The nucleic acid data:
IRESite Id: 597 Version: 1
Originaly submitted by: Martin Mokrejš Submission date: 2009-08-18 22:42:30
Reviewed by: Martin Mokrejš Last change: 2009-08-18 23:09:29
IRESite record type:
  natural_transcript
The shape of the nucleic acid molecule translated:
  linear
The quality of the mRNA/+RNA sequence:
  end-to-end_full-length_mRNA
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule:
  TMEV
The genetic origin of this natural mRNA/+RNA:
  viral
The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
335239
The mRNA/+RNA description: 
Theiler's murine encephalomyelitis virus (TMEV) RNA polyprotein, complete genome.
The mRNA/+RNA sequence represented in the +DNA notation:


Credibility of mRNA sequence:
  end-to-end_sequence_reverse_engineered_and_should_match_experiment
The organism containing this mRNA with IRES segment in its genome:
Theiler's encephalomyelitis virus BeAn 8386
A promoter reported in cDNA corresponding to IRES sequence:
  not tested
The total number of notable open-reading frames (ORFs):
  1
Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:
ORF
ORF position:   1
Version: 1 Last change: 2009-08-18 23:09:29
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
polyprotein
The description of the protein encoded in this ORF:
viral polyprotein
The translational frameshift (ribosome slippage) involved:
  0
The ribosome read-through involved:
  no
The alternative forms of this protein occur by the alternative initiation of translation:
  not tested
The ORF absolute position (the base range includes START and STOP codons or their equivalents):
  1065-7976
Remarks:
The strain GDVII is stored in Genbank under GI:62039
Citations:
Pevear DC, Calenoff M, Rozhon E, Lipton HL (1987) Analysis of the complete nucleotide sequence of the picornavirus Theiler's murine encephalomyelitis virus indicates that it is closely related to cardioviruses. J. Virol. 5(61):1507-1516
IRESs:
IRES:
Version: 3 Last change: 2009-08-18 23:14:29
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  TMEV
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  1-1040
Conclusion:
  strongly_supported_IRES
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
Bandyopadhyay et al. (1992) initially reported the IRES in BeAn strain.
Citations:
Pilipenko EV, Gmyl AP, Maslova SV, Belov GA, Sinyakov AN, Huang M, Brown TD, Agol VI (1994) Starting window, a distinct element in the cap-independent internal initiation of translation on picornaviral RNA. J. Mol. Biol. 3(241):398-414
Pilipenko EV, Gmyl AP, Maslova SV, Khitrina EV, Agol VI (1995) Attenuation of Theiler's murine encephalomyelitis virus by modifications of the oligopyrimidine/AUG tandem, a host-dependent translational cis element. J. Virol. 2(69):864-870
Bandyopadhyay PK, Wang C, Lipton HL (1992) Cap-independent translation by the 5' untranslated region of Theiler's murine encephalomyelitis virus. J. Virol. 11(66):6249-6256
Pilipenko EV, Blinov VM, Chernov BK, Dmitrieva TM, Agol VI (1989) Conservation of the secondary structure elements of the 5'-untranslated region of cardio- and aphthovirus RNAs. Nucleic Acids Res. 14(17):5701-5711
Pilipenko EV, Pestova TV, Kolupaeva VG, Khitrina EV, Poperechnaya AN, Agol VI, Hellen CU (2000) A cell cycle-dependent protein serves as a template-specific translation initiation factor. Genes Dev. 16(14):2028-2045
Regions with experimentally determined secondary structures:
A region with the experimentally determined secondary structure:
IRESite 2D Struct Id: 39
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The function of the 2D structure:
IRES
The 2D structure causes frameshift:
unknown
The absolute position of the experimentally mapped region (the range includes START and STOP codons or their equivalents):
599-1040
The underlying nucleic acid sequence and structure of the mapped region:



Remarks:
This actually a prediction model based on the EMCV structure probing data.
Citations:
Pilipenko EV, Blinov VM, Chernov BK, Dmitrieva TM, Agol VI (1989) Conservation of the secondary structure elements of the 5'-untranslated region of cardio- and aphthovirus RNAs. Nucleic Acids Res. 14(17):5701-5711
Last change to the database: 2015-04-16 16:45:23 GMT+1