Computational and Mathematical Methods in Medicine / 2013 / Article / Tab 1

Research Article

Complex Codon Usage Pattern and Compositional Features of Retroviruses

Table 1

Characteristics and codon usage pattern and AU distribution of retroviral genomes (shown in clades).

Virus*Abbrev. namesAccn. numberMean ENcSDMean AU %SDMean AU3 %SD

Orthoretrovirinae
 Alpharetrovirus
  Avian carcinoma virus ACMHV-2NC_00140240.510.0036.200.0018.500.00
  Avian leukosis virusRSA ALV-ANC_00140857.093.3244.807.3545.239.32
  Avian myelocytomatosis virus AMCVNC_00186652.790.0039.600.0032.000.00
  Fujinami sarcoma virus FuSVNC_00140342.610.0037.900.0022.200.00
  Rous sarcoma virus RSVNC_00140753.509.9344.905.2841.9015.25
  UR2 sarcoma virus UR2SVNC_00161855.680.5953.400.0056.651.77
  Y73 sarcoma virus Y73SVNC_00809439.410.0038.200.0021.200.00
 Betaretrovirus
  Enzootic nasal tumour virus of goats ENTV-2NC_00499449.861.3657.632.3370.201.53
  Jaagsiekte sheep retrovirus JSRVNC_00149449.254.2658.582.3866.089.57
  Mason-Pfizer monkey virus MPMVNC_00155050.101.3157.581.2768.131.60
  Mouse mammary tumor virus MMTVNC_00150351.842.1655.980.6262.802.42
  Ovine enzootic nasal tumour virus ENTV-1NC_00701549.232.8058.282.7271.452.87
  Squirrel monkey retrovirusHLB SMRV-HLBNC_00151453.014.6151.682.0154.783.39
 Deltaretrovirus
  Bovine leukemia virus BLVNC_00141452.052.5444.983.4947.354.83
  Primate T-lymphotropic virus 1
   Human T-lymphotropic virus 1 HTLV-1NC_00143650.881.6246.272.0545.352.82
   Simian T-lymphotropic virus 1 STLV-1NC_00085851.092.0646.732.2945.803.45
  Primate T-lymphotropic virus 2
   Human T-lymphotropic virus 2 HTLV-2NC_00148850.041.8645.583.3144.463.11
   Simian T-lymphotropic virus 2 STLV-2NC_00181551.194.2443.083.8241.975.16
  Human T-lymphotropic virus 4 HTLV-4NC_01180050.862.7142.852.6240.682.23
  Simian T-cell lymphotropic virus 6 STLV-6NC_01154654.013.8347.002.7848.734.68
  Simian T-lymphotropic virus 3 STLV-3NC_00332355.393.7244.922.7344.522.31
 Epsilonretrovirus
  Snakehead retrovirus SnRVNC_00172451.887.9150.314.7358.464.80
  Walleye dermal sarcoma virus WDSVNC_00186753.512.4557.823.3965.503.56
 Gammaretrovirus
  Abelson murine leukemia virus AbMLVNC_00149955.036.4546.738.8146.5011.23
  Feline leukemia virus FeLVNC_00194053.844.1650.301.7053.600.99
  Murine leukemia virus
   Friend murine leukemia virus FrMLVNC_00136254.951.0346.701.4147.701.82
   Moloney murine leukemia virus MoMLVNC_00150154.720.1047.001.8448.772.80
   Murine type C retrovirus MTCRNC_00170252.333.0045.900.9945.502.44
   Rauscher murine leukemia virus R-MuLVNC_00181955.420.6246.871.4047.601.32
  Gibbon ape leukemia virus GALVNC_00188555.831.3447.571.1648.830.67
  Moloney murine sarcoma virus MOMSVNC_00150256.403.2447.606.2646.088.42
  Murine osteosarcoma virus MuSVNC_00150649.970.9842.651.7737.357.14
  RD114 retrovirus RD-114NC_00988954.311.9349.703.6851.603.25
  Reticuloendotheliosis virus REVNC_00693457.090.2046.900.8046.501.44
  Spleen focus-forming virus SFFVNC_00150051.035.8545.272.2847.333.37
  Woolly monkey sarcoma virus WMSVNC_00942451.398.6542.604.0437.9713.23
  Xenotropic MuLV-related virus VP62 XMRV-VP62NC_00781552.792.4146.431.2946.802.18
Lentivirus
  Bovine immunodeficiency virus BIVNC_00141353.224.4353.263.6057.905.35
  Caprine arthritis-encephalitis virus CAEVNC_00146345.936.9657.103.4567.634.46
  Equine infectious anemia virus EIAVNC_00145047.057.9359.254.5667.431.18
  Feline immunodeficiency virus FIVNC_00148243.876.5862.013.8371.399.91
  Human immunodeficiency virus 1 HIV-1NC_00180245.054.0155.494.6664.787.24
  Human immunodeficiency virus 2 HIV-2NC_00172252.435.7351.493.0256.514.77
  Ovine lentivirus OLVNC_00151144.594.4757.723.7865.736.90
  Simian immunodeficiency virus
   Simian immunodeficiency virus SIVNC_00154948.804.1254.733.3260.627.82
   Simian immunodeficiency virus SIV-mnd 2 SIV-mnd-2NC_00445551.445.8354.912.6358.946.43
  Visna/Maedi virus VISNANC_00145244.475.3457.832.7068.256.51
Spumaretrovirinae
Bovine foamy virus BFVNC_00183155.932.3652.143.6658.765.22
Equine foamy virus EFVNC_00220145.532.6958.004.8371.165.47
Feline foamy virus FFVNC_00187148.583.7860.532.9570.403.59
Macaque simian foamy virus SFVmacNC_01081946.023.0158.524.9273.605.31
Simian foamy virus SFVNC_00136447.943.9158.034.3870.588.48
Simian foamy virus 3 SFV-3NC_01082044.333.2359.505.3175.204.35
Unclassified retroviruses
Atlantic salmon swim bladder sarcoma virus SSSVNC_00765454.692.2851.703.5457.906.65
Avian endogenous retrovirus EAV-HP EAV-HPNC_00594759.380.0047.600.0047.800.00
Xenopus laevis endogenous retrovirus Xen1 Xen-1NC_01095559.601.8053.352.7658.004.11

Viruses are shown in their respective genera.

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