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5-hydroxymethylcytosine



Description
   A nucleobase analogue that is cytosine in which the hydrogen at position 5 is replaced by a hydroxymethyl group.
Basic Information
Comman Name 5-hydroxymethylcytosine
Symbol 5hmC
Chemical Formula C5H7N3O2
Nucleoside Mass 141.13
Locations and Contents
ModificationOrganisms or CellsContentsReferences
5hmCE. coli B0.2% [5hmC/dC]https://pubmed.ncbi.nlm.nih.gov/13115372/
5hmCCrude DNA from E. coli0.6% [5hmC/dC]https://pubmed.ncbi.nlm.nih.gov/13115372/
5hmCOx.spleen0.2% [5hmC/dC]https://pubmed.ncbi.nlm.nih.gov/13115372/
5hmCPhage T51.0% [5hmC/dC]https://pubmed.ncbi.nlm.nih.gov/13115372/
5hmCPhage T72.7% [5hmC/dC]https://pubmed.ncbi.nlm.nih.gov/13115372/
5hmCCrude DNA from phage T70.5% [5hmC/dC]https://pubmed.ncbi.nlm.nih.gov/13115372/
5hmCPolyhedral virus2.4% [5hmC/dC]https://pubmed.ncbi.nlm.nih.gov/13115372/
5hmCVaccinia virus0.6% [5hmC/dC]https://pubmed.ncbi.nlm.nih.gov/13115372/
5hmCMeningo-pneumonitis virus3.9% [5hmC/dC]https://pubmed.ncbi.nlm.nih.gov/13115372/
5hmCMouse brain3.3% [5hmC/DNA]https://pubmed.ncbi.nlm.nih.gov/4538516/
5hmCMouse liver3.6% [5hmC/DNA]https://pubmed.ncbi.nlm.nih.gov/4538516/
5hmCBullfrog brain1.28% [5hmC/DNA]https://pubmed.ncbi.nlm.nih.gov/4538516/
5hmCMouse purkinje cells0.6% [5hmC/DNA]https://pubmed.ncbi.nlm.nih.gov/19372393/
5hmCMouse granule cells0.2% [5hmC/DNA]https://pubmed.ncbi.nlm.nih.gov/19372393/
5hmCMouse Spinal cord0.46% [5hmC/dG]https://pubmed.ncbi.nlm.nih.gov/21203455/
5hmCMouse Kidney, nasal epithelia0.17% [5hmC/dG]https://pubmed.ncbi.nlm.nih.gov/21203455/
5hmCMouse bladder0.16% [5hmC/dG]https://pubmed.ncbi.nlm.nih.gov/21203455/
5hmCMouse heart, muscle0.15% [5hmC/dG]https://pubmed.ncbi.nlm.nih.gov/21203455/
5hmCMouse lung0.14% [5hmC/dG]https://pubmed.ncbi.nlm.nih.gov/21203455/
5hmCMouse Pituitary gland, liver,0.06% [5hmC/dG]https://pubmed.ncbi.nlm.nih.gov/21203455/
5hmCMouse spleen, testes0.03% [5hmC/dG]https://pubmed.ncbi.nlm.nih.gov/21203455/
5hmCMouse ES cells0.39% [5hmC/dG]https://pubmed.ncbi.nlm.nih.gov/21721093/
5hmCMouse EB 2 days differentiation0.2% [5hmC/dG]https://pubmed.ncbi.nlm.nih.gov/21721093/
5hmCMouse EB 3 days differentiation0.15% [5hmC/dG]https://pubmed.ncbi.nlm.nih.gov/21721093/
5hmCHuman heart0.05% [5hmC/DNA]https://pubmed.ncbi.nlm.nih.gov/21772996/
5hmCHuman kidney0.38% [5hmC/DNA]https://pubmed.ncbi.nlm.nih.gov/21772996/
5hmCHuman colon0.45% [5hmC/DNA]https://pubmed.ncbi.nlm.nih.gov/21772996/
