PUS1, PUS10, TRUB1
intracellular membrane-bounded organelle 1 PUS1
Microsome membrane 1 MTOR
TORC1 complex 1 MTOR
TORC2 complex 1 MTOR
Secreted 4 APOE, INS, PNP, RNASET2
extracellular region 6 APOE, CDA, INS, PNP, RNASET2, TNF
cytoplasmic side of plasma membrane 1 CDK16
Mitochondrion outer membrane 1 MTOR
mitochondrial outer membrane 1 MTOR
mitochondrial matrix 1 PUS1
Extracellular side 1 ADA
Cytoplasmic vesicle lumen 1 ADA
anchoring junction 1 ADA
transcription regulator complex 1 RELA
external side of plasma membrane 3 ADA, SLC2A4, TNF
Endosome, multivesicular body 1 APOE
Extracellular vesicle 1 APOE
Secreted, extracellular space, extracellular matrix 1 APOE
chylomicron 1 APOE
high-density lipoprotein particle 1 APOE
low-density lipoprotein particle 1 APOE
multivesicular body 2 APOE, SLC2A4
very-low-density lipoprotein particle 1 APOE
T-tubule 1 SLC2A4
microtubule cytoskeleton 1 CDK16
Early endosome 1 APOE
clathrin-coated pit 1 SLC2A4
recycling endosome 1 TNF
Single-pass type II membrane protein 1 TNF
Cytoplasm, perinuclear region 1 SLC2A4
Membrane raft 2 SLC2A4, TNF
extracellular matrix 1 APOE
sarcoplasmic reticulum 1 SLC2A4
Nucleus, PML body 2 MTOR, PPARGC1A
PML body 3 CDK9, MTOR, PPARGC1A
Mitochondrion intermembrane space 1 RNASET2
mitochondrial intermembrane space 1 RNASET2
collagen-containing extracellular matrix 1 APOE
nuclear speck 1 PRKAA2
neuron projection 1 CDK16
chromatin 2 PPARGC1A, RELA
phagocytic cup 1 TNF
cytoplasmic ribonucleoprotein granule 1 CDK9
Secreted, extracellular space 1 APOE
[Isoform 1]: Mitochondrion 1 PUS1
blood microparticle 1 APOE
nuclear envelope 1 MTOR
Endomembrane system 2 MTOR, SLC2A4
endosome lumen 1 INS
Cytoplasmic vesicle membrane 1 SLC2A4
Melanosome 1 APOE
cytoplasmic stress granule 1 PRKAA2
clathrin-coated vesicle 1 SLC2A4
trans-Golgi network transport vesicle 1 SLC2A4
ficolin-1-rich granule lumen 2 CDA, PNP
secretory granule lumen 3 CDA, INS, PNP
Golgi lumen 1 INS
endoplasmic reticulum lumen 3 APOE, INS, RNASET2
tertiary granule lumen 1 CDA
transport vesicle 1 INS
transcription elongation factor complex 1 CDK9
azurophil granule lumen 1 RNASET2
Lysosome lumen 1 RNASET2
Endoplasmic reticulum-Golgi intermediate compartment membrane 1 INS
vesicle membrane 1 SLC2A4
clathrin-coated endocytic vesicle membrane 1 APOE
[Isoform 2]: Nucleus 1 PUS1
[Isoform 1]: Nucleus 1 PPARGC1A
Synapse, synaptosome 1 CDK16
synaptic cleft 1 APOE
nucleotide-activated protein kinase complex 1 PRKAA2
Cytoplasmic vesicle, phagosome 1 MTOR
cyclin/CDK positive transcription elongation factor complex 1 CDK9
P-TEFb complex 1 CDK9
cyclin-dependent protein kinase holoenzyme complex 1 CDK16
discoidal high-density lipoprotein particle 1 APOE
endocytic vesicle lumen 1 APOE
[Tumor necrosis factor, soluble form]: Secreted 1 TNF
chylomicron remnant 1 APOE
intermediate-density lipoprotein particle 1 APOE
lipoprotein particle 1 APOE
multivesicular body, internal vesicle 1 APOE
insulin-responsive compartment 1 SLC2A4
NF-kappaB p50/p65 complex 1 RELA
NF-kappaB complex 1 RELA
Ctf18 RFC-like complex 1 RFC2
DNA replication factor C complex 1 RFC2
[C-domain 2]: Secreted 1 TNF
[Tumor necrosis factor, membrane form]: Membrane 1 TNF
[C-domain 1]: Secreted 1 TNF
[Isoform B4]: Nucleus 1 PPARGC1A
[Isoform B4-8a]: Cytoplasm 1 PPARGC1A
[Isoform B5]: Nucleus 1 PPARGC1A
[Isoform 9]: Nucleus 1 PPARGC1A


文献列表