5hmCHuman rectum0.57% [5hmC/DNA]https://pubmed.ncbi.nlm.nih.gov/21772996/
5hmCHuman liver0.46% [5hmC/DNA]https://pubmed.ncbi.nlm.nih.gov/21772996/
5hmCHuman lung0.14% [5hmC/DNA]https://pubmed.ncbi.nlm.nih.gov/21772996/
5hmCHuman breast0.05% [5hmC/DNA]https://pubmed.ncbi.nlm.nih.gov/21772996/
5hmCHuman placenta0.06% [5hmC/DNA]https://pubmed.ncbi.nlm.nih.gov/21772996/
5hmCMouse brain0.15% [5hmC/DNA]https://pubmed.ncbi.nlm.nih.gov/21772996/
5hmCHeLa, HCT116, SW620, AN3CA cells<0.02% [5hmC/DNA]https://pubmed.ncbi.nlm.nih.gov/21772996/
5hmCHEK2930.009% [5hmC/dC]https://pubmed.ncbi.nlm.nih.gov/21778364/
5hmCHEK293, Tet2 CD wild type0.75% [5hmC/dC]https://pubmed.ncbi.nlm.nih.gov/21778364/
5hmCHEK293, Tet2 CD mut0.014% [5hmC/dC]https://pubmed.ncbi.nlm.nih.gov/21778364/
5hmCMouse brain cortex0.67% [5hmC/dC]https://pubmed.ncbi.nlm.nih.gov/21778364/
5hmCMouse kidney0.21%[5hmC/dC]https://pubmed.ncbi.nlm.nih.gov/21778364/
5hmCMouse lung0.16% [5hmC/dC]https://pubmed.ncbi.nlm.nih.gov/21778364/
5hmCMouse heart0.144% [5hmC/dC]https://pubmed.ncbi.nlm.nih.gov/21778364/
5hmCMouse pancreas0.093% [5hmC/dC]https://pubmed.ncbi.nlm.nih.gov/21778364/
5hmCMouse liver0.143% [5hmC/dC]https://pubmed.ncbi.nlm.nih.gov/21778364/
5hmCMouse spleen0.0575% [5hmC/dC]https://pubmed.ncbi.nlm.nih.gov/21778364/
5hmCMouse thymus0.0235% [5hmC/dC]https://pubmed.ncbi.nlm.nih.gov/21778364/
5hmCMouse embryonic stem (ES) Cells0.032% [5hmC/DNA]https://pubmed.ncbi.nlm.nih.gov/19372391/
5hmCMouse embryonic stem (ES) Cells0.13% [5hmC/dC]https://pubmed.ncbi.nlm.nih.gov/21778364/
5hmCMouse embryonic stem (ES) Cells0.0163 [5hmC/DNA]https://pubmed.ncbi.nlm.nih.gov/23658232/
5hmCHeLa cells0.0083% [5hmC/dG]https://pubmed.ncbi.nlm.nih.gov/23678980/
5hmC293T cells0.014% [5hmC/dG]https://pubmed.ncbi.nlm.nih.gov/23678980/
5hmCJurkat-T cells0.0004% [5hmC/dG]https://pubmed.ncbi.nlm.nih.gov/23678980/
5hmCDebaryomyces hansenii0.0088% [5hmC/dG]https://pubmed.ncbi.nlm.nih.gov/23678980/
5hmCKluyveromyces lactis0.0004% [5hmC/dG]https://pubmed.ncbi.nlm.nih.gov/23678980/
5hmCKluyveromyces marxianus0.003% [5hmC/dG]https://pubmed.ncbi.nlm.nih.gov/23678980/
5hmCPichia pastoris0.075% [5hmC/dG]https://pubmed.ncbi.nlm.nih.gov/23678980/
5hmCSchizosaccharomyces pombe(CICC 1056)0.34% [5hmC/dG]https://pubmed.ncbi.nlm.nih.gov/23678980/
5hmCSchizosaccharomyces pombe(CICC 1372)0.26% [5hmC/dG]https://pubmed.ncbi.nlm.nih.gov/23678980/
5hmCYarrowia lipolytica0.064% [5hmC/dG]https://pubmed.ncbi.nlm.nih.gov/23678980/
5hmCHeLa cells0.00312% [5hmC/DNA]https://pubmed.ncbi.nlm.nih.gov/23658232/