  • Yingshan Ji, Jianqiang Sun, Jingxuan Xie, Wei Wu, Stella C Shuai, Qi Zhao, Wei Chen. m5UMCB: Prediction of RNA 5-methyluridine sites using multi-scale convolutional neural network with BiLSTM. Computers in biology and medicine. 2024 01; 168(?):107793. doi: 10.1016/j.compbiomed.2023.107793. [PMID: 38048661]
  • Shangyu Gao, Yu Sun, Xiaoguang Chen, Changhua Zhu, Xiaoye Liu, Wenlei Wang, Lijun Gan, Yanwu Lu, Frank Schaarschmidt, Marco Herde, Claus-Peter Witte, Mingjia Chen. Pyrimidine catabolism is required to prevent the accumulation of 5-methyluridine in RNA. Nucleic acids research. 2023 Jun; ?(?):. doi: 10.1093/nar/gkad529. [PMID: 37334828]
  • Pengmian Feng, Wei Chen. iRNA-m5U: A sequence based predictor for identifying 5-methyluridine modification sites in Saccharomyces cerevisiae. Methods (San Diego, Calif.). 2022 07; 203(?):28-31. doi: 10.1016/j.ymeth.2021.04.013. [PMID: 33882361]
  • Hong Lin, Binghai Lou, Jonathan M Glynn, Harshavardhan Doddapaneni, Edwin L Civerolo, Chuanwu Chen, Yongping Duan, Lijuan Zhou, Cheryl M Vahling. The complete genome sequence of 'Candidatus Liberibacter solanacearum', the bacterium associated with potato zebra chip disease. PloS one. 2011 Apr; 6(4):e19135. doi: 10.1371/journal.pone.0019135. [PMID: 21552483]
  • Ofelia A Olivero, Irma L Vazquez, Catherine C Cooch, Jessica Ming, Emily Keller, Mia Yu, Jennifer P Borojerdi, Hannan M Braun, Edward McKee, Miriam C Poirier. Long-term AZT exposure alters the metabolic capacity of cultured human lymphoblastoid cells. Toxicological sciences : an official journal of the Society of Toxicology. 2010 May; 115(1):109-17. doi: 10.1093/toxsci/kfq023. [PMID: 20106944]
  • Feng-Ling Cui, Ying-Hua Yan, Qiang-Zhai Zhang, Gui-Rong Qu, Juan Du, Xiao-Jun Yao. A study on the interaction between 5-Methyluridine and human serum albumin using fluorescence quenching method and molecular modeling. Journal of molecular modeling. 2010 Feb; 16(2):255-62. doi: 10.1007/s00894-009-0548-4. [PMID: 19588173]
  • Feng-ling Cui, Ying-hua Yan, Qiang-zhai Zhang, Gui-rong Qu, Yan Lu. [Determination of protein in biological samples by synchronous fluorescence]. Guang pu xue yu guang pu fen xi = Guang pu. 2009 Sep; 29(9):2531-4. doi: NULL. [PMID: 19950668]
  • Damien Jégourel, Raphaël Delépée, Florent Breton, Antoine Rolland, Richard Vidal, Luigi A Agrofoglio. Molecularly imprinted polymer of 5-methyluridine for solid-phase extraction of pyrimidine nucleoside cancer markers in urine. Bioorganic & medicinal chemistry. 2008 Oct; 16(19):8932-9. doi: 10.1016/j.bmc.2008.08.063. [PMID: 18789867]
  • H F Becker, Y Motorin, C Florentz, R Giegé, H Grosjean. Pseudouridine and ribothymidine formation in the tRNA-like domain of turnip yellow mosaic virus RNA. Nucleic acids research. 1998 Sep; 26(17):3991-7. doi: 10.1093/nar/26.17.3991. [PMID: 9705510]
  • R H Weisbart, G Chan, A Kacena, R E Saxton. Characterization of mouse and human monoclonal antibodies cross-reactive with SLE serum antibodies to guanosine. Journal of immunology (Baltimore, Md. : 1950). 1984 Jun; 132(6):2909-12. doi: NULL. [PMID: 6725946]
  • A S Delk, J M Romeo, D P Nagle, J C Rabinowitz. Biosynthesis of ribothymidine in the transfer RNA of Streptococcus faecalis and Bacillus subtilis. A methylation of RNA involving 5,10-methylenetetrahydrofolate. The Journal of biological chemistry. 1976 Dec; 251(23):7649-56. doi: 10.1016/s0021-9258(17)32901-0. [PMID: 826533]