5hmCHEK293T-Tet10.096% [5hmC/DNA]https://pubmed.ncbi.nlm.nih.gov/23658232/
5hmCHEK293T-Tet1m0.00325% [5hmC/DNA]https://pubmed.ncbi.nlm.nih.gov/23658232/
5hmCWM-266-40.00122% [5hmC/DNA]https://pubmed.ncbi.nlm.nih.gov/23658232/
5hmCMouse brain0.38-0.54% [5hmC/ (dC+5mdC+5hmdC)]https://pubmed.ncbi.nlm.nih.gov/22644266/
5hmCMouse brain0.056% [5hmC/DNA]https://pubmed.ncbi.nlm.nih.gov/23658232/
5hmCMouse skin (red head)0.0277% [5hmC/DNA]https://pubmed.ncbi.nlm.nih.gov/23658232/
5hmCMouse skin (albino)0.0217% [5hmC/DNA]https://pubmed.ncbi.nlm.nih.gov/23658232/
5hmCMouse primordial germ cells0.05-0.2% [5hmC/dC]https://pubmed.ncbi.nlm.nih.gov/23399596/
5hmCMouse somatic cells0.05-0.2% [5hmC/dC]https://pubmed.ncbi.nlm.nih.gov/23399596/
5hmCMouse ES cells0.0013% [5hmC/dG]https://pubmed.ncbi.nlm.nih.gov/28448110/
5hmCMouse ES cells0.00089% [5hmC/dC]https://pubmed.ncbi.nlm.nih.gov/23768208/
5hmCMouse ES cells treated with ascorbic acid0.0033% [5hmC/dC]https://pubmed.ncbi.nlm.nih.gov/23768208/
5hmCHuman brain0.155% [5hmC/DNA]https://pubmed.ncbi.nlm.nih.gov/23658232/
5hmCHuman brain0.67% [5hmC/DNA]https://pubmed.ncbi.nlm.nih.gov/21772996/
5hmCArabidopsis thaliana0.000079% [5hmC/dN]https://pubmed.ncbi.nlm.nih.gov/24391970/
5hmCHuman CRC tumor tissues0.027% [5hmC/dG]https://pubmed.ncbi.nlm.nih.gov/25675106/
5hmCHuman CRC tumor-adjacent normal tissues0.0868% [5hmC/dG]https://pubmed.ncbi.nlm.nih.gov/25675106/
5hmCHeLa cells0.0068% [5hmC/dG]https://pubmed.ncbi.nlm.nih.gov/26562407/
5hmC293T cells0.0109% [5hmC/dG]https://pubmed.ncbi.nlm.nih.gov/26562407/
5hmCNHDF-Neo cells0.00087% [5hmC/dN]https://pubmed.ncbi.nlm.nih.gov/29190698/
5hmCK562 cells0.00059% [5hmC/dN]https://pubmed.ncbi.nlm.nih.gov/29190698/
5hmCMe45 cells0.00023% [5hmC/dN]https://pubmed.ncbi.nlm.nih.gov/29190698/
5hmCHCT 116 cells0.00067% [5hmC/dN]https://pubmed.ncbi.nlm.nih.gov/29190698/
5hmCRaji cells0.00013% [5hmC/dN]https://pubmed.ncbi.nlm.nih.gov/29190698/
5hmCBL cells0.0004% [5hmC/dN]https://pubmed.ncbi.nlm.nih.gov/29190698/
5hmCPeripheral blood leukocytes0.0163% [5hmC/dC]https://pubmed.ncbi.nlm.nih.gov/29410709/
5hmCCAD patients0.0191% [5hmC/dC]https://pubmed.ncbi.nlm.nih.gov/29410709/
Modification Enzymes and Reactions
Modification Enzymes:TET
Reference:https://pubmed.ncbi.nlm.nih.gov/26734843/

Modification Enzymes:NgTET1
Reference:https://pubmed.ncbi.nlm.nih.gov/25831492/











The Nucleic Acid Modification Database (NAMDB)

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